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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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2
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Abe Y, Kofman ER, Almeida M, Ouyang Z, Ponte F, Mueller JR, Cruz-Becerra G, Sakai M, Prohaska TA, Spann NJ, Resende-Coelho A, Seidman JS, Stender JD, Taylor H, Fan W, Link VM, Cobo I, Schlachetzki JCM, Hamakubo T, Jepsen K, Sakai J, Downes M, Evans RM, Yeo GW, Kadonaga JT, Manolagas SC, Rosenfeld MG, Glass CK. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Mol Cell 2023; 83:3421-3437.e11. [PMID: 37751740 PMCID: PMC10591845 DOI: 10.1016/j.molcel.2023.08.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the NCoR/HDAC3 co-repressor complex to a co-activator of AP-1 and NF-κB target genes that are required for mouse osteoclast differentiation. Accordingly, the dominant function of NCoR/HDAC3 complexes in response to RANK signaling is to activate, rather than repress, gene expression. Mechanistically, RANK signaling promotes RNA-dependent interaction of the transcriptional co-activator PGC1β with the NCoR/HDAC3 complex, resulting in the activation of PGC1β and inhibition of HDAC3 activity for acetylated histone H3. Non-coding RNAs Dancr and Rnu12, which are associated with altered human bone homeostasis, promote NCoR/HDAC3 complex assembly and are necessary for RANKL-induced osteoclast differentiation in vitro. These findings may be prototypic for signal-dependent functions of NCoR in other biological contexts.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Almeida
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Filipa Ponte
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biochemistry and Molecular Biology, Nippon Medical School Hospital, Tokyo 113-8602, Japan
| | - Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Resende-Coelho
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stavros C Manolagas
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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3
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Sluka KA, Wager TD, Sutherland SP, Labosky PA, Balach T, Bayman EO, Berardi G, Brummett CM, Burns J, Buvanendran A, Caffo B, Calhoun VD, Clauw D, Chang A, Coffey CS, Dailey DL, Ecklund D, Fiehn O, Fisch KM, Frey Law LA, Harris RE, Harte SE, Howard TD, Jacobs J, Jacobs JM, Jepsen K, Johnston N, Langefeld CD, Laurent LC, Lenzi R, Lindquist MA, Lokshin A, Kahn A, McCarthy RJ, Olivier M, Porter L, Qian WJ, Sankar CA, Satterlee J, Swensen AC, Vance CG, Waljee J, Wandner LD, Williams DA, Wixson RL, Zhou XJ. Predicting chronic postsurgical pain: current evidence and a novel program to develop predictive biomarker signatures. Pain 2023; 164:1912-1926. [PMID: 37326643 PMCID: PMC10436361 DOI: 10.1097/j.pain.0000000000002938] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 06/17/2023]
Abstract
ABSTRACT Chronic pain affects more than 50 million Americans. Treatments remain inadequate, in large part, because the pathophysiological mechanisms underlying the development of chronic pain remain poorly understood. Pain biomarkers could potentially identify and measure biological pathways and phenotypical expressions that are altered by pain, provide insight into biological treatment targets, and help identify at-risk patients who might benefit from early intervention. Biomarkers are used to diagnose, track, and treat other diseases, but no validated clinical biomarkers exist yet for chronic pain. To address this problem, the National Institutes of Health Common Fund launched the Acute to Chronic Pain Signatures (A2CPS) program to evaluate candidate biomarkers, develop them into biosignatures, and discover novel biomarkers for chronification of pain after surgery. This article discusses candidate biomarkers identified by A2CPS for evaluation, including genomic, proteomic, metabolomic, lipidomic, neuroimaging, psychophysical, psychological, and behavioral measures. Acute to Chronic Pain Signatures will provide the most comprehensive investigation of biomarkers for the transition to chronic postsurgical pain undertaken to date. Data and analytic resources generatedby A2CPS will be shared with the scientific community in hopes that other investigators will extract valuable insights beyond A2CPS's initial findings. This article will review the identified biomarkers and rationale for including them, the current state of the science on biomarkers of the transition from acute to chronic pain, gaps in the literature, and how A2CPS will address these gaps.
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Affiliation(s)
- Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Tor D. Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Patricia A. Labosky
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL
| | - Emine O. Bayman
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - John Burns
- Division of Behavioral Sciences, Rush Medical College, Chicago, IL
| | | | - Brian Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, and Emory University, Atlanta, GA
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew Chang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Christopher S. Coffey
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Dana L. Dailey
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Dixie Ecklund
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Oliver Fiehn
- University of California, Davis, Davis, CA, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
- Center for Computational Biology and Bioinformatics, University of California San Diego, San Diego, CA, United States
| | - Laura A. Frey Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Timothy D. Howard
- Department of Biochemistry, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Joshua Jacobs
- Department of Orthopedic Surgery, Rush Medical College, CHicago, IL
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | | | - Carl D. Langefeld
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
| | - Rebecca Lenzi
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Martin A. Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | | | - Ari Kahn
- Texas Advanced Computing Center, University of Texas, AUstin, TX
| | | | - Michael Olivier
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Linda Porter
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
- Office of Pain Policy and Planning National Institutes of Health, Bethesda, MD
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Cheryse A. Sankar
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | | | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Carol G.T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Jennifer Waljee
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | - David A. Williams
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | | | - Xiaohong Joe Zhou
- Center for MR Research and Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
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Baghdassarian H, Blackstone SA, Clay OS, Philips R, Matthiasardottir B, Nehrebecky M, Hua VK, McVicar R, Liu Y, Tucker SM, Randazzo D, Deuitch N, Rosenzweig S, Mark A, Sasik R, Fisch KM, Pimpale Chavan P, Eren E, Watts NR, Ma CA, Gadina M, Schwartz DM, Sanyal A, Werner G, Murdock DR, Horita N, Chowdhury S, Dimmock D, Jepsen K, Remmers EF, Goldbach-Mansky R, Gahl WA, O'Shea JJ, Milner JD, Lewis NE, Chang J, Kastner DL, Torok K, Oda H, Putnam CD, Broderick L. Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome. N Engl J Med 2023; 388:2241-2252. [PMID: 37256972 PMCID: PMC10392571 DOI: 10.1056/nejmoa2202318] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND Disabling pansclerotic morphea (DPM) is a rare systemic inflammatory disorder, characterized by poor wound healing, fibrosis, cytopenias, hypogammaglobulinemia, and squamous-cell carcinoma. The cause is unknown, and mortality is high. METHODS We evaluated four patients from three unrelated families with an autosomal dominant pattern of inheritance of DPM. Genomic sequencing independently identified three heterozygous variants in a specific region of the gene that encodes signal transducer and activator of transcription 4 (STAT4). Primary skin fibroblast and cell-line assays were used to define the functional nature of the genetic defect. We also assayed gene expression using single-cell RNA sequencing of peripheral-blood mononuclear cells to identify inflammatory pathways that may be affected in DPM and that may respond to therapy. RESULTS Genome sequencing revealed three novel heterozygous missense gain-of-function variants in STAT4. In vitro, primary skin fibroblasts showed enhanced interleukin-6 secretion, with impaired wound healing, contraction of the collagen matrix, and matrix secretion. Inhibition of Janus kinase (JAK)-STAT signaling with ruxolitinib led to improvement in the hyperinflammatory fibroblast phenotype in vitro and resolution of inflammatory markers and clinical symptoms in treated patients, without adverse effects. Single-cell RNA sequencing revealed expression patterns consistent with an immunodysregulatory phenotype that were appropriately modified through JAK inhibition. CONCLUSIONS Gain-of-function variants in STAT4 caused DPM in the families that we studied. The JAK inhibitor ruxolitinib attenuated the dermatologic and inflammatory phenotype in vitro and in the affected family members. (Funded by the American Academy of Allergy, Asthma, and Immunology Foundation and others.).
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Affiliation(s)
- Hratch Baghdassarian
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Sarah A Blackstone
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Owen S Clay
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Rachael Philips
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Brynja Matthiasardottir
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Michele Nehrebecky
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Vivian K Hua
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Rachael McVicar
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Yang Liu
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Suzanne M Tucker
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Davide Randazzo
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Natalie Deuitch
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Sofia Rosenzweig
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Adam Mark
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Roman Sasik
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Kathleen M Fisch
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Pallavi Pimpale Chavan
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Elif Eren
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Norman R Watts
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Chi A Ma
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Massimo Gadina
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Daniella M Schwartz
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Anwesha Sanyal
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Giffin Werner
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - David R Murdock
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Nobuyuki Horita
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Shimul Chowdhury
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - David Dimmock
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Kristen Jepsen
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Elaine F Remmers
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Raphaela Goldbach-Mansky
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - William A Gahl
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - John J O'Shea
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Joshua D Milner
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Nathan E Lewis
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Johanna Chang
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Daniel L Kastner
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Kathryn Torok
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Hirotsugu Oda
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Christopher D Putnam
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
| | - Lori Broderick
- From the Bioinformatics and Systems Biology Program (H.B.), the Department of Pediatrics (H.B., O.S.C., V.K.H., N.E.L.), the Center for Computational Biology and Bioinformatics, Department of Medicine (A.M., R.S., K.M.F.), the Institute for Genomic Medicine (K.J.), the Department of Bioengineering (N.E.L.), the Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics (J.C., L.B.), and the Department of Medicine (C.D.P.), University of California, San Diego, Sanford Burnham Prebys Medical Discovery Institute (R.M., Y.L.), and the San Diego Branch, Ludwig Institute for Cancer Research (C.D.P.), La Jolla, and the Department of Pathology (S.M.T.), Rady Children's Institute for Genomic Medicine (S.C., D.D.), and Rady Children's Hospital Foundation (J.C., L.B.), Rady Children's Hospital, San Diego - all in California; the Inflammatory Disease Section (S.A.B., B.M., M.N., S.R., P.P.C., N.H., E.F.R., D.L.K., H.O.), the Oncogenesis and Development Section (N.D.), and the Undiagnosed Diseases Program, Medical Genetics Branch (D.R.M., W.A.G.), National Human Genome Research Institute, the Molecular Immunology and Inflammation Branch (R.P., J.J.O.), the Light Imaging Section (D.R.) and the Translational Immunology Section (M.G.), Office of Science and Technology, and the Protein Expression Laboratory (E.E., N.R.W.), National Institute of Arthritis and Musculoskeletal and Skin Diseases, and the Genetics and Pathogenesis of Allergy Section, Laboratory of Allergic Diseases (C.A.M.), and the Translational Autoinflammatory Disease Section (R.G.-M.), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park (B.M.) - all in Maryland; Sanford School of Medicine, University of South Dakota, Sioux Falls (S.A.B.); the Division of Rheumatology and Clinical Immunology, University of Pittsburgh (D.M.S.), University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh (A.S., G.W., K.T.), and the University of Pittsburgh Scleroderma Center (A.S., G.W., K.T.) - all in Pittsburgh; the Division of Pediatric Allergy, Immunology, and Rheumatology, Columbia University, New York (J.D.M.); and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases and the Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany (H.O.)
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am 2023; 19:100449. [PMID: 36844610 PMCID: PMC9939935 DOI: 10.1016/j.lana.2023.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Victor J. Cantu
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Laura Kohn
- Kohn Education Consulting, San Diego, CA, USA
| | - Natasha K. Martin
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adriane Wynn
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Marlene Flores
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Araz Majnoonian
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Patricia Gonzalez-Zuniga
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Megan Nguyen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Anh V. Vo
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Tina Le
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dawn Duong
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ashkan Hassani
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Samantha Tweeten
- County of San Diego, Health and Human Services Agency, 1600 Pacific Highway, San Diego, CA, 92101, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abbas Hakim
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Peter De Hoff
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adam M. Mark
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chanond A. Nasamran
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kathleen M. Fisch
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Justin Morris
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Electrical and Computer Engineering, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Jaeyoung Kang
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Behnam Khaleghi
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Colin Young
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ameen D. Akel
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Sean Eilert
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Justin Eno
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Ken Curewitz
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Louise C. Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tajana Rosing
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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6
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv 2023:2021.10.19.21265226. [PMID: 34704096 PMCID: PMC8547528 DOI: 10.1101/2021.10.19.21265226] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 - March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88% - 98%); 67% were associated with a positive wastewater sample (95% CI: 57% - 77%), and 40% were associated with a positive surface sample (95% CI: 29% - 52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | | | - Tommi Gaines
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Richard S. Garfein
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Victor J. Cantu
- University of California San Diego, Department of Bioengineering
| | | | - Natasha K Martin
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Adriane Wynn
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Carrissa Wijaya
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Marlene Flores
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Vinton Omaleki
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Araz Majnoonian
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Patricia Gonzalez-Zuniga
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Megan Nguyen
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Anh V Vo
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Tina Le
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Dawn Duong
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Ashkan Hassani
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Kristen Jepsen
- University of California San Diego, Institute for Genomic Medicine
| | - Benjamin Henson
- University of California San Diego, Institute for Genomic Medicine
| | - Abbas Hakim
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
| | - Amanda Birmingham
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Peter De Hoff
- University of California San Diego, Department of Pediatrics
| | - Adam M. Mark
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Chanond A Nasamran
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Sara Brin Rosenthal
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Niema Moshiri
- University of California San Diego, Department of Computer Science & Engineering
| | - Kathleen M. Fisch
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Greg Humphrey
- University of California San Diego, Department of Pediatrics
| | - Sawyer Farmer
- University of California San Diego, Department of Pediatrics
| | - Helena M. Tubb
- University of California San Diego, Department of Pediatrics
| | - Tommy Valles
- University of California San Diego, Department of Pediatrics
| | - Justin Morris
- University of California San Diego, Department of Computer Science & Engineering
- San Diego State University, Department of Electrical and Computer Engineering
| | - Jaeyoung Kang
- University of California San Diego, Department of Electrical and Computer Engineering
| | - Behnam Khaleghi
- University of California San Diego, Department of Computer Science & Engineering
| | - Colin Young
- University of California San Diego, Department of Computer Science & Engineering
| | | | | | | | | | - Louise C Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Tajana Rosing
- University of California San Diego, Department of Computer Science & Engineering
| | - Rob Knight
- University of California San Diego, Department of Pediatrics
- University of California San Diego, Department of Bioengineering
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7
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022; 609:101-108. [PMID: 35798029 PMCID: PMC9433318 DOI: 10.1038/s41586-022-05049-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.,Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego, USA
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. .,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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8
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Hepokoski ML, Odish M, Lam MT, Coufal NG, Rolfsen ML, Shadel GS, Moyzis AG, Sainz AG, Takiar PG, Patel S, Leonard AJ, Samandari N, Hansen E, Trescott S, Nguyen C, Jepsen K, Cutter G, Gillespie MN, Spragg RG, Sasik R, Ix JH. Absolute quantification of plasma mitochondrial DNA by droplet digital PCR marks COVID-19 severity over time during intensive care unit admissions. Am J Physiol Lung Cell Mol Physiol 2022; 323:L84-L92. [PMID: 35699291 PMCID: PMC9273271 DOI: 10.1152/ajplung.00128.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
Increased plasma mitochondrial DNA concentrations are associated with poor outcomes in multiple critical illnesses, including COVID-19. However, current methods of cell-free mitochondrial DNA quantification in plasma are time-consuming and lack reproducibility. Here, we used next-generation sequencing to characterize the size and genome location of circulating mitochondrial DNA in critically ill subjects with COVID-19 to develop a facile and optimal method of quantification by droplet digital PCR. Sequencing revealed a large percentage of small mitochondrial DNA fragments in plasma with wide variability in coverage by genome location. We identified probes for the mitochondrial DNA genes, cytochrome B and NADH dehydrogenase 1, in regions of relatively high coverage that target small sequences potentially missed by other methods. Serial assessments of absolute mitochondrial DNA concentrations were then determined in plasma from 20 critically ill subjects with COVID-19 without a DNA isolation step. Mitochondrial DNA concentrations on the day of enrollment were increased significantly in patients with moderate or severe acute respiratory distress syndrome (ARDS) compared with those with no or mild ARDS. Comparisons of mitochondrial DNA concentrations over time between patients with no/mild ARDS who survived, patients with moderate/severe ARDS who survived, and nonsurvivors showed the highest concentrations in patients with more severe disease. Absolute mitochondrial DNA quantification by droplet digital PCR is time-efficient and reproducible; thus, we provide a valuable tool and rationale for future studies evaluating mitochondrial DNA as a real-time biomarker to guide clinical decision-making in critically ill subjects with COVID-19.
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Affiliation(s)
- Mark L Hepokoski
- VA San Diego Healthcare System, San Diego, California
- Division of Pulmonary and Critical Care and Sleep Medicine, University of California San Diego, San Diego, California
| | - Mazen Odish
- Division of Pulmonary and Critical Care and Sleep Medicine, University of California San Diego, San Diego, California
| | - Michael T Lam
- VA San Diego Healthcare System, San Diego, California
- Division of Pulmonary and Critical Care and Sleep Medicine, University of California San Diego, San Diego, California
- Salk Institute for Biological Sciences, La Jolla, California
| | - Nicole G Coufal
- Department of Pediatrics, University of California San Diego, San Diego, California
- Rady Children's Hospital, San Diego, California
| | - Mark L Rolfsen
- Department of Medicine, School of Medicine, University of California San Diego, San Diego, California
| | - Gerald S Shadel
- Salk Institute for Biological Sciences, La Jolla, California
| | | | - Alva G Sainz
- Salk Institute for Biological Sciences, La Jolla, California
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Puja G Takiar
- Department of Medicine, School of Medicine, University of California San Diego, San Diego, California
| | - Sagar Patel
- Division of Pulmonary and Critical Care and Sleep Medicine, University of California San Diego, San Diego, California
| | - Austin J Leonard
- Department of Medicine, School of Medicine, University of California San Diego, San Diego, California
| | | | - Emily Hansen
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Samantha Trescott
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Celina Nguyen
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California
| | - Gary Cutter
- Department of Biostatistics, School of Public Health, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Mark N Gillespie
- Department of Pharmacology, University of South Alabama, Mobile, Alabama
| | - Roger G Spragg
- Division of Pulmonary and Critical Care and Sleep Medicine, University of California San Diego, San Diego, California
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics, University of California San Diego, La Jolla, California
| | - Joachim H Ix
- VA San Diego Healthcare System, San Diego, California
- Division of Nephrology and Hypertension, University of California San Diego, San Diego, California
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9
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Berardi G, Frey-Law L, Sluka KA, Bayman EO, Coffey CS, Ecklund D, Vance CGT, Dailey DL, Burns J, Buvanendran A, McCarthy RJ, Jacobs J, Zhou XJ, Wixson R, Balach T, Brummett CM, Clauw D, Colquhoun D, Harte SE, Harris RE, Williams DA, Chang AC, Waljee J, Fisch KM, Jepsen K, Laurent LC, Olivier M, Langefeld CD, Howard TD, Fiehn O, Jacobs JM, Dakup P, Qian WJ, Swensen AC, Lokshin A, Lindquist M, Caffo BS, Crainiceanu C, Zeger S, Kahn A, Wager T, Taub M, Ford J, Sutherland SP, Wandner LD. Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol. Front Med (Lausanne) 2022; 9:849214. [PMID: 35547202 PMCID: PMC9082267 DOI: 10.3389/fmed.2022.849214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or "omics," quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
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Affiliation(s)
- Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Laura Frey-Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Emine O. Bayman
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Coffey
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Dixie Ecklund
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Carol G. T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Dana L. Dailey
- Department of Physical Therapy, St. Ambrose University, Davenport, IA, United States
| | - John Burns
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, United States
| | - Asokumar Buvanendran
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Robert J. McCarthy
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Joshua Jacobs
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, United States
| | - Xiaohong Joe Zhou
- Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
| | - Richard Wixson
- NorthShore Orthopaedic and Spine Institute, NorthShore University HealthSystem, Skokie, IL, United States
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL, United States
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
| | - Douglas Colquhoun
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - David A. Williams
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States
| | - Andrew C. Chang
- Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Waljee
- Section of Plastic and Reconstructive Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kristen Jepsen
- Institute of Genomic Medicine Genomics Center, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Michael Olivier
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Panshak Dakup
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna Lokshin
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Martin Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Brian S. Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ciprian Crainiceanu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Scott Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ari Kahn
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, United States
| | - Tor Wager
- Presidential Cluster in Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States
| | - Margaret Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - James Ford
- Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, The National Institutes of Health, Bethesda, MD, United States
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10
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022:2021.12.21.21268143. [PMID: 35411350 PMCID: PMC8996633 DOI: 10.1101/2021.12.21.21268143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M. Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B. Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C. Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K. Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R. MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T. Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K. Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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11
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022. [PMID: 35411350 DOI: 10.1101/2022.01.27.22269965] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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12
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Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. NPJ Breast Cancer 2022; 8:6. [PMID: 35027560 PMCID: PMC8758681 DOI: 10.1038/s41523-021-00365-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Hidetoshi Mori
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Jonathan Gordon
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Mark F Evans
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Joseph Steward
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Thomas O'Keefe
- Department of Surgery, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Farnaz Hasteh
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Gary S Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Donald L Weaver
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Brian L Sprague
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Surgery, University of Vermont, Burlington, VT, 05405, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Janet L Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
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13
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Xian S, Dosset M, Almanza G, Searles S, Sahani P, Waller TC, Jepsen K, Carter H, Zanetti M. The unfolded protein response links tumor aneuploidy to local immune dysregulation. EMBO Rep 2021; 22:e52509. [PMID: 34698427 PMCID: PMC8647024 DOI: 10.15252/embr.202152509] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 12/19/2022] Open
Abstract
Aneuploidy is a chromosomal abnormality associated with poor prognosis in many cancer types. Here, we tested the hypothesis that the unfolded protein response (UPR) mechanistically links aneuploidy and local immune dysregulation. Using a single somatic copy number alteration (SCNA) score inclusive of whole‐chromosome, chromosome arm, and focal alterations in a pan‐cancer analysis of 9,375 samples in The Cancer Genome Atlas (TCGA) database, we found an inverse correlation with a cytotoxicity (CYT) score across disease stages. Co‐expression patterns of UPR genes changed substantially between SCNAlow and SCNAhigh groups. Pathway activity scores showed increased activity of multiple branches of the UPR in response to aneuploidy. The PERK branch showed the strongest association with a reduced CYT score. The conditioned medium of aneuploid cells transmitted XBP1 splicing and caused IL‐6 and arginase 1 transcription in receiver bone marrow‐derived macrophages and markedly diminished the production of IFN‐γ and granzyme B in activated human T cells. We propose the UPR as a mechanistic link between aneuploidy and immune dysregulation in the tumor microenvironment.
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Affiliation(s)
- Su Xian
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Magalie Dosset
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Gonzalo Almanza
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Stephen Searles
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Paras Sahani
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - T Cameron Waller
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
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14
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Nachmanson D, Evans MF, Steward J, Officer A, Yao H, O'Keefe TJ, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky A, Stein JL, Harismendy O. Abstract 2176: Mutational profiling of premalignant breast microbiopsies. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ductal carcinoma in situ (DCIS) comprises ~20% of all breast cancer diagnoses in the United States. Nearly all DCIS are treated to prevent progression to potentially lethal invasive cancer, yet it is estimated about half of DCIS progress within 10 years making the systematic treatment controversial. This highlights an urgent need for reliable molecular markers to stratify patients by risk. Small, degraded biopsies have made molecular profiling historically challenging; furthermore, a single biopsy can have several regions varying in nuclear grade, hormone receptor status, and histological architecture requiring laser-capture microdissection. Recent advances in whole-exome sequencing now enable mutational profiling from limited quantities (<10ng) of damaged, formalin-fixed, paraffin-embedded (FFPE) DNA, and present an opportunity to sequence individual regions and relate the phenotypic heterogeneity with genetic alterations. Here, we apply these advances to obtain mutational profiles from pure DCIS microbiopsies, enabling a comprehensive molecular profile of pure DCIS, direct measurement of genetic heterogeneity, and associations between molecular and histopathological features.
Whole-exome sequencing was performed on 59 regions across 31 pure DCIS cases varying in nuclear grade (including 19% low-grade), and histological architecture (52% cribriform, 39% solid). Driver analysis revealed breast cancer-like driver alterations in 30/31 cases, and evidence for multiple putative drivers in 26/31, even in low-grade DCIS. The most frequently mutated genes across patients were common breast cancer driver genes: PIK3CA (37%), TP53 (22%), and GATA3 (11%). Phylogenetic trees constructed on multi-region biopsies revealed that regions of the same biopsy shared 12-336 alterations, and all pathogenic driver point mutations. Nevertheless, 1-22 region-specific alterations were found in each biopsy, some of which were likely driver CNA. We identified several histological associations with genetic alterations including high grade (p=2x10-4) and solid DCIS (p=3x10-4) associated with high copy number burden, and a non-significant increase in GATA3 (13% vs 0%) and PIK3CA (50% vs 28%) pathogenic mutations in cribriform vs solid architecture. Lastly, the most genetically diverse DCIS were HER2+/ER- (p=0.07) and those displaying necrosis (p=0.006). Overall, using novel methodology we performed detailed multi-region mutational profiling on difficult to sequence precancer lesions, revealing varying genetic diversity within a biopsy and novel associations between histology and underlying genetic landscape. We illustrate multiple driver genetic alterations and diversity present even in low-grade, pure DCIS lesions, providing key insight into early breast carcinogenesis and representing a critical step towards the development of prognostic markers of progression.
Citation Format: Daniela Nachmanson, Mark F. Evans, Joseph Steward, Adam Officer, Huazhen Yao, Thomas J. O'Keefe, Farnaz Hasteh, Gary S. Stein, Kristen Jepsen, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, Alexander Borowsky, Janet L. Stein, Olivier Harismendy. Mutational profiling of premalignant breast microbiopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2176.
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Affiliation(s)
| | | | | | - Adam Officer
- 1University of California San Diego, La Jolla, CA
| | - Huazhen Yao
- 4Institute for Genomic Medicine, University of California San Diego, La Jolla, CA
| | | | | | | | - Kristen Jepsen
- 4Institute for Genomic Medicine, University of California San Diego, La Jolla, CA
| | | | - Gillian L. Hirst
- 5Hellen Diller Family Comprehensive Cancer Center, San Francisco, CA
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. Alzheimers Dement (Amst) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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Harismendy O, Nachmanson D, Evans MF, Mori H, Officer A, Yau C, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Campbell M, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Gordon JA, Borowsky A, Stein JL. Abstract GS2-01: The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-gs2-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: With the implementation of widespread breast cancer screening, the diagnosis of Ductal Carcinoma In Situ (DCIS) has increased 5 fold. Most cases are treated with combinations of surgery, radiation and endocrine therapy, reducing the risk of second events, including ipsilateral invasive cancer. Without standard markers to confidently identify the most indolent lesions, a subset of cases are likely over-treated. The mutational landscapes of DCIS and invasive ductal carcinoma (IDC) are similar and not sufficient to identify higher risk lesions with recent studies suggesting that clonal selection plays a limited role in progression. Histological analysis highlighted the role of the extracellular matrix and immune-surveillance to maintain duct integrity and limit progression. Due to the small size, limited availability and quality of research specimens, few biomarker studies investigated pure DCIS with adequate follow-up or genome-wide methods, let alone integrated more than one type of biomarker. Unlike breast cancer, there is no comprehensive, systematic, multi-modal atlas of DCIS, limiting the ability to test broad and novel hypotheses and characterize processes maintaining breast tissue homeostasis.
Methods: Through sequential sectioning of pure DCIS archived specimens, a total of 70 histological regions from 40 cases were annotated and profiled using up to 3 platforms: multiplex immuno-histochemistry (mIHC), RNA-seq, and whole-exome sequencing. Stromal and epithelial spatial distribution of immune cells and states were quantified using mIHC. The epithelial compartments were microdissected and profiled using genome-wide gene expression, DNA mutations and copy number alterations.
Results: Epithelial regions were classified according to expression subtypes consistent with histological markers, highlighting associations with the lesion architecture and grade. Compared to solid pattern, cribriform pattern DCIS has induced EMT processes and repressed proliferation processes, a trend reminiscent of low-recurrence-risk expression signatures measured in IDC. The DNA copy number burden increased with grade and the mutational burden was the highest in solid DCIS. Both were higher in Her2+ cases. The clustering of mutations at chromosome 17p - attributed to the APOBEC-driven Kataegis phenomenon - was observed in a subset of regions, suggesting this event can occur in pre-invasive lesions. All DCIS had somatic alterations of at least one known driver gene with some associated with grade (TP53) or expression subtype (ERBB2). Multi-region profiling available in a subset of samples revealed genetic heterogeneity of likely-driver events between proximal regions of similar histological characteristics. The density and proliferative states of selected immune cells - including T-cells, B-cells and Macrophages - highlights the diversity of the tumor immune environment with the highest densities observed in Her2+ ducts and stroma, minimal ductal infiltration in other lesions, fewer dividing B- and T-cells around the more proliferative areas and a small number of regions depleted from any adaptive immune cells.
Conclusion: This first multi-modal profiling of pure DCIS reveals an unsuspected diversity of molecular and microenvironmental states and presents their association with progression risk factors. The observations support the need for stronger integration of molecular and clinicopathology features, especially at sub-histological levels, to ensure the findings can be interpreted in the correct clinical and phenotypic context. The compatibility of the approach with archived specimens supports the expansion to larger retrospective DCIS collections with outcomes.
Citation Format: Olivier Harismendy, Daniela Nachmanson, Mark F. Evans, Hidetoshi Mori, Adam Officer, Christina Yau, Joseph Steward, Huazhen Yao, Thomas O'Keefe, Farnaz Hasteh, Gary S. Stein, Kristen Jepsen, Michael Campbell, Donald L. Weaver, Gillian L. Hirst, Brian L. Sprague, Laura J. Esserman, Jonathan A. Gordon, Alexander Borowsky, Janet L. Stein. The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr GS2-01.
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Yamasaki AE, Warshaw JN, Kyalwazi BL, Matsui H, Jepsen K, Panopoulos AD. An iPSC line derived from a human acute myeloid leukemia cell line (HL-60-iPSC) retains leukemic abnormalities and displays myeloid differentiation defects. Stem Cell Res 2020; 49:102096. [PMID: 33370871 PMCID: PMC8031422 DOI: 10.1016/j.scr.2020.102096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022] Open
Abstract
Cancer-derived iPSCs have provided valuable insight into oncogenesis, but human cancer cells can often be difficult to reprogram, especially in cases of complex genetic abnormalities. Here we report, to our knowledge, the first successful generation of an iPSC line from a human immortalized acute myeloid leukemia (AML) cell line, the cell line HL-60. This iPSC line retains a majority of the leukemic genotype and displays defects in myeloid differentiation, thus providing a tool for modeling and studying AML.
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Affiliation(s)
- Amanda E Yamasaki
- Department of Biological Sciences, University of Notre Dame, IN 46556, USA; Center for Stem Cells and Regenerative Medicine, University of Notre Dame, IN 46556, USA
| | - Jane N Warshaw
- Department of Biological Sciences, University of Notre Dame, IN 46556, USA
| | - Beverly L Kyalwazi
- Department of Biological Sciences, University of Notre Dame, IN 46556, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California San Diego, CA 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, CA 92093, USA
| | - Athanasia D Panopoulos
- Department of Biological Sciences, University of Notre Dame, IN 46556, USA; Center for Stem Cells and Regenerative Medicine, University of Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, IN 46556, USA.
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Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. Mutational profiling of micro-dissected pre-malignant lesions from archived specimens. BMC Med Genomics 2020; 13:173. [PMID: 33208147 PMCID: PMC7672910 DOI: 10.1186/s12920-020-00820-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA. METHODS Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm2) from 3 breast ductal carcinoma in situ (DCIS). RESULTS Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity. CONCLUSION Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Joseph Steward
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Eliza Jeong
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Thomas J O'Keefe
- Division of Breast Surgery and The Comprehensive Breast Health Center - UC San Diego School of Medicine, 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Farnaz Hasteh
- Department of Pathology - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine - UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, 2279 45th Street, Sacramento, CA, 95817, USA
| | - Olivier Harismendy
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA. .,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
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Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
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Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
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Nachmanson D, Steward J, Kim T, Yao H, Jeong E, O'Keefe T, Hirst GL, Esserman L, Borowsky A, Hasteh F, Jepsen K, Harismendy O. Abstract 2499: Genomic spatial profiling of archived pre-malignant lesions of the breast epithelium. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The widespread adoption of breast cancer screening has increased the detection of pre-malignant lesions such as ductal carcinoma in situ (DCIS) but there are currently no reliable biomarkers to stratify DCIS and avoid over-treatment. Importantly, the identification of novel biomarkers in DCIS is notoriously difficult. The rare and late recurrence to subsequent breast cancer (10% at 10 years) poses challenges in experimental design that only a few established, retrospective studies can solve. Most tissue specimens in the associated registries are small, fixed and archived in paraffin (FFPE), precluding their characterization via standard genomic assays. Besides, pure DCIS often present multi-focal heterogenous histology of unclear mutational make-up. Here, we present an approach combining laser capture microdissection with state-of-the-art genomic library preparation methods to enable molecular profiling from minute amounts of damaged nucleic acids and demonstrate its validity for the spatial molecular characterization of DCIS specimen.
Targeted DNA sequencing was performed on limited dilutions of a test DNA from archived breast tissue. Three library preparation strategies were evaluated, included adaptation of classic A-tailing (AT), alternate single-strand (SS) or blunt-end (BE) adapter ligations. The use of an AT protocol resulted less than 10% of targeted base pairs covered at more than 20x (Cov20) from lower than 50ng of DNA and suggested the adapter ligation as initial bottleneck. In contrast, SS or BE adapter ligation from 3ng of DNA reduced the fraction of duplicate reads, increasing the Cov20 to 49% and 100% respectively. Artifactual C to T substitutions, a signature of formalin damage, were restricted to variants of low allelic fraction (<5%). As a result, the use of ensemble variant calling and heuristic filtering to eliminate artifacts and germline variants, led to exome-wide mutational profile of 89% precision and 88% recall from 3ng input, comparable to replicate deep sequencing from a mirrored fresh frozen specimen. The presence of an ERBB2 amplification was validated in all tested conditions. The BE approach for whole exomes was validated on DCIS regions (N=8) and normal epithelium (N=1) dissected from 3 FFPE DCIS blocks. The normal epithelium was unaltered and copy number alterations both consistent and inconsistent within specimen were identified, including FGFR1 and ERBB2 gains or TP53 loss restricted to high-grade lesions. Short variants and indels were rare (~123 per region), mostly shared within each specimen and unlikely to represent driver mutations. The proposed approach can support the spatial mutational profiling of pre-malignant lesions. Compatible with a limited quantity of tissue from archived specimens, the approach sets a new paradigm for the retrospective molecular characterization of specimen with longitudinal follow-up and associated long-term outcome.
Citation Format: Daniela Nachmanson, Joseph Steward, Taeyong Kim, Huazhen Yao, Eliza Jeong, Thomas O'Keefe, Gillian L. Hirst, Laura Esserman, Alexander Borowsky, Farnaz Hasteh, Kristen Jepsen, Olivier Harismendy. Genomic spatial profiling of archived pre-malignant lesions of the breast epithelium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2499.
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Affiliation(s)
| | | | | | - Huazhen Yao
- 1University of California San Diego, La Jolla, CA
| | | | | | | | - Laura Esserman
- 3University of California San Francisco, San Francisco, CA
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Yang BH, Wang K, Wan S, Liang Y, Yuan X, Dong Y, Cho S, Xu W, Jepsen K, Feng GS, Lu LF, Xue HH, Fu W. TCF1 and LEF1 Control Treg Competitive Survival and Tfr Development to Prevent Autoimmune Diseases. Cell Rep 2020; 27:3629-3645.e6. [PMID: 31216480 PMCID: PMC6701704 DOI: 10.1016/j.celrep.2019.05.061] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/26/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022] Open
Abstract
CD4+ Foxp3+ T regulatory (Treg) cells are key players in preventing lethal autoimmunity. Tregs undertake differentiation processes and acquire diverse functional properties. However, how Treg’s differentiation and functional specification are regulated remains incompletely understood. Here, we report that gradient expression of TCF1 and LEF1 distinguishes Tregs into three distinct subpopulations, particularly highlighting a subset of activated Treg (aTreg) cells. Treg-specific ablation of TCF1 and LEF1 renders the mice susceptible to systemic autoimmunity. TCF1 and LEF1 are dispensable for Treg’s suppressive capacity but essential for maintaining a normal aTreg pool and promoting Treg’s competitive survival. As a consequence, the development of T follicular regulatory (Tfr) cells, which are a subset of aTreg, is abolished in TCF1/LEF1-conditional knockout mice, leading to unrestrained T follicular helper (Tfh) and germinal center B cell responses. Thus, TCF1 and LEF1 act redundantly to control the maintenance and functional specification of Treg subsets to prevent autoimmunity. Transcriptional regulation of Treg differentiation and function remains incompletely understood. Yang et al. report that two TCF family transcription factors regulate the survival and functional specification of a subset of Treg cells to prevent autoimmunity.
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Affiliation(s)
- Bi-Huei Yang
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ke Wang
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shuo Wan
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Liang
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; PhD Program, Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Xiaomei Yuan
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Yi Dong
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sunglim Cho
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wanqing Xu
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gen-Sheng Feng
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Li-Fan Lu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Hai-Hui Xue
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Iowa City Veterans Affairs Health Care System, Iowa City, IA 52246, USA.
| | - Wenxian Fu
- Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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Batista A, Rodvold JJ, Xian S, Searles SC, Lew A, Iwawaki T, Almanza G, Waller TC, Lin J, Jepsen K, Carter H, Zanetti M. IRE1α regulates macrophage polarization, PD-L1 expression, and tumor survival. PLoS Biol 2020; 18:e3000687. [PMID: 32520957 PMCID: PMC7307794 DOI: 10.1371/journal.pbio.3000687] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/22/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
In the tumor microenvironment, local immune dysregulation is driven in part by macrophages and dendritic cells that are polarized to a mixed proinflammatory/immune-suppressive phenotype. The unfolded protein response (UPR) is emerging as the possible origin of these events. Here we report that the inositol-requiring enzyme 1 (IRE1α) branch of the UPR is directly involved in the polarization of macrophages in vitro and in vivo, including the up-regulation of interleukin 6 (IL-6), IL-23, Arginase1, as well as surface expression of CD86 and programmed death ligand 1 (PD-L1). Macrophages in which the IRE1α/X-box binding protein 1 (Xbp1) axis is blocked pharmacologically or deleted genetically have significantly reduced polarization and CD86 and PD-L1 expression, which was induced independent of IFNγ signaling, suggesting a novel mechanism in PD-L1 regulation in macrophages. Mice with IRE1α- but not Xbp1-deficient macrophages showed greater survival than controls when implanted with B16.F10 melanoma cells. Remarkably, we found a significant association between the IRE1α gene signature and CD274 gene expression in tumor-infiltrating macrophages in humans. RNA sequencing (RNASeq) analysis showed that bone marrow-derived macrophages with IRE1α deletion lose the integrity of the gene connectivity characteristic of regulated IRE1α-dependent decay (RIDD) and the ability to activate CD274 gene expression. Thus, the IRE1α/Xbp1 axis drives the polarization of macrophages in the tumor microenvironment initiating a complex immune dysregulation leading to failure of local immune surveillance.
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Affiliation(s)
- Alyssa Batista
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Jeffrey J. Rodvold
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Su Xian
- Division of Medical Genetics; Department of Medicine, and Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America
| | - Stephen C. Searles
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Alyssa Lew
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Takao Iwawaki
- Laboratory for Cell Recovery Mechanisms, Brain Science Institute, RIKEN, Hirosawa, Japan
| | - Gonzalo Almanza
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
| | - T. Cameron Waller
- Division of Medical Genetics; Department of Medicine, and Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America
| | - Jonathan Lin
- Department of Pathology, Stanford University, Palo Alto, California, United States of America
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, California, United States of America
| | - Hannah Carter
- Division of Medical Genetics; Department of Medicine, and Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America
| | - Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California, United States of America
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Nachamanson D, Steward J, Kim T, Yao H, Jeong E, O'Keefe T, Hirst GL, Hasteh F, Jepsen K, Esserman LJ, Borowsky A, Harismendy O. Abstract P4-05-05: A high-sensitivity molecular profiling approach to spatially characterize archived pre-cancer lesions. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-05-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The widespread adoption of breast cancer screening has increased the detection of pre-malignant lesions such as ductal carcinoma in situ (DCIS) but has not translated into increased survival rates. There are currently no reliable biomarkers to stratify DCIS into those which would not develop into an aggressive invasive cancer from those that do, and avoid over-treatment. The interaction with the DCIS microenvironment has likely been under-appreciated or not studied in the adequate clinical context. Importantly, the identification of novel biomarkers in DCIS is notoriously difficult. The rare and late recurrence to subsequent breast cancer (10% at 10 years) poses challenges in experimental design that only a few established, retrospective studies can solve. Most tissue specimens in the associated registries are small, fixed and archived in paraffin (FFPE), precluding their characterization via standard genomic assays. Here, we present an approach combining laser capture microdissection (LCM) with state-of-the-art genomic library preparation methods to enable molecular profiling from minute amounts of damaged nucleic acids and demonstrate its validity for the spatial molecular characterization of DCIS specimen. Methods: Targeted DNA sequencing (whole exome and cancer gene panel) was performed on limited dilutions (200, 50, 10,3 ng) of a test DNA from archived breast tissue, or validation DNA from 10 LCM regions from 3 DCIS specimens. Three library preparation strategies were evaluated, included adaptation of classic A-tailing (AT), or alternate single-strand (SS) or blunt-end (BE) adapter ligations. The expression profiling was performed using SMART-3SEQ protocol on 15 LCM regions from 8 DCIS specimen.
Results: The use of an FFPE-optimized hybrid-capture AT protocol resulted in poor coverage performance (7% of targeted base pairs covered at ≥20x) from test DNA inputs lower than 50 ng and suggested the ligation of the sequencing adapter as the initial bottleneck. Alternatively steps using SS or BE adapter ligation from 3 ng of test DNA (~500 cells) increased the library complexity, reducing the fraction of duplicate reads and increasing the fraction of targeted base pairs covered at 20x to 49% and 100% respectively. Artifactual cytosine to tyrosine substitutions, a signature of formalin damage, were restricted to variants of low allelic fraction (<5%). As a result, the use of molecular barcodes, ensemble variant calling and heuristic variant filtering, resulted in 98% precision and 96% recall in variant calling accuracy from 3ng input, when compared to 200 ng input from a fresh frozen mirrored specimen. Similarly, the presence of an ERBB2 amplification was validated in all tested conditions. The validation of the BE approach on 10 LCM regions from 3 DCIS showed decreasing levels of clonal relationships when comparing regions from adjacent sections, then from matching distinct regions, then from distinct specimen. The heterogeneity of TP53 loss of heterozygosity within a specimen was consistent with high-grade. Furthermore, gene expression profiling of 15 regions from 8 archived DCIS specimen differentiated expression profiles of stromal and epithelial regions, within and between specimen, highlighting sets of genes associated with DCIS subtype and the immune make-up of the micro-environment. Conclusion: The proposed approach - from coordinated specimen preparation to mutational and expression profiling - was therefore validated to support the spatial characterization of pre-cancerous lesions and the microenvironment in which they evolve. Compatible with a limited quantity of tissue from archived specimens, the approach sets a new paradigm for the retrospective molecular characterization of specimen with longitudinal follow-up and associated long-term outcome.
Citation Format: Daniela Nachamanson, Joseph Steward, Taeyong Kim, Huazhen Yao, Eliza Jeong, Thomas O'Keefe, Gillian L. Hirst, Farnaz Hasteh, Kristen Jepsen, Laura J. Esserman, Alexander Borowsky, Olivier Harismendy. A high-sensitivity molecular profiling approach to spatially characterize archived pre-cancer lesions [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-05-05.
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Yamasaki AE, King NE, Matsui H, Jepsen K, Panopoulos AD. Two iPSC lines generated from the bone marrow of a relapsed/refractory AML patient display normal karyotypes and myeloid differentiation potential. Stem Cell Res 2019; 41:101587. [DOI: 10.1016/j.scr.2019.101587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/31/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
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Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol 2019; 20:226. [PMID: 31672156 PMCID: PMC6822431 DOI: 10.1186/s13059-019-1834-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/23/2019] [Indexed: 01/05/2023] Open
Abstract
As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.
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Affiliation(s)
- Jon G Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Rodolfo A Salido
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jeremiah Minich
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Marcus Fedarko
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Timothy D Arthur
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | | | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Greg C Humphrey
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - James Gaffney
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cliff Green
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marlon Liyanage
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Jason W Dang
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Vanessa V Phelan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA
| | - Robert A Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anton Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Douglas J Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P. DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. Epigenetics 2019; 14:365-382. [PMID: 30871403 DOI: 10.1080/15592294.2019.1588682] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Parkinson's Disease (PD) is a common neurodegenerative disorder currently diagnosed based on the presentation of characteristic movement symptoms. Unfortunately, patients exhibiting these symptoms have already undergone significant dopaminergic neuronal loss. Earlier diagnosis, aided by molecular biomarkers specific to PD, would improve overall patient care. Epigenetic mechanisms, which are modified by both environment and disease pathophysiology, are emerging as important components of neurodegeneration. Alterations to the PD methylome have been reported in epigenome-wide association studies. However, the extent to which methylation changes correlate with disease progression has not yet been reported; nor the degree to which methylation is affected by PD medication. We performed a longitudinal genome-wide methylation study surveying ~850,000 CpG sites in whole blood from 189 well-characterized PD patients and 191 control individuals obtained at baseline and at a follow-up visit ~2 y later. We identified distinct patterns of methylation in PD cases versus controls. Importantly, we identified genomic sites where methylation changes longitudinally as the disease progresses. Moreover, we identified methylation changes associated with PD pathology through the analysis of PD cases that were not exposed to anti-parkinsonian therapy. In addition, we identified methylation sites modulated by exposure to dopamine replacement drugs. These results indicate that DNA methylation is dynamic in PD and changes over time during disease progression. To the best of our knowledge, this is the first longitudinal epigenome-wide methylation analysis for Parkinson's disease and reveals changes associated with disease progression and in response to dopaminergic medications in the blood methylome.
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Affiliation(s)
- Adrienne Henderson-Smith
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA.,b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Kathleen M Fisch
- c Center for Computational Biology & Bioinformatics, Department of Medicine , University of California San Diego , La Jolla , CA , USA
| | - Jianping Hua
- d Center for Bioinformatics and Genomics Systems Engineering, Texas A&M Engineering Experiment Station , Texas A&M University , College Station , TX , USA
| | - Ganqiang Liu
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Eugenia Ricciardelli
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Kristen Jepsen
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Mathew Huentelman
- b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Gabriel Stalberg
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA.,g Harvard Biomarkers Study investigators are listed in the Acknowledgement section
| | - Steven D Edland
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA
| | - Clemens R Scherzer
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Travis Dunckley
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Paula Desplats
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA.,i Department of Pathology , University of California San Diego , La Jolla , CA , USA
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27
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Almanza G, Rodvold JJ, Tsui B, Jepsen K, Carter H, Zanetti M. Extracellular vesicles produced in B cells deliver tumor suppressor miR-335 to breast cancer cells disrupting oncogenic programming in vitro and in vivo. Sci Rep 2018; 8:17581. [PMID: 30514916 PMCID: PMC6279829 DOI: 10.1038/s41598-018-35968-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023] Open
Abstract
The successful implementation of miRNA (miR) therapies in humans will ultimately rely on the use of vehicles with improved cellular delivery capability. Here we tested a new system that leverages extracellular vesicles (EVs) laden with a tumor suppressor miRNA (miR-335) produced in B cells by plasmid DNA induction (iEVs). We demonstrate that iEVs-335 efficiently and durably restored the endogenous miR-335 pool in human triple negative breast cancer cells, downregulated the expression of the miR-335 target gene SOX4 transcription factor, and markedly inhibited tumor growth in vivo. Remarkably, iEVs-335 mediated transcriptional effects that persisted in tumors after 60 days post orthotopic implantation. Genome-wide RNASeq analysis of cancer cells treated in vitro with iEVs-335 showed the regulation of a discrete number of genes only, without broad transcriptome perturbations. This new technology may be ideally suited for therapies aimed to restore tumor suppressor miRNAs in cancer cells, disrupting the oncogenic program established after escape from miRNA control.
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Affiliation(s)
- Gonzalo Almanza
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0815, USA
| | - Jeffrey J Rodvold
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0815, USA
| | - Brian Tsui
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0815, USA.
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28
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Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics 2018; 19:199. [PMID: 29703133 PMCID: PMC6389247 DOI: 10.1186/s12864-018-4585-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/08/2018] [Indexed: 01/23/2023] Open
Abstract
Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Electronic supplementary material The online version of this article (10.1186/s12864-018-4585-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jamie P Kershner
- BioFrontiers Institute, Next-Gen Sequencing Facility, University of Colorado Boulder, Boulder, CO, USA
| | - Vincent L Butty
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, MA, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, TX, USA
| | - Edward Wilcox
- DNA Sequencing Center, Brigham Young University, Provo, UT, USA
| | - Jenny Gipson
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Allison Gillaspy
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Krystalynne Morris
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leslie Grimmett
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Prohaska TA, Que X, Diehl CJ, Hendrikx S, Chang MW, Jepsen K, Glass CK, Benner C, Witztum JL. Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies. J Immunol 2018; 200:1702-1717. [PMID: 29378911 PMCID: PMC5821571 DOI: 10.4049/jimmunol.1700568] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022]
Abstract
B-1 cells are a unique subset of B cells that are positively selected for expressing autoreactive BCRs. We isolated RNA from peritoneal (B-1a, B-1b, B-2) and splenic (B-1a, marginal zone, follicular) B cells from C57BL/6 mice and used 5'-RACE to amplify the IgH V region using massively parallel sequencing. By analyzing 379,000 functional transcripts, we demonstrate that B-1a cells use a distinct and restricted repertoire. All B-1 cell subsets, especially peritoneal B-1a cells, had a high proportion of sequences without N additions, suggesting predominantly prenatal development. Their transcripts differed markedly and uniquely contained VH11 and VH12 genes, which were rearranged only with a restricted selection of D and J genes, unlike other V genes. Compared to peritoneal B-1a, the peritoneal B-1b repertoire was larger, had little overlap with B-1a, and most sequences contained N additions. Similarly, the splenic B-1a repertoire differed from peritoneal B-1a sequences, having more unique sequences and more frequent N additions, suggesting influx of B-1a cells into the spleen from nonperitoneal sites. Two CDR3s, previously described as Abs to bromelain-treated RBCs, comprised 43% of peritoneal B-1a sequences. We show that a single-chain variable fragment designed after the most prevalent B-1a sequence bound oxidation-specific epitopes such as the phosphocholine of oxidized phospholipids. In summary, we provide the IgH V region library of six murine B cell subsets, including, to our knowledge for the first time, a comparison between B-1a and B-1b cells, and we highlight qualities of B-1 cell Abs that indicate unique selection processes.
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Affiliation(s)
- Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Xuchu Que
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Cody J Diehl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sabrina Hendrikx
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093; and
| | - Christopher K Glass
- Department of Medicine, University of California San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joseph L Witztum
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
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Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports 2017; 8:1086-1100. [PMID: 28410642 PMCID: PMC5390244 DOI: 10.1016/j.stemcr.2017.03.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 03/08/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.
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Affiliation(s)
- Athanasia D Panopoulos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roy Williams
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sherin I Hashem
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernhard M Schuldt
- Zentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany
| | - Christopher DeBoever
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo D Arias
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Melvin Garcia
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley C Nelson
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Harismendy
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - David A Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - William W Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - KathyJean Farnam
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Cook
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Borja
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carl A Miller
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan D Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Frauke Drees
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Okubo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Yuriko Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Veronica Modesto
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carl T Dargitz
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rachel Feiring
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chang Zhao
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aitor Aguirre
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas J McGarry
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joaquin Reyna
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fangwen Rao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel T O'Connor
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sylvia M Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neil C Chi
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Franz-Josef Müller
- Zentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany
| | - Lawrence S B Goldstein
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Eric Adler
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - W Travis Berggren
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Erin N Smith
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell 2017; 20:533-546.e7. [PMID: 28388430 PMCID: PMC5444918 DOI: 10.1016/j.stem.2017.03.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 12/27/2016] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes. We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally. We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions. In addition, we were able to identify effects on gene expression of rare genic CNVs and regulatory single-nucleotide variants and found that reactivation of gene expression on the X chromosome depends on gene chromosomal position. Our work highlights the value of iPSCs for genetic association analyses and provides a unique resource for investigating the genetic regulation of gene expression in pluripotent cells.
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Affiliation(s)
- Christopher DeBoever
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Paola Benaglio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Joaquin Reyna
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Katrina M Olson
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Hui Huang
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | | | | | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Angelo Arias
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Bing Ren
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Naoki Nariai
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | | | - Emma K Farley
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0419, USA.
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA.
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Sartori E, Carvalho L, Zutin E, Mendonca D, Smith L, Vasconcellos L, Jepsen K, Krebsbach P, Mendonca G. Effect of titanium nanotopography on mobilization of mesenchymal stem cells. Dent Mater 2016. [DOI: 10.1016/j.dental.2016.08.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jepsen K, Jepsen S, Laine M, Anssari Moin D, Pilloni A, Zeza B, Sanz M, Ortiz-Vigon A, Roos-Jansåker A, Renvert S. Reconstruction of Peri-implant Osseous Defects. J Dent Res 2015; 95:58-66. [DOI: 10.1177/0022034515610056] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
There is a paucity of data for the effectiveness of reconstructive procedures in the treatment of peri-implantitis. The objective of this study was to compare reconstruction of peri-implant osseous defects with open flap debridement (OFD) plus porous titanium granules (PTGs) compared with OFD alone. Sixty-three patients (36 female, 27 male; mean age 58.4 y [SD 12.3]), contributing one circumferential peri-implant intraosseous defect, were included in a multinational, multicenter randomized trial using a parallel-group design. After OFD and surface decontamination using titanium brushes and hydrogen peroxide, 33 defects received PTGs. The implants were not submerged. All patients received adjunctive perioperative systemic antibiotics. The primary outcome variable (defect fill) was assessed on digitalized radiographs. Clinical measurements of probing depth (PPD), bleeding on probing (BoP), suppuration, and plaque were taken by blinded examiners. After 12 mo, the test group (OFD plus PTG) showed a mean radiographic defect fill (mesial/distal) of 3.6/3.6 mm compared with 1.1/1.0 in the control group (OFD). Differences were statistically significant in favor of the test group ( P < 0.0001). The OFD plus PTG group showed a mean reduction in PPD of 2.8 mm compared with 2.6 mm in the OFD group. BoP was reduced from 89.4% to 33.3% and from 85.8% to 40.4% for the test and control groups, respectively. There was no significant difference in complete resolution of peri-implantitis (PPD ≤4 mm and no BoP at six implant sites and no further bone loss), because this finding was accomplished at 30% of implants in the test group and 23% of implants in the control group. Reconstructive surgery using PTGs resulted in significantly enhanced radiographic defect fill compared with OFD. However, limitations in the lack of ability to discern biomaterial from osseous tissue could not be verified to determine new bone formation. Similar improvements according to clinical measures were obtained after both surgical treatment modalities (ClinicalTrials.gov NCT02406001).
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Affiliation(s)
- K. Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Bonn, Germany
| | - S. Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Bonn, Germany
| | - M.L. Laine
- Department of Periodontology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
| | - D. Anssari Moin
- Department of Periodontology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University, Amsterdam, The Netherlands
| | - A. Pilloni
- Section of Periodontics, University of Rome, Sapienza, Italy
| | - B. Zeza
- Section of Periodontics, University of Rome, Sapienza, Italy
| | - M. Sanz
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group, University Complutense, Madrid, Spain
| | - A. Ortiz-Vigon
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group, University Complutense, Madrid, Spain
| | - A.M. Roos-Jansåker
- Department of Periodontology, Public Dental Health Service,
Kristianstad, Sweden
- Department of Oral Sciences, Kristianstad University, Kristianstad, Sweden
| | - S. Renvert
- Department of Periodontology, Public Dental Health Service,
Kristianstad, Sweden
- Department of Oral Sciences, Kristianstad University, Kristianstad, Sweden
- Blekinge Institute of Technology, Karlskrona, Sweden
- School of Dental Sciences, Trinity College, Dublin, Ireland
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Harismendy O, Alakus H, Yost S, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM. Abstract 4803: BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Malignant mesothelioma (MM) arises from mesothelial cells that line the pleural, peritoneal and pericardial surfaces. The majority of MMs are pleural and have been associated with asbestos exposure. Previously, pleural MMs have been genetically characterized by the loss of BAP1 (40-60%) as well as loss of NF2 (75%) and CDKN2A (60%). The rare peritoneal form of MM occurs in ∼10% cases. With only ∼300 cases diagnosed in the US per year, its link to asbestos exposure is not clear and its mutational landscape unknown. We analyzed the somatic mutational landscape of 12 peritoneal MM of epitheloid subtype using copy number analysis (N = 9), whole exome sequencing (N = 7) and targeted sequencing (N = 12). Peritoneal MM display few copy number alterations, with most samples having less than 10 Mbp total changes, mostly through deletions and no high copy number amplification. Chromosome band 3p21 encoding BAP1 is the most recurrently deleted region (5/9), while, in contrast to pleural MM, NF2 and CDKN2A are not affected. We further identified 87 non-silent mutations across 7 sequenced tumors, with a median of 8 mutated genes per tumor, resulting in a very low mutation rate (median 1.3 10-6). BAP1 was the only recurrently mutated gene (N = 3/7). In one additional case, loss of the entire chromosome 3 leaves a non-functional copy of BAP1 carrying a rare nonsense germline variant, thus suggesting a potential genetic predisposition in this patient. Finally, with targeted sequencing of BAP1 in 3 additional cases, we conclude that BAP1 is frequently altered through copy number losses (N = 3/12), mutations (N = 3/12) or both (N = 2/12) sometimes at a sub-clonal level. Our findings suggest a major role for BAP1 in peritoneal MM susceptibility and oncogenesis and indicate important molecular differences to pleural MM as well as potential strategies for therapy and prevention.
Citation Format: Olivier Harismendy, Hakan Alakus, Shawn Yost, Brian Woo, Randall French, Grace Y. Lin, Kristen Jepsen, Kelly A. Frazer, Andrew M. Lowy. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4803. doi:10.1158/1538-7445.AM2015-4803
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Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med 2015; 13:122. [PMID: 25889843 PMCID: PMC4422481 DOI: 10.1186/s12967-015-0485-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malignant mesothelioma (MM) arises from mesothelial cells that line the pleural, peritoneal and pericardial surfaces. The majority of MMs are pleural and have been associated with asbestos exposure. Previously, pleural MMs have been genetically characterized by the loss of BAP1 (40-60%) as well as loss of NF2 (75%) and CDKN2A (60%). The rare peritoneal form of MM occurs in ~10% cases. With only ~300 cases diagnosed in the US per year, its link to asbestos exposure is not clear and its mutational landscape unknown. METHODS We analyzed the somatic mutational landscape of 12 peritoneal MM of epitheloid subtype using copy number analysis (N = 9), whole exome sequencing (N = 7) and targeted sequencing (N = 12). RESULTS Peritoneal MM display few copy number alterations, with most samples having less than 10 Mbp total changes, mostly through deletions and no high copy number amplification. Chromosome band 3p21 encoding BAP1 is the most recurrently deleted region (5/9), while, in contrast to pleural MM, NF2 and CDKN2A are not affected. We further identified 87 non-silent mutations across 7 sequenced tumors, with a median of 8 mutated genes per tumor, resulting in a very low mutation rate (median 1.3 10(-6)). BAP1 was the only recurrently mutated gene (N = 3/7). In one additional case, loss of the entire chromosome 3 leaves a non-functional copy of BAP1 carrying a rare nonsense germline variant, thus suggesting a potential genetic predisposition in this patient. Finally, with targeted sequencing of BAP1 in 3 additional cases, we conclude that BAP1 is frequently altered through copy number losses (N = 3/12), mutations (N = 3/12) or both (N = 2/12) sometimes at a sub-clonal level. CONCLUSION Our findings suggest a major role for BAP1 in peritoneal MM susceptibility and oncogenesis and indicate important molecular differences to pleural MM as well as potential strategies for therapy and prevention.
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Affiliation(s)
- Hakan Alakus
- Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany. .,Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Shawn E Yost
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA.
| | - Brian Woo
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA.
| | - Randall French
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Grace Y Lin
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA. .,Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Andrew M Lowy
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
| | - Olivier Harismendy
- Moores UCSD Cancer Center, 3855 Health Science Drive, Maildrop 0820, 92093, La Jolla, USA. .,Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CHM, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J 2015; 5:e303. [PMID: 25860294 PMCID: PMC4450323 DOI: 10.1038/bcj.2015.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023] Open
Abstract
We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
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Affiliation(s)
- E N Smith
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - E M Ghia
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - C M DeBoever
- Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA
| | - L Z Rassenti
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K Jepsen
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K-A Yoon
- Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA
| | - H Matsui
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - S Rozenzhak
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - H Alakus
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - P J Shepard
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Y Dai
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - M Khosroheidari
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - M Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - K L Gunderson
- Illumina, Inc., 5200 Illumina Way, San Diego, CA, USA
| | - K Messer
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - L Muthuswamy
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - T J Hudson
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - O Harismendy
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C L Barrett
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C H M Jamieson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA [3] Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - D A Carson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - T J Kipps
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K A Frazer
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [3] Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA [4] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
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DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CHM, Carson D, Kipps TJ, Frazer KA. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol 2015; 11:e1004105. [PMID: 25768983 PMCID: PMC4358997 DOI: 10.1371/journal.pcbi.1004105] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/12/2023] Open
Abstract
Mutations in the splicing factor SF3B1 are found in several cancer types and have been associated with various splicing defects. Using transcriptome sequencing data from chronic lymphocytic leukemia, breast cancer and uveal melanoma tumor samples, we show that hundreds of cryptic 3’ splice sites (3’SSs) are used in cancers with SF3B1 mutations. We define the necessary sequence context for the observed cryptic 3’ SSs and propose that cryptic 3’SS selection is a result of SF3B1 mutations causing a shift in the sterically protected region downstream of the branch point. While most cryptic 3’SSs are present at low frequency (<10%) relative to nearby canonical 3’SSs, we identified ten genes that preferred out-of-frame cryptic 3’SSs. We show that cancers with mutations in the SF3B1 HEAT 5-9 repeats use cryptic 3’SSs downstream of the branch point and provide both a mechanistic model consistent with published experimental data and affected targets that will guide further research into the oncogenic effects of SF3B1 mutation. A key goal of cancer genomics studies is to identify genes that are recurrently mutated at a rate above background and likely contribute to cancer development. Many such recurrently mutated genes have been identified over the last few years, but we often do not know the underlying mechanisms by which they contribute to cancer growth. Unexpectedly, several genes in the spliceosome, the collection of RNAs and proteins that remove introns from transcribed RNAs, are recurrently mutated in different cancers. Here, we have examined mutations in the splicing factor SF3B1, a key component of the spliceosome, and identified a global splicing defect present in different cancers with SF3B1 mutations by comparing the expression of splice junctions using generalized linear models. While prior studies have reported a limited number of aberrant splicing events in SF3B1-mutated cancers, we have established that SF3B1 mutations are associated with usage of hundreds of atypical splice sites at the 3’ end of the intron. We have identified nucleotide sequence requirements for these cryptic splice sites that are consistent with a proposed mechanistic model. These findings greatly expand our understanding of the effect of SF3B1 mutations on splicing and provide new targets for determining the oncogenic effect of SF3B1 mutations.
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Affiliation(s)
- Christopher DeBoever
- Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Emanuela M. Ghia
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Peter J. Shepard
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Laura Rassenti
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Christian L. Barrett
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Catriona H. M. Jamieson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Dennis Carson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Kelly A. Frazer
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Boland BS, Widjaja CE, Banno A, Zhang B, Kim SH, Stoven S, Peterson MR, Jones MC, Su HI, Crowe SE, Bui JD, Ho SB, Okugawa Y, Goel A, Marietta EV, Khosroheidari M, Jepsen K, Aramburu J, López-Rodríguez C, Sandborn WJ, Murray JA, Harismendy O, Chang JT. Immunodeficiency and autoimmune enterocolopathy linked to NFAT5 haploinsufficiency. J Immunol 2015; 194:2551-60. [PMID: 25667416 DOI: 10.4049/jimmunol.1401463] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The link between autoimmune diseases and primary immunodeficiency syndromes has been increasingly appreciated. Immunologic evaluation of a young man with autoimmune enterocolopathy and unexplained infections revealed evidence of immunodeficiency, including IgG subclass deficiency, impaired Ag-induced lymphocyte proliferation, reduced cytokine production by CD8(+) T lymphocytes, and decreased numbers of NK cells. Genetic evaluation identified haploinsufficiency of NFAT5, a transcription factor regulating immune cell function and cellular adaptation to hyperosmotic stress, as a possible cause of this syndrome. Inhibition or deletion of NFAT5 in normal human and murine cells recapitulated several of the immune deficits identified in the patient. These results provide evidence of a primary immunodeficiency disorder associated with organ-specific autoimmunity linked to NFAT5 deficiency.
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Affiliation(s)
- Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093
| | | | - Asoka Banno
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Bing Zhang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Stephanie H Kim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | | | - Michael R Peterson
- Western Washington Pathology and Multicare Health System, Tacoma, WA 98405
| | - Marilyn C Jones
- Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA 92093
| | - H Irene Su
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sheila E Crowe
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Samuel B Ho
- Department of Pathology, University of California San Diego, La Jolla, CA 92093
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246; Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Epigenetics, Cancer Prevention and Cancer Genomics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246; Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246
| | | | - Mahdieh Khosroheidari
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kristen Jepsen
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jose Aramburu
- Immunology Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003 Spain; and
| | - Cristina López-Rodríguez
- Immunology Unit, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003 Spain; and
| | - William J Sandborn
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093
| | | | - Olivier Harismendy
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093; Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA 92093;
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Alakus H, Babicky M, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels M, Mose E, Peterson M, Lowy A, Frazer K, Harismendy O. Abstract 5191: Genome-wide mutational analysis reveals core signaling pathways in mucinous neoplasms of the appendix. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mucinous Neoplasm of the Appendix (MNA) is a rare malignancy often diagnosed after metastasis to the peritoneal surfaces resulting in Mucinous Carcinomatosis Peritonei (MCP). Genetic alterations in MNA are poorly characterized due to its low incidence, the hypo-cellularity of MCPs and a lack of relevant pre-clinical models. As such, application of targeted therapies to this disease is limited to those developed for colorectal cancer (CRC) and not based on molecular rationale. We sequenced the whole exomes of 10 MCPs to identify genome-wide somatic mutations and copy number aberrations and validated significant findings in 19 additional cases using deep sequencing and microdroplet PCR. These studies demonstrate that MNA has a different molecular makeup than CRC. Most tumors have co-existing oncogenic mutations in KRAS (26/29) and GNAS (21/29) and are characterized by cAMP-PKA pathway activation. High-grade tumors are GNAS wild-type (5/6), suggesting they do not progress from low-grade tumors. MNAs do share some genetic alterations with CRC including gain of 1q (5/10), Wnt and TGFβ pathway alteration. In contrast, mutations in TP53 (1/10) and APC (0/10), common in CRC, are rare in MNA. Coincident activation of the Ras-Raf-MEK-ERK and cAMP-PKA signaling pathways appears to be shared with pancreatic intraductal papillary mucinous neoplasm. Thus, MNA genome-wide mutational analysis reveals genetic alterations distinct from CRC, in support its unique pathophysiology and suggests MEK and PKA inhibition as new therapeutic opportunities.
Citation Format: Hakan Alakus, Michele Babicky, Pradipta Ghosh, Shawn Yost, Kristen Jepsen, Yang Dai, Angelo Arias, Michael Samuels, Evangeline Mose, Michael Peterson, Andrew Lowy, Kelly Frazer, Olivier Harismendy. Genome-wide mutational analysis reveals core signaling pathways in mucinous neoplasms of the appendix. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5191. doi:10.1158/1538-7445.AM2014-5191
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Castelo-Branco G, Lilja T, Wallenborg K, Falcão AM, Marques SC, Gracias A, Solum D, Paap R, Walfridsson J, Teixeira AI, Rosenfeld MG, Jepsen K, Hermanson O. Neural stem cell differentiation is dictated by distinct actions of nuclear receptor corepressors and histone deacetylases. Stem Cell Reports 2014; 3:502-15. [PMID: 25241747 PMCID: PMC4266002 DOI: 10.1016/j.stemcr.2014.07.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 01/16/2023] Open
Abstract
Signaling factors including retinoic acid (RA) and thyroid hormone (T3) promote neuronal, oligodendrocyte, and astrocyte differentiation of cortical neural stem cells (NSCs). However, the functional specificity of transcriptional repressor checkpoints controlling these differentiation programs remains unclear. Here, we show by genome-wide analysis that histone deacetylase (HDAC)2 and HDAC3 show overlapping and distinct promoter occupancy at neuronal and oligodendrocyte-related genes in NSCs. The absence of HDAC3, but not HDAC2, initiated a neuronal differentiation pathway in NSCs. The ablation of the corepressor NCOR or HDAC2, in conjunction with T3 treatment, resulted in increased expression of oligodendrocyte genes, revealing a direct HDAC2-mediated repression of Sox8 and Sox10 expression. Interestingly, Sox10 was required also for maintaining the more differentiated state by repression of stem cell programming factors such as Sox2 and Sox9. Distinct and nonredundant actions of NCORs and HDACs are thus critical for control of lineage progression and differentiation programs in neural progenitors. ChIP-seq reveals distinct and overlapping occupancy of HDAC2 and HDAC3 in NSCs Absence of NCOR promotes oligodendrocyte differentiation of NSCs HDAC2 controls Sox10 expression in OL differentiation via a SOX2-occupied enhancer Sox10 is required for maintaining the differentiated state in late OL precursors
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Affiliation(s)
- Gonçalo Castelo-Branco
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Tobias Lilja
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Karolina Wallenborg
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ana M Falcão
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Sueli C Marques
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Aileen Gracias
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Derek Solum
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0648, USA
| | - Ricardo Paap
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julian Walfridsson
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Ana I Teixeira
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0648, USA
| | - Kristen Jepsen
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0648, USA
| | - Ola Hermanson
- Linnaeus Center in Developmental Biology for Regenerative Medicine (DBRM), Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden.
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Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol 2014; 15:420. [PMID: 25103687 PMCID: PMC4165357 DOI: 10.1186/s13059-014-0420-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/07/2014] [Indexed: 11/17/2022] Open
Abstract
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
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Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer KA, Harismendy O. Correction: Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med 2014; 6:53. [PMID: 25228923 PMCID: PMC4165363 DOI: 10.1186/s13073-014-0053-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/04/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Hakan Alakus
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA ; Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany
| | - Michele L Babicky
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA USA
| | - Pradipta Ghosh
- Department of Medicine, University of California San Diego, La Jolla, CA USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA USA
| | - Shawn Yost
- Bioinformatics Graduate Program, University of California San Diego, La Jolla, CA USA
| | - Kristen Jepsen
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA
| | - Yang Dai
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA
| | - Angelo Arias
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA
| | | | - Evangeline S Mose
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA USA
| | - Richard B Schwab
- Department of Medicine, University of California San Diego, La Jolla, CA USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA USA
| | - Michael R Peterson
- Department of Pathology, University of California San Diego, La Jolla, CA USA
| | - Andrew M Lowy
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA USA
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA USA ; Clinical and Translational Science Institute, University of California San Diego, La Jolla, CA USA ; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA USA
| | - Olivier Harismendy
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA USA ; Clinical and Translational Science Institute, University of California San Diego, La Jolla, CA USA
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Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer KA, Harismendy O. Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med 2014; 6:43. [PMID: 24944587 PMCID: PMC4062050 DOI: 10.1186/gm559] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/23/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mucinous neoplasms of the appendix (MNA) are rare tumors which may progress from benign to malignant disease with an aggressive biological behavior. MNA is often diagnosed after metastasis to the peritoneal surfaces resulting in mucinous carcinomatosis peritonei (MCP). Genetic alterations in MNA are poorly characterized due to its low incidence, the hypo-cellularity of MCPs, and a lack of relevant pre-clinical models. As such, application of targeted therapies to this disease is limited to those developed for colorectal cancer and not based on molecular rationale. METHODS We sequenced the whole exomes of 10 MCPs of appendiceal origin to identify genome-wide somatic mutations and copy number aberrations and validated significant findings in 19 additional cases. RESULTS Our study demonstrates that MNA has a different molecular makeup than colorectal cancer. Most tumors have co-existing oncogenic mutations in KRAS (26/29) and GNAS (20/29) and are characterized by downstream PKA activation. High-grade tumors are GNAS wild-type (5/6), suggesting they do not progress from low-grade tumors. MNAs do share some genetic alterations with colorectal cancer including gain of 1q (5/10), Wnt, and TGFβ pathway alterations. In contrast, mutations in TP53 (1/10) and APC (0/10), common in colorectal cancer, are rare in MNA. Concurrent activation of the KRAS and GNAS mediated signaling pathways appears to be shared with pancreatic intraductal papillary mucinous neoplasm. CONCLUSIONS MNA genome-wide mutational analysis reveals genetic alterations distinct from colorectal cancer, in support of its unique pathophysiology and suggests new targeted therapeutic opportunities.
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Affiliation(s)
- Hakan Alakus
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA ; Department of General, Visceral and Cancer Surgery, University of Cologne, Köln, Germany
| | - Michele L Babicky
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Department of Medicine, University of California San Diego, La Jolla, CA, USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Shawn Yost
- Bioinformatics Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA
| | - Yang Dai
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA
| | - Angelo Arias
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA
| | | | - Evangeline S Mose
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Richard B Schwab
- Department of Medicine, University of California San Diego, La Jolla, CA, USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Peterson
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Andrew M Lowy
- Division of Surgical Oncology, Department of Surgery, University of California San Diego, La Jolla, CA, USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA ; Clinical and Translational Science Institute, University of California San Diego, La Jolla, CA, USA ; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Olivier Harismendy
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children's Hospital, University of California San Diego, La Jolla, CA, USA ; Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA ; Clinical and Translational Science Institute, University of California San Diego, La Jolla, CA, USA
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Smith EN, Jepsen K, Arias AD, Shepard PJ, Chambers CD, Frazer KA. Genetic ancestry of participants in the National Children's Study. Genome Biol 2014; 15:R22. [PMID: 24490717 PMCID: PMC4053981 DOI: 10.1186/gb-2014-15-2-r22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/03/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The National Children's Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes. RESULTS We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories. CONCLUSIONS Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.
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He G, Dhar D, Nakagawa H, Font-Burgada J, Ogata H, Jiang Y, Shalapour S, Seki E, Yost SE, Jepsen K, Frazer KA, Harismendy O, Hatziapostolou M, Iliopoulos D, Suetsugu A, Hoffman RM, Tateishi R, Koike K, Karin M. Identification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling. Cell 2013; 155:384-96. [PMID: 24120137 DOI: 10.1016/j.cell.2013.09.031] [Citation(s) in RCA: 340] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 06/04/2013] [Accepted: 09/19/2013] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a slowly developing malignancy postulated to evolve from premalignant lesions in chronically damaged livers. However, it was never established that premalignant lesions actually contain tumor progenitors that give rise to cancer. Here, we describe isolation and characterization of HCC progenitor cells (HcPCs) from different mouse HCC models. Unlike fully malignant HCC, HcPCs give rise to cancer only when introduced into a liver undergoing chronic damage and compensatory proliferation. Although HcPCs exhibit a similar transcriptomic profile to bipotential hepatobiliary progenitors, the latter do not give rise to tumors. Cells resembling HcPCs reside within dysplastic lesions that appear several months before HCC nodules. Unlike early hepatocarcinogenesis, which depends on paracrine IL-6 production by inflammatory cells, due to upregulation of LIN28 expression, HcPCs had acquired autocrine IL-6 signaling that stimulates their in vivo growth and malignant progression. This may be a general mechanism that drives other IL-6-producing malignancies.
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Affiliation(s)
- Guobin He
- Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, University of California San Diego, School of Medicine, 9500 Gilman Drive, San Diego, CA 92093, USA
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Harismendy O, Schwab RB, Alakus H, Yost SE, Matsui H, Hasteh F, Wallace AM, Park HL, Madlensky L, Parker B, Carpenter PM, Jepsen K, Anton-Culver H, Frazer KA. Evaluation of ultra-deep targeted sequencing for personalized breast cancer care. Breast Cancer Res 2013; 15:R115. [PMID: 24326041 PMCID: PMC3978701 DOI: 10.1186/bcr3584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 12/06/2013] [Indexed: 01/24/2023] Open
Abstract
INTRODUCTION The increasing number of targeted therapies, together with a deeper understanding of cancer genetics and drug response, have prompted major healthcare centers to implement personalized treatment approaches relying on high-throughput tumor DNA sequencing. However, the optimal way to implement this transformative methodology is not yet clear. Current assays may miss important clinical information such as the mutation allelic fraction, the presence of sub-clones or chromosomal rearrangements, or the distinction between inherited variants and somatic mutations. Here, we present the evaluation of ultra-deep targeted sequencing (UDT-Seq) to generate and interpret the molecular profile of 38 breast cancer patients from two academic medical centers. METHODS We sequenced 47 genes in matched germline and tumor DNA samples from 38 breast cancer patients. The selected genes, or the pathways they belong to, can be targeted by drugs or are important in familial cancer risk or drug metabolism. RESULTS Relying on the added value of sequencing matched tumor and germline DNA and using a dedicated analysis, UDT-Seq has a high sensitivity to identify mutations in tumors with low malignant cell content. Applying UDT-Seq to matched tumor and germline specimens from the 38 patients resulted in a proposal for at least one targeted therapy for 22 patients, the identification of tumor sub-clones in 3 patients, the suggestion of potential adverse drug effects in 3 patients and a recommendation for genetic counseling for 2 patients. CONCLUSION Overall our study highlights the additional benefits of a sequencing strategy, which includes germline DNA and is optimized for heterogeneous tumor tissues.
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Affiliation(s)
- Olivier Harismendy
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
- Moores UCSD Cancer Center, School of Medicine, University of California San Diego, 3855 Health Science Drive, La Jolla CA 92093, USA
- Clinical and Translational Science Institute, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Richard B Schwab
- Moores UCSD Cancer Center, School of Medicine, University of California San Diego, 3855 Health Science Drive, La Jolla CA 92093, USA
- Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Hakan Alakus
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Shawn E Yost
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
- Department of Surgery, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Hiroko Matsui
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Farnaz Hasteh
- Bioinformatics Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Anne M Wallace
- Moores UCSD Cancer Center, School of Medicine, University of California San Diego, 3855 Health Science Drive, La Jolla CA 92093, USA
- Department of Family and Preventive Medicine, School of Medicine, University of California San Diego, La Jolla CA, USA
| | - Hannah L Park
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Lisa Madlensky
- Moores UCSD Cancer Center, School of Medicine, University of California San Diego, 3855 Health Science Drive, La Jolla CA 92093, USA
- Department of Epidemiology, School of Medicine, University of California Irvine, 252 Irvine Hall, Irvine CA 92697, USA
| | - Barbara Parker
- Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Philip M Carpenter
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, 252 Irvine Hall, Irvine CA 92697, USA
| | - Kristen Jepsen
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Hoda Anton-Culver
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Kelly A Frazer
- Division of Genome Information Sciences, Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
- Moores UCSD Cancer Center, School of Medicine, University of California San Diego, 3855 Health Science Drive, La Jolla CA 92093, USA
- Clinical and Translational Science Institute, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
- Department of General, Visceral and Cancer Surgery, University of Cologne, Frangenheimstraße 4, 50931, Köln Germany
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Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. ACTA ACUST UNITED AC 2013; 29:1908-9. [PMID: 23712659 PMCID: PMC3712217 DOI: 10.1093/bioinformatics/btt305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Summary: We present Mutascope, a sequencing analysis pipeline specifically developed for the identification of somatic variants present at low-allelic fraction from high-throughput sequencing of amplicons from matched tumor-normal specimen. Using datasets reproducing tumor genetic heterogeneity, we demonstrate that Mutascope has a higher sensitivity and generates fewer false-positive calls than tools designed for shotgun sequencing or diploid genomes. Availability: Freely available on the web at http://sourceforge.net/projects/mutascope/. Contact:oharismendy@ucsd.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shawn E Yost
- Bioinformatics Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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Grossman TR, Gamliel A, Wessells RJ, Taghli-Lamallem O, Jepsen K, Ocorr K, Korenberg JR, Peterson KL, Rosenfeld MG, Bodmer R, Bier E. Over-expression of DSCAM and COL6A2 cooperatively generates congenital heart defects. PLoS Genet 2011; 7:e1002344. [PMID: 22072978 PMCID: PMC3207880 DOI: 10.1371/journal.pgen.1002344] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/29/2011] [Indexed: 11/19/2022] Open
Abstract
A significant current challenge in human genetics is the identification of interacting genetic loci mediating complex polygenic disorders. One of the best characterized polygenic diseases is Down syndrome (DS), which results from an extra copy of part or all of chromosome 21. A short interval near the distal tip of chromosome 21 contributes to congenital heart defects (CHD), and a variety of indirect genetic evidence suggests that multiple candidate genes in this region may contribute to this phenotype. We devised a tiered genetic approach to identify interacting CHD candidate genes. We first used the well vetted Drosophila heart as an assay to identify interacting CHD candidate genes by expressing them alone and in all possible pairwise combinations and testing for effects on rhythmicity or heart failure following stress. This comprehensive analysis identified DSCAM and COL6A2 as the most strongly interacting pair of genes. We then over-expressed these two genes alone or in combination in the mouse heart. While over-expression of either gene alone did not affect viability and had little or no effect on heart physiology or morphology, co-expression of the two genes resulted in ≈50% mortality and severe physiological and morphological defects, including atrial septal defects and cardiac hypertrophy. Cooperative interactions between DSCAM and COL6A2 were also observed in the H9C2 cardiac cell line and transcriptional analysis of this interaction points to genes involved in adhesion and cardiac hypertrophy. Our success in defining a cooperative interaction between DSCAM and COL6A2 suggests that the multi-tiered genetic approach we have taken involving human mapping data, comprehensive combinatorial screening in Drosophila, and validation in vivo in mice and in mammalian cells lines should be applicable to identifying specific loci mediating a broad variety of other polygenic disorders.
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Affiliation(s)
- Tamar R. Grossman
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Amir Gamliel
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | | | - Ouarda Taghli-Lamallem
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Kristen Jepsen
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Karen Ocorr
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Julie R. Korenberg
- The Brain Institute, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Kirk L. Peterson
- School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Rolf Bodmer
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
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Solá S, Xavier JM, Santos DM, Aranha MM, Morgado AL, Jepsen K, Rodrigues CMP. p53 interaction with JMJD3 results in its nuclear distribution during mouse neural stem cell differentiation. PLoS One 2011; 6:e18421. [PMID: 21483786 PMCID: PMC3069089 DOI: 10.1371/journal.pone.0018421] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 03/02/2011] [Indexed: 12/15/2022] Open
Abstract
Conserved elements of apoptosis are also integral components of cellular differentiation. In this regard, p53 is involved in neurogenesis, being required for neurite outgrowth in primary neurons and for axonal regeneration in mice. Interestingly, demethylases regulate p53 activity and its interaction with co-activators by acting on non-histone proteins. In addition, the histone H3 lysine 27-specific demethylase JMJD3 induces ARF expression, thereby stabilizing p53 in mouse embryonic fibroblasts. We hypothesized that p53 interacts with key regulators of neurogenesis to redirect stem cells to differentiation, as an alternative to cell death. Specifically, we investigated the potential cross-talk between p53 and JMJD3 during mouse neural stem cell (NSC) differentiation. Our results demonstrated that JMJD3 mRNA and protein levels were increased early in mouse NSC differentiation, when JMJD3 activity was readily detected. Importantly, modulation of JMJD3 in NSCs resulted in changes of total p53 protein, coincident with increased ARF mRNA and protein expression. ChIP analysis revealed that JMJD3 was present at the promoter and exon 1 regions of ARF during neural differentiation, although without changes in H3K27me3. Immunoprecipitation assays demonstrated a direct interaction between p53 and JMJD3, independent of the C-terminal region of JMJD3, and modulation of p53 methylation by JMJD3-demethylase activity. Finally, transfection of mutant JMJD3 showed that the demethylase activity of JMJD3 was crucial in regulating p53 cellular distribution and function. In conclusion, JMJD3 induces p53 stabilization in mouse NSCs through ARF-dependent mechanisms, directly interacts with p53 and, importantly, causes nuclear accumulation of p53. This suggests that JMJD3 and p53 act in a common pathway during neurogenesis.
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Affiliation(s)
- Susana Solá
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.
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Abstract
A crucial aspect of development, homeostasis and prevention of disease is the strict maintenance of patterns of gene repression. Gene repression is largely achieved by the combinatorial action of various enzymatic complexes - known as co-repressor complexes - that are recruited to DNA by transcription factors and often act through enzymatic modification of histone protein tails. Our understanding of how co-repressors act has begun to change over recent years owing to the increased availability of genome-scale data. Here, we consider specific strategies that underlie repression events - for example, those mediated by the nuclear receptor co-repressor (NCoR, also known as NCOR1) and silencing mediator of retinoic acid and thyroid hormone receptor (SMRT, also known as NCOR2) co-repressor complexes - and discuss emerging themes in gene repression.
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Affiliation(s)
- Valentina Perissi
- Department of Medicine, Howard Hughes Medical Institute, School of Medicine, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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