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Gernez Y, Narula M, Cepika AM, Valdes Camacho J, Hoyte EG, Mouradian K, Glader B, Singh D, Sathi B, Rao L, Tolin AL, Weinberg KI, Lewis DB, Bacchetta R, Weinacht KG. Case report: Refractory Evans syndrome in two patients with spondyloenchondrodysplasia with immune dysregulation treated successfully with JAK1/JAK2 inhibition. Front Immunol 2024; 14:1328005. [PMID: 38347954 PMCID: PMC10859398 DOI: 10.3389/fimmu.2023.1328005] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/28/2023] [Indexed: 02/15/2024] Open
Abstract
Biallelic mutations in the ACP5 gene cause spondyloenchondrodysplasia with immune dysregulation (SPENCDI). SPENCDI is characterized by the phenotypic triad of skeletal dysplasia, innate and adaptive immune dysfunction, and variable neurologic findings ranging from asymptomatic brain calcifications to severe developmental delay with spasticity. Immune dysregulation in SPENCDI is often refractory to standard immunosuppressive treatments. Here, we present the cases of two patients with SPENCDI and recalcitrant autoimmune cytopenias who demonstrated a favorable clinical response to targeted JAK inhibition over a period of more than 3 years. One of the patients exhibited steadily rising IgG levels and a bone marrow biopsy revealed smoldering multiple myeloma. A review of the literature uncovered that approximately half of the SPENCDI patients reported to date exhibited increased IgG levels. Screening for multiple myeloma in SPENCDI patients with rising IgG levels should therefore be considered.
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Affiliation(s)
- Yael Gernez
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Mansi Narula
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Alma-Martina Cepika
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Juanita Valdes Camacho
- Division of Allergy and Immunology, Department of Pediatrics, Louisiana State University (LSU) Health, Shreveport, LA, United States
| | - Elisabeth G. Hoyte
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Kirsten Mouradian
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Bertil Glader
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Deepika Singh
- Division of Rheumatology, Department of Pediatrics, Valley Children Hospital, Madera, CA, United States
| | - Bindu Sathi
- Division of Hematology, Department of Pediatrics, Valley Children Hospital, Madera, CA, United States
| | - Latha Rao
- Division of Hematology, Department of Pediatrics, Valley Children Hospital, Madera, CA, United States
| | - Ana L. Tolin
- Division of Immunology, Department of Pediatrics, Hospital Pediatrico Dr. Humberto Notti, Mendoza, Argentina
| | - Kenneth I. Weinberg
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - David B. Lewis
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Rosa Bacchetta
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
| | - Katja G. Weinacht
- Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, CA, United States
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2
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Guo J, Chowdhury RR, Mallajosyula V, Xie J, Dubey M, Liu Y, Li J, Wei YL, Palanski BA, Wang C, Qiu L, Ohanyan M, Kask O, Sola E, Kamalyan L, Lewis DB, Scriba TJ, Davis MM, Dodd D, Zeng X, Chien YH. γδ T cell antigen receptor polyspecificity enables T cell responses to a broad range of immune challenges. Proc Natl Acad Sci U S A 2024; 121:e2315592121. [PMID: 38227652 PMCID: PMC10823224 DOI: 10.1073/pnas.2315592121] [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: 09/15/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
γδ T cells are essential for immune defense and modulating physiological processes. While they have the potential to recognize large numbers of antigens through somatic gene rearrangement, the antigens which trigger most γδ T cell response remain unidentified, and the role of antigen recognition in γδ T cell function is contentious. Here, we show that some γδ T cell receptors (TCRs) exhibit polyspecificity, recognizing multiple ligands of diverse molecular nature. These ligands include haptens, metabolites, neurotransmitters, posttranslational modifications, as well as peptides and proteins of microbial and host origin. Polyspecific γδ T cells are enriched among activated cells in naive mice and the responding population in infection. They express diverse TCR sequences, have different functional potentials, and include the innate-like γδ T cells, such as the major IL-17 responders in various pathological/physiological conditions. We demonstrate that encountering their antigenic microbiome metabolite maintains their homeostasis and functional response, indicating that their ability to recognize multiple ligands is essential for their function. Human γδ T cells with similar polyspecificity also respond to various immune challenges. This study demonstrates that polyspecificity is a prevalent feature of γδ T cell antigen recognition, which enables rapid and robust T cell responses to a wide range of challenges, highlighting a unique function of γδ T cells.
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Affiliation(s)
- Jing Guo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Roshni Roy Chowdhury
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA94305
| | - Jianming Xie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Megha Dubey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Yuanyuan Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Jing Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA94305
| | - Yu-ling Wei
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | | | - Conghua Wang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Lingfeng Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou310003, China
- National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou310003, China
| | - Mané Ohanyan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Oliver Kask
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
| | - Elsa Sola
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA94305
| | - Lilit Kamalyan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA94305
| | - David B. Lewis
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA94305
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town7700, South Africa
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Xun Zeng
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou310003, China
- National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou310003, China
- Research Units of Infectious disease and Microecology, Chinese Academy of Medical Sciences, Beijing100730, China
| | - Yueh-hsiu Chien
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA94305
- Program in Immunology, Stanford University School of Medicine, Stanford, CA94305
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3
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Maas-Bauer K, Köhler N, Stell AV, Zwick M, Acharya S, Rensing-Ehl A, König C, Kroll J, Baker J, Koßmann S, Pradier A, Wang S, Docquier M, Lewis DB, Negrin RS, Simonetta F. Single-cell transcriptomics reveal different maturation stages and sublineage commitment of human thymic invariant natural killer T cells. J Leukoc Biol 2024; 115:401-409. [PMID: 37742056 PMCID: PMC10799303 DOI: 10.1093/jleuko/qiad113] [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: 01/20/2023] [Revised: 07/08/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023] Open
Abstract
Invariant natural killer T cells are a rare, heterogeneous T-cell subset with cytotoxic and immunomodulatory properties. During thymic development, murine invariant natural killer T cells go through different maturation stages differentiating into distinct sublineages, namely, invariant natural killer T1, 2, and 17 cells. Recent reports indicate that invariant natural killer T2 cells display immature properties and give rise to other subsets, whereas invariant natural killer T1 cells seem to be terminally differentiated. Whether human invariant natural killer T cells follow a similar differentiation model is still unknown. To define the maturation stages and assess the sublineage commitment of human invariant natural killer T cells during thymic development, in this study, we performed single-cell RNA sequencing analysis on human Vα24+Vβ11+ invariant natural killer T cells isolated from thymocytes. We show that these invariant natural killer T cells displayed heterogeneity, and our unsupervised analysis identified 5 clusters representing different maturation stages, from an immature profile with high expression of genes important for invariant natural killer T cell development and proliferation to a mature, fully differentiated profile with high levels of cytotoxic effector molecules. Evaluation of expression of sublineage-defining gene sets revealed mainly cells with an invariant natural killer T2 signature in the most immature cluster, whereas the more differentiated ones displayed an invariant natural killer T1 signature. Combined analysis with a publicly available single-cell RNA sequencing data set of human invariant natural killer T cells from peripheral blood suggested that the 2 main subsets exist both in thymus and in the periphery, while a third more immature one was restricted to the thymus. Our data point to the existence of different maturation stages of human thymic invariant natural killer T cells and provide evidence for sublineage commitment of invariant natural killer T cells in the human thymus.
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Affiliation(s)
- Kristina Maas-Bauer
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Natalie Köhler
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, Freiburg 79104, Germany
| | - Anna-Verena Stell
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Melissa Zwick
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Swati Acharya
- Sean N. Parker Center for Asthma and Allergy Research, Department of Medicine, Stanford University, 240 Pasteur Dr, Stanford, CA 94304, United States
| | - Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Str. 115, Freiburg 79106, Germany
| | - Christoph König
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Str. 115, Freiburg 79106, Germany
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Johannes Kroll
- Department of Cardiovascular Surgery, Heart Center Freiburg University, Hugstetter Straße 55, Freiburg 79106, Germany
| | - Jeanette Baker
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
| | - Stefanie Koßmann
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Amandine Pradier
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva 1205, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - Sisi Wang
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
- Department of Genetics & Evolution, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - David B Lewis
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, United States
| | - Robert S Negrin
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
| | - Federico Simonetta
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva 1205, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
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4
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Balerna JA, Kramer AM, Landry SM, Rains MC, Lewis DB. Synergistic effects of precipitation and groundwater extraction on freshwater wetland inundation. J Environ Manage 2023; 337:117690. [PMID: 36933535 DOI: 10.1016/j.jenvman.2023.117690] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/10/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Wetlands provide essential ecosystem services, including nutrient cycling, flood protection, and biodiversity support, that are sensitive to changes in wetland hydrology. Wetland hydrological inputs come from precipitation, groundwater discharge, and surface run-off. Changes to these inputs via climate variation, groundwater extraction, and land development may alter the timing and magnitude of wetland inundation. Here, we use a long-term (14-year) comparative study of 152 depressional wetlands in west-central Florida to identify sources of variation in wetland inundation during two key time periods, 2005-2009 and 2010-2018. These time periods are separated by the enactment of water conservation policies in 2009, which included regional reductions in groundwater extraction. We investigated the response of wetland inundation to the interactive effects of precipitation, groundwater extraction, surrounding land development, basin geomorphology, and wetland vegetation class. Results show that water levels were lower and hydroperiods were shorter in wetlands of all vegetation classes during the first (2005-2009) time period, which corresponded with low rainfall conditions and high rates of groundwater extraction. Under water conservation policies enacted in the second (2010-2018) time period, median wetland water depths increased 1.35 m and median hydroperiods increased from 46 % to 83 %. Water-level variation was additionally less sensitive to groundwater extraction. The increase in inundation differed among vegetation classes with some wetlands not displaying signs of hydrological recovery. After accounting for effects of several explanatory factors, inundation still varied considerably among wetlands, suggesting a diversity of hydrological regimes, and thus ecological function, among individual wetlands across the landscape. Policies seeking to balance human water demand with the preservation of depressional wetlands would benefit by recognizing the heightened sensitivity of wetland inundation to groundwater extraction during periods of low precipitation.
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Affiliation(s)
- Jessica A Balerna
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA.
| | - Andrew M Kramer
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Shawn M Landry
- School of Geosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Mark C Rains
- School of Geosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - David B Lewis
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
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5
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Durieux DM, Scrogham GD, Fender C, Lewis DB, Deban SM, Gemmell BJ. Benthic jellyfish act as suction pumps to facilitate release of interstitial porewater. Sci Rep 2023; 13:3770. [PMID: 36882452 PMCID: PMC9992524 DOI: 10.1038/s41598-023-30101-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Upside-down jellyfish, genus Cassiopea (Péron and Lesueur, 1809), are found in shallow coastal habitats in tropical and subtropical regions circumglobally. These animals have previously been demonstrated to produce flow both in the water column as a feeding current, and in the interstitial porewater, where they liberate porewater at rates averaging 2.46 mL h-1. Since porewater in Cassiopea habitat can be nutrient-rich, this is a potential source of nutrient enrichment in these ecosystems. This study experimentally determines that porewater release by Cassiopea sp. jellyfish is due to suction pumping, and not the Bernoulli effect. This suggests porewater release is directly coupled to bell pulsation rate, and unlike vertical jet flux, should be unaffected by population density. In addition, we show that bell pulsation rate is positively correlated with temperature, and negatively correlated with animal size. As such, we would predict an increase in the release of nutrient-rich porewater during the warm summer months. Furthermore, we show that, at our field site in Lido Key, Florida, at the northernmost limit of Cassiopea range, population densities decline during the winter, increasing seasonal differences in porewater release.
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Affiliation(s)
- David M Durieux
- University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | | | - Christian Fender
- University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - David B Lewis
- University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Stephen M Deban
- University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Brad J Gemmell
- University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA.
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6
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Bertaina A, Grimm PC, Weinberg K, Parkman R, Kristovich KM, Barbarito G, Lippner E, Dhamdhere G, Ramachandran V, Spatz JM, Fathallah-Shaykh S, Atkinson TP, Al-Uzri A, Aubert G, van der Elst K, Green SG, Agarwal R, Slepicka PF, Shah AJ, Roncarolo MG, Gallo A, Concepcion W, Lewis DB. Sequential Stem Cell-Kidney Transplantation in Schimke Immuno-osseous Dysplasia. N Engl J Med 2022; 386:2295-2302. [PMID: 35704481 PMCID: PMC10545450 DOI: 10.1056/nejmoa2117028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 12/25/2022]
Abstract
Lifelong immunosuppression is required for allograft survival after kidney transplantation but may not ultimately prevent allograft loss resulting from chronic rejection. We developed an approach that attempts to abrogate immune rejection and the need for post-transplantation immunosuppression in three patients with Schimke immuno-osseous dysplasia who had both T-cell immunodeficiency and renal failure. Each patient received sequential transplants of αβ T-cell-depleted and CD19 B-cell-depleted haploidentical hematopoietic stem cells and a kidney from the same donor. Full donor hematopoietic chimerism and functional ex vivo T-cell tolerance was achieved, and the patients continued to have normal renal function without immunosuppression at 22 to 34 months after kidney transplantation. (Funded by the Kruzn for a Kure Foundation.).
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Affiliation(s)
- Alice Bertaina
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Paul C Grimm
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Kenneth Weinberg
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Robertson Parkman
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Karen M Kristovich
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Giulia Barbarito
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Elizabeth Lippner
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Girija Dhamdhere
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Vasavi Ramachandran
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Jordan M Spatz
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Sahar Fathallah-Shaykh
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - T Prescott Atkinson
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Amira Al-Uzri
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Geraldine Aubert
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Kim van der Elst
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Sean G Green
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Rajni Agarwal
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Priscila F Slepicka
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Ami J Shah
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Maria G Roncarolo
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Amy Gallo
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - Waldo Concepcion
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
| | - David B Lewis
- From the Division of Hematology, Oncology, Stem Cell Transplantation, and Regenerative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), the Center for Definitive and Curative Medicine (A.B., K.W., R.P., K.M.K., G.B., R.A., P.F.S., A.J.S., M.G.R.), and the Divisions of Nephrology (P.C.G., W.C.) and Allergy, Immunology, and Rheumatology (E.L., G.D., V.R., J.M.S., D.B.L.), Department of Pediatrics, and the Departments of Surgery (A.G., W.C.) and Pediatrics (W.C.), Stanford University School of Medicine, and Department of Pharmacy (S.G.G.), Stanford Children's Health - both in Stanford, CA; the Divisions of Pediatric Nephrology (S.F.-S.) and Pediatric Allergy and Immunology (T.P.A.), Department of Pediatrics, University of Alabama, Birmingham; the Division of Nephrology, Department of Pediatrics, Oregon Health Sciences University, Portland (A. A.-U.); the Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada (G.A.); and the Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands (K.E.)
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Zeng L, Liu Y, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA, La Russa MF, Qi LS. Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Nat Commun 2022; 13:2766. [PMID: 35589813 PMCID: PMC9119983 DOI: 10.1038/s41467-022-30546-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 10/28/2021] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.
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Affiliation(s)
- Leiping Zeng
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xammy Huu Nguyenla
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA
| | - Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Mengting Han
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Draven A Rane
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jordan M Spatz
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Saket Jain
- University of California San Francisco, San Francisco, CA, 94143, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin Pinsky
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Chatham, Kent ME4 4TB, UK
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Annelise E Barron
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Catherine A Blish
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA
| | - David B Lewis
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Sarah A Stanley
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA.
| | - Marie F La Russa
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA.
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8
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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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9
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Gernez Y, Murugesan K, Cortales CR, Banaei N, Hoyte L, Pinsky BA, Lewis DB, Pham MN. Immunogenicity of a third COVID-19 messenger RNA vaccine dose in primary immunodeficiency disorder patients with functional B-cell defects. J Allergy Clin Immunol Pract 2022; 10:1385-1388.e2. [PMID: 35259538 PMCID: PMC8897836 DOI: 10.1016/j.jaip.2022.02.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 01/06/2023]
Affiliation(s)
- Yael Gernez
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif
| | - Cristina R Cortales
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Clinical Microbiology Laboratory, Stanford Health Care, Stanford, Calif
| | - Lisa Hoyte
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Clinical Virology Laboratory, Stanford Health Care, Stanford, Calif
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif
| | - Michele N Pham
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Internal Medicine, University of California, San Francisco, Calif.
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10
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Bertaina A, Barbarito G, Ramachandran V, Kristovich K, Lippner EA, Fathallah-Shaykh S, Al-Uzri A, Shah AJ, Slepicka PF, Oppizzi L, Agarwal R, Roncarolo MG, Gallo A, Concepcion W, Weinberg KI, Parkman R, Lewis DB, Grimm PC. Functional Immune Tolerance Induced By Sequential Hematopoietic Stem Cell-Solid Organ Transplantation. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00617-0] [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: 11/16/2022]
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11
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Pham MN, Murugesan K, Banaei N, Pinsky BA, Tang M, Hoyte E, Lewis DB, Gernez Y. Immunogenicity and Tolerability of COVID-19 mRNA Vaccines in PID patients with functional B-cell defects. J Allergy Clin Immunol 2021; 149:907-911.e3. [PMID: 34952033 PMCID: PMC8690218 DOI: 10.1016/j.jaci.2021.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/29/2021] [Accepted: 11/05/2021] [Indexed: 12/03/2022]
Abstract
Background Data on the safety and efficacy of coronavirus disease 2019 (COVID-19) vaccination in people with a range of primary immunodeficiencies (PIDs) are lacking because these patients were excluded from COVID-19 vaccine trials. This information may help in clinical management of this vulnerable patient group. Objective We assessed humoral and T-cell immune responses after 2 doses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) messenger RNA (mRNA) vaccines in patients with PID and functional B-cell defects. Methods A double-center retrospective review was performed of patients with PID who completed COVID-19 mRNA vaccination and who had humoral responses assessed through SARS-CoV-2 spike protein receptor binding domain (RBD) IgG antibody levels with reflex assessment of the antibody to block RBD binding to angiotensin-converting enzyme 2 (ACE2; hereafter referred to as ACE2 receptor blocking activity, as a surrogate test for neutralization) and T-cell response evaluated by an IFN-γ release assay. Immunization reactogenicity was also reviewed. Results A total of 33 patients with humoral defect were evaluated; 69.6% received BNT162b2 vaccine (Pfizer-BioNTech) and 30.3% received mRNA-1273 (Moderna). The mRNA vaccines were generally well tolerated without severe reactions. The IFN-γ release assay result was positive in 24 (77.4%) of 31 patients. Sixteen of 33 subjects had detectable RBD-specific IgG responses, but only 2 of these 16 subjects had an ACE2 receptor blocking activity level of ≥50%. Conclusion Vaccination of this cohort of patients with PID with COVID-19 mRNA vaccines was safe, and cellular immunity was stimulated in most subjects. However, antibody responses to the spike protein RBD were less consistent, and, when detected, were not effective at ACE2 blocking.
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Affiliation(s)
- Michele N Pham
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Internal Medicine, University of California, San Francisco, Calif
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Clinical Microbiology Laboratory, Stanford Health Care, Stanford, Calif
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Clinical Virology Laboratory, Stanford Health Care, Stanford, Calif
| | - Monica Tang
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Internal Medicine, University of California, San Francisco, Calif
| | - Elisabeth Hoyte
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif
| | - David B Lewis
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif
| | - Yael Gernez
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, Calif.
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12
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Peterson LS, Hedou J, Ganio EA, Stelzer IA, Feyaerts D, Harbert E, Adusumelli Y, Ando K, Tsai ES, Tsai AS, Han X, Ringle M, Houghteling P, Reiss JD, Lewis DB, Winn VD, Angst MS, Aghaeepour N, Stevenson DK, Gaudilliere B. Single-Cell Analysis of the Neonatal Immune System Across the Gestational Age Continuum. Front Immunol 2021; 12:714090. [PMID: 34497610 PMCID: PMC8420969 DOI: 10.3389/fimmu.2021.714090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/24/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Although most causes of death and morbidity in premature infants are related to immune maladaptation, the premature immune system remains poorly understood. We provide a comprehensive single-cell depiction of the neonatal immune system at birth across the spectrum of viable gestational age (GA), ranging from 25 weeks to term. A mass cytometry immunoassay interrogated all major immune cell subsets, including signaling activity and responsiveness to stimulation. An elastic net model described the relationship between GA and immunome (R=0.85, p=8.75e-14), and unsupervised clustering highlighted previously unrecognized GA-dependent immune dynamics, including decreasing basal MAP-kinase/NFκB signaling in antigen presenting cells; increasing responsiveness of cytotoxic lymphocytes to interferon-α; and decreasing frequency of regulatory and invariant T cells, including NKT-like cells and CD8+CD161+ T cells. Knowledge gained from the analysis of the neonatal immune landscape across GA provides a mechanistic framework to understand the unique susceptibility of preterm infants to both hyper-inflammatory diseases and infections.
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Affiliation(s)
- Laura S Peterson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Julien Hedou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Eliza Harbert
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Yamini Adusumelli
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Eileen S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Megan Ringle
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Pearl Houghteling
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Jonathan D Reiss
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - David B Lewis
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, United States
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Nima Aghaeepour
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States.,Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Brice Gaudilliere
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States.,Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
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13
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Brar N, Spinner MA, Baker MC, Advani RH, Natkunam Y, Lewis DB, Silva O. Increased double-negative αβ+ T-cells reveal adult-onset autoimmune lymphoproliferative syndrome in a patient with IgG4-related disease. Haematologica 2021; 107:347-350. [PMID: 34474549 PMCID: PMC8719087 DOI: 10.3324/haematol.2021.279297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Nivaz Brar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Michael A Spinner
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Matthew C Baker
- Division of Immunology and Rheumatology, Department of Medicine Stanford University School of Medicine, Stanford, CA
| | - Ranjana H Advani
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Oscar Silva
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.
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14
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Mounger J, Boquete MT, Schmid MW, Granado R, Robertson MH, Voors SA, Langanke KL, Alvarez M, Wagemaker CAM, Schrey AW, Fox GA, Lewis DB, Lira CF, Richards CL. Inheritance of DNA methylation differences in the mangrove Rhizophora mangle. Evol Dev 2021; 23:351-374. [PMID: 34382741 DOI: 10.1111/ede.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/15/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022]
Abstract
The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - M Teresa Boquete
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Department of Evolutionary Ecology, CSIC, Estación Biológica de Doñana, Sevilla, Spain
| | | | - Renan Granado
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Marta H Robertson
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Sandy A Voors
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Kristen L Langanke
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Mariano Alvarez
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Avalo, Durham, NC, USA
| | | | - Aaron W Schrey
- Department of Biology, Georgia Southern University, Armstrong Campus, Savannah, Georgia, USA
| | - Gordon A Fox
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - David B Lewis
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Catarina Fonseca Lira
- Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Plant Evolutionary Ecology, University of Tübingen, Institute of Evolution & Ecology, Tübingen, Germany
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15
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Pressley M, Salvioli M, Lewis DB, Richards CL, Brown JS, Staňková K. Evolutionary Dynamics of Treatment-Induced Resistance in Cancer Informs Understanding of Rapid Evolution in Natural Systems. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rapid evolution is ubiquitous in nature. We briefly review some of this quite broadly, particularly in the context of response to anthropogenic disturbances. Nowhere is this more evident, replicated and accessible to study than in cancer. Curiously cancer has been late - relative to fisheries, antibiotic resistance, pest management and evolution in human dominated landscapes - in recognizing the need for evolutionarily informed management strategies. The speed of evolution matters. Here, we employ game-theoretic modeling to compare time to progression with continuous maximum tolerable dose to that of adaptive therapy where treatment is discontinued when the population of cancer cells gets below half of its initial size and re-administered when the cancer cells recover, forming cycles with and without treatment. We show that the success of adaptive therapy relative to continuous maximum tolerable dose therapy is much higher if the population of cancer cells is defined by two cell types (sensitive vs. resistant in a polymorphic population). Additionally, the relative increase in time to progression increases with the speed of evolution. These results hold with and without a cost of resistance in cancer cells. On the other hand, treatment-induced resistance can be modeled as a quantitative trait in a monomorphic population of cancer cells. In that case, when evolution is rapid, there is no advantage to adaptive therapy. Initial responses to therapy are blunted by the cancer cells evolving too quickly. Our study emphasizes how cancer provides a unique system for studying rapid evolutionary changes within tumor ecosystems in response to human interventions; and allows us to contrast and compare this system to other human managed or dominated systems in nature.
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16
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Abstract
Coronavirus disease 2019 (COVID-19), caused by a strain of coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic that has affected the lives of billions of individuals. Extensive studies have revealed that SARS-CoV-2 shares many biological features with SARS-CoV, the zoonotic virus that caused the 2002 outbreak of severe acute respiratory syndrome, including the system of cell entry, which is triggered by binding of the viral spike protein to angiotensin-converting enzyme 2. Clinical studies have also reported an association between COVID-19 and cardiovascular disease. Pre-existing cardiovascular disease seems to be linked with worse outcomes and increased risk of death in patients with COVID-19, whereas COVID-19 itself can also induce myocardial injury, arrhythmia, acute coronary syndrome and venous thromboembolism. Potential drug-disease interactions affecting patients with COVID-19 and comorbid cardiovascular diseases are also becoming a serious concern. In this Review, we summarize the current understanding of COVID-19 from basic mechanisms to clinical perspectives, focusing on the interaction between COVID-19 and the cardiovascular system. By combining our knowledge of the biological features of the virus with clinical findings, we can improve our understanding of the potential mechanisms underlying COVID-19, paving the way towards the development of preventative and therapeutic solutions.
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Affiliation(s)
- Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford, CA, USA. .,Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yaling Han
- Cardiovascular Research Institute, Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford, CA, USA. .,Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L, Chemparathy A, Chmura S, Heaton NS, Debs R, Pande T, Endy D, La Russa MF, Lewis DB, Qi LS. Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza. Cell 2020; 181:865-876.e12. [PMID: 32353252 PMCID: PMC7189862 DOI: 10.1016/j.cell.2020.04.020] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/24/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, has highlighted the need for antiviral approaches that can target emerging viruses with no effective vaccines or pharmaceuticals. Here, we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (prophylactic antiviral CRISPR in human cells), for viral inhibition that can effectively degrade RNA from SARS-CoV-2 sequences and live influenza A virus (IAV) in human lung epithelial cells. We designed and screened CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs targeting SARS-CoV-2. This approach effectively reduced H1N1 IAV load in respiratory epithelial cells. Our bioinformatic analysis showed that a group of only six crRNAs can target more than 90% of all coronaviruses. With the development of a safe and effective system for respiratory tract delivery, PAC-MAN has the potential to become an important pan-coronavirus inhibition strategy.
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Affiliation(s)
- Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Girija Dhamdhere
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Laine Goudy
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Leiping Zeng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Augustine Chemparathy
- Department of Management Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | | | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Tara Pande
- Los Altos High School, Los Altos, CA 94022, USA
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Marie F La Russa
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - David B Lewis
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA.
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18
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Bertaina A, Bacchetta R, Lewis DB, Grimm PC, Shah AJ, Agarwal R, Concepcion W, Czechowicz A, Bhatia N, Lahiri P, Weinberg KI, Parkman R, Porteus M, Roncarolo MG. Αβ T-Cell/CD19 B-Cell Depleted Haploidentical Stem Cell Transplantation: A New Platform for Curing Rare and Monogenic Disorders. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.560] [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: 10/25/2022]
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19
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Siddiqi AE, Liu AY, Charville GW, Kunder CA, Uzel G, Sadighi Akha AA, Oak J, Martin B, Sacha J, Lewis DB, Gernez Y. Disseminated Pneumocystis jirovecii Infection with Osteomyelitis in a Patient with CTLA-4 Haploinsufficiency. J Clin Immunol 2020; 40:412-414. [PMID: 31955317 DOI: 10.1007/s10875-020-00748-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
Affiliation(s)
- Aminaa E Siddiqi
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford School of Medicine, 269 Campus Drive, CCSR Suite 3215, Stanford, CA, 94305-5366, USA
| | - Anne Y Liu
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford School of Medicine, 269 Campus Drive, CCSR Suite 3215, Stanford, CA, 94305-5366, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | | | | | - Gulbu Uzel
- National Institutes of Allergy and Infectious Disease NIH, Bethesda, MD, USA
| | - Amir A Sadighi Akha
- Division of Clinical Biochemistry & Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jean Oak
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Beth Martin
- Division of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joshua Sacha
- Division of Allergy and Clinical Immunology, David Grant USAF Medical Center in Travis AFB, Fairfield, CA, USA
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford School of Medicine, 269 Campus Drive, CCSR Suite 3215, Stanford, CA, 94305-5366, USA
| | - Yael Gernez
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford School of Medicine, 269 Campus Drive, CCSR Suite 3215, Stanford, CA, 94305-5366, USA.
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20
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Handumrongkul C, Ye AL, Chmura SA, Soroceanu L, Mack M, Ice RJ, Thistle R, Myers M, Ursu SJ, Liu Y, Kashani-Sabet M, Heath TD, Liggitt D, Lewis DB, Debs R. Durable multitransgene expression in vivo using systemic, nonviral DNA delivery. Sci Adv 2019; 5:eaax0217. [PMID: 31807699 PMCID: PMC6881169 DOI: 10.1126/sciadv.aax0217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 10/02/2019] [Indexed: 05/05/2023]
Abstract
Recombinant adeno-associated virus (AAV) vectors are transforming therapies for rare human monogenic deficiency diseases. However, adaptive immune responses to AAV and its limited DNA insert capacity, restrict their therapeutic potential. HEDGES (high-level extended duration gene expression system), a nonviral DNA- and liposome-based gene delivery platform, overcomes these limitations in immunocompetent mice. Specifically, one systemic HEDGES injection durably produces therapeutic levels of transgene-encoded human proteins, including FDA-approved cytokines and monoclonal antibodies, without detectable integration into genomic DNA. HEDGES also controls protein production duration from <3 weeks to >1.5 years, does not induce anti-vector immune responses, is reexpressed for prolonged periods following reinjection, and produces only transient minimal toxicity. HEDGES can produce extended therapeutic levels of multiple transgene-encoded therapeutic human proteins from DNA inserts >1.5-fold larger than AAV-based therapeutics, thus creating combinatorial interventions to effectively treat common polygenic diseases driven by multigenic abnormalities.
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Affiliation(s)
| | | | | | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Ryan J. Ice
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Robert Thistle
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Sarah J. Ursu
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Yong Liu
- DNARx LLC, San Francisco, CA, USA
| | | | | | - Denny Liggitt
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - David B. Lewis
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert Debs
- DNARx LLC, San Francisco, CA, USA
- Corresponding author.
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21
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Gernez Y, de Jesus AA, Alsaleem H, Macaubas C, Roy A, Lovell D, Jagadeesh KA, Alehashemi S, Erdman L, Grimley M, Talarico S, Bacchetta R, Lewis DB, Canna SW, Laxer RM, Mellins ED, Goldbach-Mansky R, Weinacht KG. Severe autoinflammation in 4 patients with C-terminal variants in cell division control protein 42 homolog (CDC42) successfully treated with IL-1β inhibition. J Allergy Clin Immunol 2019. [PMID: 31271789 DOI: 10.1016/j.jaci.2019.06.017)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Yael Gernez
- Division of Allergy and Immunology, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif.
| | - Adriana A de Jesus
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Hanouf Alsaleem
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudia Macaubas
- Division of Human Gene Therapy, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Amitava Roy
- Bioinformatics and Computational Biosciences Branch (BCBB) OCICB Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Mont
| | - Daniel Lovell
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Sara Alehashemi
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Laura Erdman
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Grimley
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Susanna Talarico
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosa Bacchetta
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - David B Lewis
- Division of Allergy and Immunology, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Scott W Canna
- Division of Rheumatology/RK Mellon Institute, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pa
| | - Ron M Laxer
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth D Mellins
- Division of Human Gene Therapy, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Katja G Weinacht
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif.
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22
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Gernez Y, de Jesus AA, Alsaleem H, Macaubas C, Roy A, Lovell D, Jagadeesh KA, Alehashemi S, Erdman L, Grimley M, Talarico S, Bacchetta R, Lewis DB, Canna SW, Laxer RM, Mellins ED, Goldbach-Mansky R, Weinacht KG. Severe autoinflammation in 4 patients with C-terminal variants in cell division control protein 42 homolog (CDC42) successfully treated with IL-1β inhibition. J Allergy Clin Immunol 2019; 144:1122-1125.e6. [PMID: 31271789 DOI: 10.1016/j.jaci.2019.06.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Yael Gernez
- Division of Allergy and Immunology, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif.
| | - Adriana A de Jesus
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Hanouf Alsaleem
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudia Macaubas
- Division of Human Gene Therapy, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Amitava Roy
- Bioinformatics and Computational Biosciences Branch (BCBB) OCICB Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Mont
| | - Daniel Lovell
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Sara Alehashemi
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Laura Erdman
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Grimley
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Susanna Talarico
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosa Bacchetta
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - David B Lewis
- Division of Allergy and Immunology, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Scott W Canna
- Division of Rheumatology/RK Mellon Institute, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pa
| | - Ron M Laxer
- Department of Pediatric Rheumatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth D Mellins
- Division of Human Gene Therapy, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Md
| | - Katja G Weinacht
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, Calif.
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23
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Lippner E, Lewis DB. The Clinical Spectrum of Hypomorphic IL2RG Severe Combined Immunodeficiency (SCID). J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.360] [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: 10/27/2022]
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24
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Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics 2019; 35:95-103. [PMID: 30561547 PMCID: PMC6298056 DOI: 10.1093/bioinformatics/bty537] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [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: 01/24/2018] [Revised: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 12/12/2022] Open
Abstract
Motivation Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mohammad Sajjad Ghaemi
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Département de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, QC, Canada
- Groupe d’Études et de Recherche en Analyse des Décision (GERAD), Montréal, QC, Canada
- Centre Interuniversitaire de Recherche sur les Réseaux d’Entreprise, la Logistique et le Transport (CIRRELT), Montréal, QC, Canada
| | - Daniel B DiGiulio
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin Callahan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Thuy T M Ngo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute and Department of Molecular and Medical Genetics, Oregon Health Sciences University, Portland, OR, USA
| | | | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Robaczewska
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - David Mcilwain
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Yael Rosenberg-Hasson
- Institute for Immunity, Transplantation and Infection, Human Immune Monitoring Center Stanford, CA, USA
| | - Ronald J Wong
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecele Quaintance
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Natalie Stanley
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Athena Tanada
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dyani Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie McNeil
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul Wise
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivana Maric
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Sirota
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurice L Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary L Darmstadt
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David B Lewis
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vahid Partovi Nia
- Département de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, QC, Canada
- Groupe d’Études et de Recherche en Analyse des Décision (GERAD), Montréal, QC, Canada
| | - Bruno Agard
- Département de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, QC, Canada
- Centre Interuniversitaire de Recherche sur les Réseaux d’Entreprise, la Logistique et le Transport (CIRRELT), Montréal, QC, Canada
| | - Robert Tibshirani
- Departments of Biomedical Data Sciences and Statistics, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Gary M Shaw
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
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25
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Rosa JS, Hernandez JD, Sherr JA, Smith BM, Brown KD, Farhadian B, Mahony T, McGhee SA, Lewis DB, Thienemann M, Frankovich JD. Allergic Diseases and Immune-Mediated Food Disorders in Pediatric Acute-Onset Neuropsychiatric Syndrome. Pediatr Allergy Immunol Pulmonol 2018; 31:158-165. [PMID: 30283713 DOI: 10.1089/ped.2018.0888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/26/2018] [Indexed: 12/26/2022]
Abstract
Background: The prevalence and impact of allergic and immune-mediated food disorders in pediatric acute-onset neuropsychiatric syndrome (PANS) are mostly unknown. Objective: We sought to explore the prevalence of atopic dermatitis (AD), asthma, allergic rhinitis (AR), IgE-mediated food allergies (FAs), and other immune-mediated food disorders requiring food avoidance in patients with PANS. In addition, to further understand the extent of food restriction in this population, we investigated the empiric use of dietary measures to improve PANS symptoms. Methods: Pediatric patients in a PANS Clinic and Research Program were given surveys regarding their caregiver burdens, allergic and food-related medical history, and whether food elimination resulted in perception of improvement of PANS symptoms. A review of health records was conducted to confirm that all responses in the survey were concordant with documentation of each patient's medical chart. Results: Sixty-nine (ages 4-20 years) of 80 subjects who fulfilled PANS criteria completed the surveys. Thirteen (18.8%) had AD, 11 (15.9%) asthma, 33 (47.8%) AR, 11 (15.9%) FA, 1 (1.4%) eosinophilic gastrointestinal disorders, 1 (1.4%) food protein-induced enterocolitis syndrome, 3 (4.3%) milk protein-induced proctocolitis syndrome, and 3 (4.3%) celiac disease. Thirty subjects (43.5%) avoided foods due to PANS; elimination of gluten and dairy was most common and was associated with perceived improvement of PANS symptoms (by parents). This perceived improvement was not confirmed with objective data. Conclusions: The prevalence of allergic and immune-mediated food disorders in PANS is similar to the general population as reported in the literature, with the exception of AR that appears to be more prevalent in our PANS cohort. More research will be required to establish whether diet or allergies influence PANS symptoms.
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Affiliation(s)
- Jaime S Rosa
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.,PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Joseph D Hernandez
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.,PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Janell A Sherr
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.,PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Bridget M Smith
- Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Center of Innovation for Complex Chronic Healthcare, Hines Veterans Affairs Hospital, Hines, Illinois
| | - Kayla D Brown
- PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Bahare Farhadian
- PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Talia Mahony
- PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Sean A McGhee
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - David B Lewis
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.,PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Margo Thienemann
- PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
| | - Jennifer D Frankovich
- Division of Immunology, Allergy and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California.,PANS Clinic and Research Program, Stanford Children's Health, Palo Alto, California
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26
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Kuehn HS, Niemela JE, Sreedhara K, Stoddard JL, Grossman J, Wysocki CA, de la Morena MT, Garofalo M, Inlora J, Snyder MP, Lewis DB, Stratakis CA, Fleisher TA, Rosenzweig SD. Novel nonsense gain-of-function NFKB2 mutations associated with a combined immunodeficiency phenotype. Blood 2017; 130:1553-1564. [PMID: 28778864 PMCID: PMC5620416 DOI: 10.1182/blood-2017-05-782177] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/09/2017] [Indexed: 11/20/2022] Open
Abstract
NF-κB signaling through its NFKB1-dependent canonical and NFKB2-dependent noncanonical pathways plays distinctive roles in a diverse range of immune processes. Recently, mutations in these 2 genes have been associated with common variable immunodeficiency (CVID). While studying patients with genetically uncharacterized primary immunodeficiencies, we detected 2 novel nonsense gain-of-function (GOF) NFKB2 mutations (E418X and R635X) in 3 patients from 2 families, and a novel missense change (S866R) in another patient. Their immunophenotype was assessed by flow cytometry and protein expression; activation of canonical and noncanonical pathways was examined in peripheral blood mononuclear cells and transfected HEK293T cells through immunoblotting, immunohistochemistry, luciferase activity, real-time polymerase chain reaction, and multiplex assays. The S866R change disrupted a C-terminal NF-κΒ2 critical site affecting protein phosphorylation and nuclear translocation, resulting in CVID with adrenocorticotropic hormone deficiency, growth hormone deficiency, and mild ectodermal dysplasia as previously described. In contrast, the nonsense mutations E418X and R635X observed in 3 patients led to constitutive nuclear localization and activation of both canonical and noncanonical NF-κΒ pathways, resulting in a combined immunodeficiency (CID) without endocrine or ectodermal manifestations. These changes were also found in 2 asymptomatic relatives. Thus, these novel NFKB2 GOF mutations produce a nonfully penetrant CID phenotype through a different pathophysiologic mechanism than previously described for mutations in NFKB2.
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Affiliation(s)
- Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Karthik Sreedhara
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Jennifer L Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Jennifer Grossman
- Division of Hematology and Hematologic Malignancies, Alberta Health Services, Calgary, AB, Canada
| | - Christian A Wysocki
- Division of Allergy and Immunology, Department of Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - M Teresa de la Morena
- Division of Allergy and Immunology, Department of Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mary Garofalo
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | | | | | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA; and
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics
- Program on Developmental Endocrinology and Genetics, and
- Pediatric Endocrinology Inter-institute Training Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, MD
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27
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Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B. An immune clock of human pregnancy. Sci Immunol 2017; 2:2/15/eaan2946. [PMID: 28864494 PMCID: PMC5701281 DOI: 10.1126/sciimmunol.aan2946] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022]
Abstract
Themaintenance of pregnancy relies on finely tuned immune adaptations.We demonstrate that these adaptations are precisely timed, reflecting an immune clock of pregnancy in women delivering at term. Using mass cytometry, the abundance and functional responses of allmajor immune cell subsets were quantified in serial blood samples collected throughout pregnancy. Cell signaling–based Elastic Net, a regularized regressionmethod adapted from the elastic net algorithm, was developed to infer and prospectively validate a predictive model of interrelated immune events that accurately captures the chronology of pregnancy. Model components highlighted existing knowledge and revealed previously unreported biology, including a critical role for the interleukin-2–dependent STAT5ab signaling pathway in modulating T cell function during pregnancy. These findings unravel the precise timing of immunological events occurring during a term pregnancy and provide the analytical framework to identify immunological deviations implicated in pregnancy-related pathologies.
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Affiliation(s)
- Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - David Mcilwain
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94121, USA
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Sofie Van Gassen
- Department of Information Technology, Ghent University, and the Center for Inflammation Research, Ghent, Belgium
| | - Dyani K Gaudilliere
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Quentin Baca
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Leslie McNeil
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Robin Okada
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Mohammad S Ghaemi
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - David Furman
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Immunogenetics, Jose de San Martin Clinical Hospital, National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Maurice L Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Yaser Y El-Sayed
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Cecele Quaintance
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Ronald Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Robert Tibshirani
- Departments of Biomedical Data Sciences and Statistics, Stanford University, Stanford, CA 94121, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94121, USA
| | - David B Lewis
- Division of Pediatric Immunology and Allergy, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121, USA.
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Fearon WF, Okada K, Kobashigawa JA, Kobayashi Y, Luikart H, Sana S, Daun T, Chmura SA, Sinha S, Cohen G, Honda Y, Pham M, Lewis DB, Bernstein D, Yeung AC, Valantine HA, Khush K. Angiotensin-Converting Enzyme Inhibition Early After Heart Transplantation. J Am Coll Cardiol 2017; 69:2832-2841. [PMID: 28595700 DOI: 10.1016/j.jacc.2017.03.598] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/27/2017] [Accepted: 03/31/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Cardiac allograft vasculopathy (CAV) remains a leading cause of mortality after heart transplantation (HT). Angiotensin-converting enzyme inhibitors (ACEIs) may retard the development of CAV but have not been well studied after HT. OBJECTIVES This study tested the safety and efficacy of the ACEI ramipril on the development of CAV early after HT. METHODS In this prospective, multicenter, randomized, double-blind, placebo-controlled trial, 96 HT recipients were randomized to undergo ramipril or placebo therapy. They underwent coronary angiography, endothelial function testing; measurements of fractional flow reserve (FFR) and coronary flow reserve (CFR) and the index of microcirculatory resistance (IMR); and intravascular ultrasonography (IVUS) of the left anterior descending coronary artery, within 8 weeks of HT. At 1 year, the invasive assessment was repeated. Circulating endothelial progenitor cells (EPCs) were quantified at baseline and 1 year. RESULTS Plaque volumes at 1 year were similar between the ramipril and placebo groups (162.1 ± 70.5 mm3 vs. 177.3 ± 94.3 mm3, respectively; p = 0.73). Patients receiving ramipril had improvement in microvascular function as shown by a significant decrease in IMR (21.4 ± 14.7 to 14.4 ± 6.3; p = 0.001) and increase in CFR (3.8 ± 1.7 to 4.8 ± 1.5; p = 0.017), from baseline to 1 year. This did not occur with IMR (17.4 ± 8.4 to 21.5 ± 20.0; p = 0.72) or CFR (4.1 ± 1.8 to 4.1 ± 2.2; p = 0.60) in the placebo-treated patients. EPCs decreased significantly at 1 year in the placebo group but not in the ramipril group. CONCLUSIONS Ramipril does not slow development of epicardial plaque volume but does stabilize levels of endothelial progenitor cells and improve microvascular function, which have been associated with improved long-term survival after HT. (Angiotensin Converting Enzyme [ACE] Inhibition and Cardiac Allograft Vasculopathy; NCT01078363).
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Affiliation(s)
- William F Fearon
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California; Cardiology Section, Palo Alto Veterans Affairs Health Care System, Palo Alto, California.
| | - Kozo Okada
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Jon A Kobashigawa
- Advanced Heart Disease Section, Cedars-Sinai Heart Institute, Los Angeles, California
| | - Yuhei Kobayashi
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Helen Luikart
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Sean Sana
- Advanced Heart Disease Section, Cedars-Sinai Heart Institute, Los Angeles, California
| | - Tiffany Daun
- Advanced Heart Disease Section, Cedars-Sinai Heart Institute, Los Angeles, California
| | - Steven A Chmura
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, Stanford, California
| | - Seema Sinha
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Garett Cohen
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Yasuhiro Honda
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Michael Pham
- Cardiology Section, Palo Alto Veterans Affairs Health Care System, Palo Alto, California
| | - David B Lewis
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, Stanford, California
| | - Daniel Bernstein
- Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, California
| | - Alan C Yeung
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Hannah A Valantine
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
| | - Kiran Khush
- Stanford Cardiovascular Institute and Division of Cardiovascular Medicine, Stanford, California
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29
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Lal RA, Bachrach LK, Hoffman AR, Inlora J, Rego S, Snyder MP, Lewis DB. A Case Report of Hypoglycemia and Hypogammaglobulinemia: DAVID Syndrome in a Patient With a Novel NFKB2 Mutation. J Clin Endocrinol Metab 2017; 102:2127-2130. [PMID: 28472507 DOI: 10.1210/jc.2017-00341] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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] [Received: 02/06/2017] [Accepted: 04/25/2017] [Indexed: 11/19/2022]
Abstract
Context Deficient anterior pituitary with variable immune deficiency (DAVID) syndrome is a rare disorder in which children present with symptomatic adrenocorticotropic hormone (ACTH) deficiency preceded by hypogammaglobulinemia from B-cell dysfunction with recurrent infections, called common variable immunodeficiency (CVID). Subsequent whole exome sequencing studies have revealed germline heterozygous C-terminal mutations of NFKB2 as a cause of DAVID syndrome or of CVID without clinical hypopituitarism. However, to the best of our knowledge there have been no cases in which the endocrinopathy has presented in the absence of a prior clinical history of CVID. Case Description A previously healthy 7-year-old boy with no history of clinical immunodeficiency presented with profound hypoglycemia and seizures. He was found to have secondary adrenal insufficiency and was started on glucocorticoid replacement. An evaluation for autoimmune disease, including for antipituitary antibodies, was negative. Evaluation unexpectedly revealed hypogammaglobulinemia [decreased immunoglobulin G (IgG), IgM, and IgA]. He had moderately reduced serotype-specific IgG responses after pneumococcal polysaccharide vaccine. Subsequently, he was found to have growth hormone deficiency. Six years after initial presentation, whole exome sequencing revealed a de novo heterozygous NFKB2 missense mutation c.2596A>C (p.Ser866Arg) in the C-terminal region predicted to abrogate the processing of the p100 NFKB2 protein to its active p52 form. Conclusions Isolated early-onset ACTH deficiency is rare, and C-terminal region NFKB2 mutations should be considered as an etiology even in the absence of a clinical history of CVID. Early immunologic evaluation is indicated in the diagnosis and management of isolated ACTH deficiency.
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Affiliation(s)
- Rayhan A Lal
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
- Division of Endocrinology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305
| | - Laura K Bachrach
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Andrew R Hoffman
- Division of Endocrinology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305
| | - Jingga Inlora
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Shannon Rego
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - David B Lewis
- Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
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30
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Creed IF, Lane CR, Serran JN, Alexander LC, Basu NB, Calhoun AJK, Christensen JR, Cohen MJ, Craft C, D’Amico E, DeKeyser E, Fowler L, Golden HE, Jawitz JW, Kalla P, Kirkman LK, Lang M, Leibowitz SG, Lewis DB, Marton J, McLaughlin DL, Raanan-Kiperwas H, Rains MC, Rains KC, Smith L. Enhancing protection for vulnerable waters. Nat Geosci 2017; 10:809-815. [PMID: 30079098 PMCID: PMC6071434 DOI: 10.1038/ngeo3041] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/08/2017] [Indexed: 05/20/2023]
Abstract
Governments worldwide do not adequately protect their limited freshwater systems and therefore place freshwater functions and attendant ecosystem services at risk. The best available scientific evidence compels enhanced protections for freshwater systems, especially for impermanent streams and wetlands outside of floodplains that are particularly vulnerable to alteration or destruction. New approaches to freshwater sustainability - implemented through scientifically informed adaptive management - are required to protect freshwater systems through periods of changing societal needs. One such approach introduced in the US in 2015 is the Clean Water Rule, which clarified the jurisdictional scope for federally protected waters. However, within hours of its implementation litigants convinced the US Court of Appeals for the Sixth Circuit to stay the rule, and the subsequently elected administration has now placed it under review for potential revision or rescission. Regardless of its outcome at the federal level, policy and management discussions initiated by the propagation of this rare rulemaking event have potential far-reaching implications at all levels of government across the US and worldwide. At this timely juncture, we provide a scientific rationale and three policy options for all levels of government to meaningfully enhance protection of these vulnerable waters. A fourth option, a 'do-nothing' approach, is wholly inconsistent with the well-established scientific evidence of the importance of these vulnerable waters.
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Affiliation(s)
- Irena F. Creed
- Department of Biology, Western University, London, ON N6A 5B7, Canada
| | - Charles R. Lane
- US Environmental Protection Agency (US EPA) Office of Research and Development, National Exposure Research Laboratory, Cincinnati, Ohio 45268, USA
| | | | | | - Nandita B. Basu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Aram J. K. Calhoun
- Department of Wildlife, Fisheries, and Conservation Biology, University of Maine, Orono, Maine 04469, USA
| | - Jay R. Christensen
- US EPA Office of Research and Development, National Exposure Research Laboratory, Las Vegas, Nevada 89119, USA
| | - Matthew J. Cohen
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Christopher Craft
- School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Edward DeKeyser
- School of Natural Resource Sciences, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Laurie Fowler
- Odum School of Ecology, The University of Georgia, Athens, Georgia 30602, USA
| | - Heather E. Golden
- US EPA Office of Research and Development, National Exposure Research Laboratory, Cincinnati, Ohio 45268, USA
| | - James W. Jawitz
- Soil and Water Science Department, University of Florida, Gainesville, Florida 32611, USA
| | - Peter Kalla
- US EPA Region 4 Laboratory, Athens, Georgia 30605, USA
| | | | - Megan Lang
- US Fish and Wildlife Service, Falls Church, Virginia 22041, USA
| | - Scott G. Leibowitz
- US EPA National Health and Environmental Effects Research Laboratory, Western Ecology Division, Corvallis, Oregon 97333, USA
| | - David B. Lewis
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA
| | - John Marton
- CDM Smith, Inc., Indianapolis, Indiana 46204, USA
| | - Daniel L. McLaughlin
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Hadas Raanan-Kiperwas
- ORISE Fellow, US EPA Office of Wetlands, Oceans, and Watersheds, Washington, DC 20460, USA
| | - Mark C. Rains
- School of Geosciences, University of South Florida, Tampa, Florida 33620, USA
| | - Kai C. Rains
- School of Geosciences, University of South Florida, Tampa, Florida 33620, USA
| | - Lora Smith
- Joseph W. Jones Ecological Research Center, Newton, Georgia 39870, USA
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31
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Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL. Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol 2016; 197:4482-4492. [PMID: 27793998 DOI: 10.4049/jimmunol.1601195] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/20/2016] [Indexed: 12/17/2022]
Abstract
Preterm labor and infections are the leading causes of neonatal deaths worldwide. During pregnancy, immunological cross talk between the mother and her fetus is critical for the maintenance of pregnancy and the delivery of an immunocompetent neonate. A precise understanding of healthy fetomaternal immunity is the important first step to identifying dysregulated immune mechanisms driving adverse maternal or neonatal outcomes. This study combined single-cell mass cytometry of paired peripheral and umbilical cord blood samples from mothers and their neonates with a graphical approach developed for the visualization of high-dimensional data to provide a high-resolution reference map of the cellular composition and functional organization of the healthy fetal and maternal immune systems at birth. The approach enabled mapping of known phenotypical and functional characteristics of fetal immunity (including the functional hyperresponsiveness of CD4+ and CD8+ T cells and the global blunting of innate immune responses). It also allowed discovery of new properties that distinguish the fetal and maternal immune systems. For example, examination of paired samples revealed differences in endogenous signaling tone that are unique to a mother and her offspring, including increased ERK1/2, MAPK-activated protein kinase 2, rpS6, and CREB phosphorylation in fetal Tbet+CD4+ T cells, CD8+ T cells, B cells, and CD56loCD16+ NK cells and decreased ERK1/2, MAPK-activated protein kinase 2, and STAT1 phosphorylation in fetal intermediate and nonclassical monocytes. This highly interactive functional map of healthy fetomaternal immunity builds the core reference for a growing data repository that will allow inferring deviations from normal associated with adverse maternal and neonatal outcomes.
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Affiliation(s)
- Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Quentin J Baca
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Pier Federico Gherardini
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Dyani K Gaudilliere
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Hope L Lancero
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Leslie S McNeil
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Karl G Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Brendan Carvalho
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - David B Lewis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305.,Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Brice L Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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Butte MJ, Park KT, Lewis DB. Treatment of CGD-associated Colitis with the IL-23 Blocker Ustekinumab. J Clin Immunol 2016; 36:619-20. [PMID: 27465505 DOI: 10.1007/s10875-016-0318-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/13/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Manish J Butte
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University, 300 Pasteur Drive, Grant Building Room H307A, Stanford, CA, 94305, USA.
| | - K T Park
- Division of Gastroenterology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University, 300 Pasteur Drive, Grant Building Room H307A, Stanford, CA, 94305, USA
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Liu F, Sun X, Fairman J, Lewis DB, Katz JM, Levine M, Tumpey TM, Lu X. A cationic liposome-DNA complexes adjuvant (JVRS-100) enhances the immunogenicity and cross-protective efficacy of pre-pandemic influenza A (H5N1) vaccine in ferrets. Virology 2016; 492:197-203. [PMID: 26967975 PMCID: PMC5796654 DOI: 10.1016/j.virol.2016.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 12/09/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
Abstract
Influenza A (H5N1) viruses continue to pose a public health threat. As inactivated H5N1 vaccines are poorly immunogenic, adjuvants are needed to improve the immunogenicity of H5N1 vaccine in humans. Here, we investigated the immunogenicity and cross-protective efficacy in ferrets of a clade 2.2-derived vaccine with addition of JVRS-100, an adjuvant consisting of cationic liposome-DNA complexes (CLDC). After the first vaccination, significantly higher levels of hemagglutination-inhibition (HAI) and neutralizing antibody titers were detected in ferrets immunized with adjuvanted vaccine compared to unadjuvanted vaccine. Following a second dose of adjuvanted vaccine, HAI antibody titers of ≥ 40 were detected against viruses from multiple H5N1 clades. HAI antibodies against newly isolated H5N2 and H5N8 viruses were also augmented by JVRS-100. Ferrets were challenged with a heterologous H5N1 virus. All ferrets that received two doses of adjuvanted vaccine exhibited mild illness, significantly reduced nasal wash virus titers and protection from lethal challenge. In contrast, ferrets that received unadjuvanted vaccine showed greater weight loss, high viral titers and 3 of 6 animals succumbed to the lethal challenge. Our results indicate that the addition of JVRS-100 to H5N1 vaccine enhanced immunogenicity and cross-protection against lethal H5N1 virus disease in ferrets. JVRS-100 warrants further investigation as a potential adjuvant for influenza vaccines.
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Affiliation(s)
- Feng Liu
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiangjie Sun
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - David B Lewis
- Department of Pediatrics, Interdepartmental Program in Immunology, and Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Jacqueline M Katz
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Min Levine
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Terrence M Tumpey
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiuhua Lu
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Chen SF, Holmes TH, Slifer T, Ramachandran V, Mackey S, Hebson C, Arvin AM, Lewis DB, Dekker CL. Longitudinal Kinetics of Cytomegalovirus-Specific T-Cell Immunity and Viral Replication in Infants With Congenital Cytomegalovirus Infection. J Pediatric Infect Dis Soc 2016; 5:14-20. [PMID: 26908487 PMCID: PMC4765489 DOI: 10.1093/jpids/piu089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 08/08/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Congenital cytomegalovirus (CMV) is reported to affect up to 1% of all live births in the United States. T-cell immunity may be important for controlling CMV replication in congenital CMV-infected infants. We describe the natural history of CMV-specific T-cell evolution and CMV replication in infants with congenital CMV infection. METHODS Cytomegalovirus viral load, CMV urine culture, and CMV-specific CD4 and CD8 T-cell responses were assessed in a prospective longitudinal cohort of 51 infants with congenital CMV infection who were observed from birth to 3 years of age. RESULTS We found a kinetic pattern of decreasing urinary CMV replication and increasing CMV-specific CD4 and CD8 T-cell responses during the first 3 years of life. We also found higher CMV-specific CD8 T-cell responses were associated with subsequent reduction of urine CMV viral load. CONCLUSION For infants with congenital CMV infection, our data suggest an age-related maturation of both CMV-specific CD4 and CD8 T-cell immunity that is associated with an age-related decline in urinary CMV replication.
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Affiliation(s)
| | - Tyson H. Holmes
- Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California
| | | | | | | | - Cathleen Hebson
- Department of Pediatrics, Santa Clara Valley Medical Center, San Jose, California
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Sanyal M, Morimoto M, Baradaran-Heravi A, Choi K, Kambham N, Jensen K, Dutt S, Dionis-Petersen KY, Liu LX, Felix K, Mayfield C, Dekel B, Bokenkamp A, Fryssira H, Guillen-Navarro E, Lama G, Brugnara M, Lücke T, Olney AH, Hunley TE, Polat AI, Yis U, Bogdanovic R, Mitrovic K, Berry S, Najera L, Najafian B, Gentile M, Nur Semerci C, Tsimaratos M, Lewis DB, Boerkoel CF. Lack of IL7Rα expression in T cells is a hallmark of T-cell immunodeficiency in Schimke immuno-osseous dysplasia (SIOD). Clin Immunol 2015; 161:355-65. [DOI: 10.1016/j.clim.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 10/16/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
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Bruckner TA, Mayo JA, Gould JB, Stevenson DK, Lewis DB, Shaw GM, Carmichael SL. Heightened risk of preterm birth and growth restriction after a first-born son. Ann Epidemiol 2015; 25:743-7.e1. [DOI: 10.1016/j.annepidem.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/07/2015] [Accepted: 07/10/2015] [Indexed: 12/20/2022]
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37
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Gaudillière B, Ganio EA, Tingle M, Lancero HL, Fragiadakis GK, Baca QJ, Aghaeepour N, Wong RJ, Quaintance C, El-Sayed YY, Shaw GM, Lewis DB, Stevenson DK, Nolan GP, Angst MS. Implementing Mass Cytometry at the Bedside to Study the Immunological Basis of Human Diseases: Distinctive Immune Features in Patients with a History of Term or Preterm Birth. Cytometry A 2015; 87:817-29. [PMID: 26190063 PMCID: PMC4758855 DOI: 10.1002/cyto.a.22720] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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] [Indexed: 11/12/2022]
Abstract
Single-cell technologies have immense potential to shed light on molecular and biological processes that drive human diseases. Mass cytometry (or Cytometry by Time Of Flight mass spectrometry, CyTOF) has already been employed in clinical studies to comprehensively survey patients' circulating immune system. As interest in the "bedside" application of mass cytometry is growing, the delineation of relevant methodological issues is called for. This report uses a newly generated dataset to discuss important methodological considerations when mass cytometry is implemented in a clinical study. Specifically, the use of whole blood samples versus peripheral blood mononuclear cells (PBMCs), design of mass-tagged antibody panels, technical and analytical implications of sample barcoding, and application of traditional and unsupervised approaches to analyze high-dimensional mass cytometry datasets are discussed. A mass cytometry assay was implemented in a cross-sectional study of 19 women with a history of term or preterm birth to determine whether immune traits in peripheral blood differentiate the two groups in the absence of pregnancy. Twenty-seven phenotypic and 11 intracellular markers were simultaneously analyzed in whole blood samples stimulated with lipopolysaccharide (LPS at 0, 0.1, 1, 10, and 100 ng mL(-1)) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. Complementary analyses, grounded in traditional or unsupervised gating strategies of immune cell subsets, indicated that the prpS6 and pMAPKAPK2 responses in classical monocytes are accentuated in women with a history of preterm birth (FDR<1%). The results suggest that women predisposed to preterm birth may be prone to mount an exacerbated TLR4 response during the course of pregnancy. This important hypothesis-generating finding points to the power of single-cell mass cytometry to detect biologically important differences in a relatively small patient cohort.
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Affiliation(s)
- Brice Gaudillière
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Edward A. Ganio
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Martha Tingle
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Hope L. Lancero
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Gabriela K. Fragiadakis
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Quentin J. Baca
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
| | - Nima Aghaeepour
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Cele Quaintance
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Yasser Y. El-Sayed
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94305
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - David B. Lewis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305
| | - Garry P. Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, School of Medicine, Stanford, California 94305
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Acharya S, Petersen KY, Golubkov V, Kwong M, Adams CM, Jackson PK, Lewis DB. Abstract 5002: Abstract Submission. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-5002] [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
Protein tyrosine kinase 7 (PTK7), a catalytically inactive receptor tyrosine kinase (RTK) that is highly expressed by T-lineage cells during intrathymic development, is a novel marker for human CD4+ recent thymic emigrants (RTEs), and is also highly expressed on some T-lineage thymomas, e.g., Jurkat cells as well as inprimary T-Acute Lymphoblastic leukemia. The function of PTK7 in normal human T-cell development and in oncogenesis remains unclear. Here, using RNAi-mediated gene silencing in T-lineage tumor cells, primary human peripheral T-cells, and thymocytes, we found that targeting PTK7 consistently decreased cell survival by augmenting caspase-3 activation of apoptosis. The PTK7 knockdown also decreased AKT phosphorylation and PI3 kinase activity, suggesting an essential role for PTK7 in survival of RTEs and developing thymocytes involving the PI3K/AKT pathway. Using mass spectrometry we identified insulin-like growth factor-1 (IGF-1) receptor as an active kinase partner of PTK7. This interaction was biologically relevant in that PTK7 downregulation also reduced IGF-1R-dependent survival signals in T-lineage cells. As enhanced IGF-1-dependent signaling is a frequent event in oncogenesis, the intersection of PTK7 with the IGF-1 signaling pathway suggests the potential of PTK7-directed therapy of T-lineage tumors.
Citation Format: Swati Acharya, Kira Y.D Petersen, Vladislav Golubkov, Mandy Kwong, Christopher M. Adams, Peter K. Jackson, David B. Lewis. Abstract Submission. [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 5002. doi:10.1158/1538-7445.AM2015-5002
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Affiliation(s)
- Swati Acharya
- 1Stanford University School of Medicine, Stanford, CA
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O'Gorman WE, Hsieh EWY, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM. Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus. J Allergy Clin Immunol 2015; 136:1326-36. [PMID: 26037552 DOI: 10.1016/j.jaci.2015.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [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: 12/20/2014] [Revised: 03/20/2015] [Accepted: 04/01/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND Activation of Toll-like receptors (TLRs) induces inflammatory responses involved in immunity to pathogens and autoimmune pathogenesis, such as in patients with systemic lupus erythematosus (SLE). Although TLRs are differentially expressed across the immune system, a comprehensive analysis of how multiple immune cell subsets respond in a system-wide manner has not been described. OBJECTIVE We sought to characterize TLR activation across multiple immune cell subsets and subjects, with the goal of establishing a reference framework against which to compare pathologic processes. METHODS Peripheral whole-blood samples were stimulated with TLR ligands and analyzed by means of mass cytometry simultaneously for surface marker expression, activation states of intracellular signaling proteins, and cytokine production. We developed a novel data visualization tool to provide an integrated view of TLR signaling networks with single-cell resolution. We studied 17 healthy volunteer donors and 8 patients with newly diagnosed and untreated SLE. RESULTS Our data revealed the diversity of TLR-induced responses within cell types, with TLR ligand specificity. Subsets of natural killer cells and T cells selectively induced nuclear factor κ light chain enhancer of activated B cells in response to TLR2 ligands. CD14(hi) monocytes exhibited the most polyfunctional cytokine expression patterns, with more than 80 distinct cytokine combinations. Monocytic TLR-induced cytokine patterns were shared among a group of healthy donors, with minimal intraindividual and interindividual variability. Furthermore, autoimmune disease altered baseline cytokine production; newly diagnosed untreated SLE patients shared a distinct monocytic chemokine signature, despite clinical heterogeneity. CONCLUSION Mass cytometry defined a systems-level reference framework for human TLR activation, which can be applied to study perturbations in patients with inflammatory diseases, such as SLE.
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Affiliation(s)
- William E O'Gorman
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif
| | - Elena W Y Hsieh
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif; Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, Calif
| | - Erica S Savig
- Cancer Biology Program, Stanford University, Stanford, Calif
| | | | - Joseph D Hernandez
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, Calif; Department of Pathology, Stanford University, Stanford, Calif
| | - Leo Hansmann
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif
| | - Imelda M Balboni
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, Calif
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, Calif
| | - Wendy J Fantl
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif; Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University, Stanford, Calif
| | - David B Lewis
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University, Stanford, Calif
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif.
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif; Howard Hughes Medical Institute, Stanford University, Stanford, Calif.
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Ozen M, Zhao H, Lewis DB, Wong RJ, Stevenson DK. Heme oxygenase and the immune system in normal and pathological pregnancies. Front Pharmacol 2015; 6:84. [PMID: 25964759 PMCID: PMC4408852 DOI: 10.3389/fphar.2015.00084] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [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: 02/27/2015] [Accepted: 04/02/2015] [Indexed: 11/22/2022] Open
Abstract
Normal pregnancy is an immunotolerant state. Many factors, including environmental, socioeconomic, genetic, and immunologic changes by infection and/or other causes of inflammation, may contribute to inter-individual differences resulting in a normal or pathologic pregnancy. In particular, imbalances in the immune system can cause many pregnancy-related diseases, such as infertility, abortions, pre-eclampsia, and preterm labor, which result in maternal/fetal death, prematurity, or small-for-gestational age newborns. New findings imply that myeloid regulatory cells and regulatory T cells (Tregs) may mediate immunotolerance during normal pregnancy. Effector T cells (Teffs) have, in contrast, been implicated to cause adverse pregnancy outcomes. Furthermore, feto-maternal tolerance affects the developing fetus. It has been shown that the Treg/Teff balance affects litter size and adoptive transfer of pregnancy-induced Tregs can prevent fetal rejection in the mouse. Heme oxygenase-1 (HO-1) has a protective role in many conditions through its anti-inflammatory, anti-apoptotic, antioxidative, and anti-proliferative actions. HO-1 is highly expressed in the placenta and plays a role in angiogenesis and placental vascular development and in regulating vascular tone in pregnancy. In addition, HO-1 is a major regulator of immune homeostasis by mediating crosstalk between innate and adaptive immune systems. Moreover, HO-1 can inhibit inflammation-induced phenotypic maturation of immune effector cells and pro-inflammatory cytokine secretion and promote anti-inflammatory cytokine production. HO-1 may also be associated with T-cell activation and can limit immune-based tissue injury by promoting Treg suppression of effector responses. Thus, HO-1 and its byproducts may protect against pregnancy complications by its immunomodulatory effects, and the regulation of HO-1 or its downstream effects has the potential to prevent or treat pregnancy complications and prematurity.
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Affiliation(s)
- Maide Ozen
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine , Stanford, CA, USA
| | - Hui Zhao
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine , Stanford, CA, USA
| | - David B Lewis
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine , Stanford, CA, USA
| | - Ronald J Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine , Stanford, CA, USA
| | - David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine , Stanford, CA, USA
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Marton JM, Creed IF, Lewis DB, Lane CR, Basu NB, Cohen MJ, Craft CB. Geographically Isolated Wetlands are Important Biogeochemical Reactors on the Landscape. Bioscience 2015. [DOI: 10.1093/biosci/biv009] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jing H, Zhang Q, Zhang Y, Hill BJ, Dove CG, Gelfand EW, Atkinson TP, Uzel G, Matthews HF, Mustillo PJ, Lewis DB, Kavadas FD, Hanson IC, Kumar AR, Geha RS, Douek DC, Holland SM, Freeman AF, Su HC. Somatic reversion in dedicator of cytokinesis 8 immunodeficiency modulates disease phenotype. J Allergy Clin Immunol 2014; 133:1667-75. [PMID: 24797421 DOI: 10.1016/j.jaci.2014.03.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/21/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Autosomal recessive loss-of-function mutations in dedicator of cytokinesis 8 (DOCK8) cause a combined immunodeficiency characterized by atopy, recurrent infections, and cancer susceptibility. A genotype-phenotype explanation for the variable disease expression is lacking. OBJECTIVE We investigated whether reversions contributed to the variable disease expression. METHODS Patients followed at the National Institutes of Health's Clinical Center were studied. We performed detailed genetic analyses and intracellular flow cytometry to detect DOCK8 protein expression within lymphocyte subsets. RESULTS We identified 17 of 34 DOCK8-deficient patients who had germline mutations with variable degrees of reversion caused by somatic repair. Somatic repair of the DOCK8 mutations resulted from second-site mutation, original-site mutation, gene conversion, and intragenic crossover. Higher degrees of reversion were associated with recombination-mediated repair. DOCK8 expression was restored primarily within antigen-experienced T cells or natural killer cells but less so in naive T or B cells. Several patients exhibited multiple different repair events. Patients who had reversions were older and had less severe allergic disease, although infection susceptibility persisted. No patients were cured without hematopoietic cell transplantation. CONCLUSIONS In patients with DOCK8 deficiency, only certain combinations of germline mutations supported secondary somatic repair. Those patients had an ameliorated disease course with longer survival but still had fatal complications or required hematopoietic cell transplantation. These observations support the concept that some DOCK8-immunodeficient patients have mutable mosaic genomes that can modulate disease phenotype over time.
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Affiliation(s)
- Huie Jing
- Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Qian Zhang
- Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Yu Zhang
- Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Brenna J Hill
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Christopher G Dove
- Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Erwin W Gelfand
- Division of Allergy and Immunology, Department of Pediatrics, Division of Cell Biology, National Jewish Health, Denver, Colo
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Gulbu Uzel
- Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Helen F Matthews
- Laboratory of Immunology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Peter J Mustillo
- Division of Infectious Diseases and Immunology, Nationwide Children's Hospital, Columbus, Ohio
| | - David B Lewis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Stanford University, Stanford, Calif
| | - Fotini D Kavadas
- Section of Clinical Immunology and Allergy, Department of Pediatrics, Alberta Children's Hospital and University of Calgary, Calgary, Alberta, Canada
| | - I Celine Hanson
- Section of Allergy and Immunology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex
| | - Ashish R Kumar
- Cancer and Blood Diseases Institute, Division of Bone Marrow Transplantation and Immune Deficiency and Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Raif S Geha
- Division of Immunology and Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, Mass
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md
| | - Helen C Su
- Laboratory of Host Defenses, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Md.
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Zheng J, Liu Y, Liu Y, Liu M, Xiang Z, Lam KT, Lewis DB, Lau YL, Tu W. Human CD8+ regulatory T cells inhibit GVHD and preserve general immunity in humanized mice. Sci Transl Med 2013; 5:168ra9. [PMID: 23325802 DOI: 10.1126/scitranslmed.3004943] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Graft-versus-host disease (GVHD) is a lethal complication of allogeneic bone marrow transplantation (BMT). Immunosuppressive agents are currently used to control GVHD but may cause general immune suppression and limit the effectiveness of BMT. Adoptive transfer of regulatory T cells (T(regs)) can prevent GVHD in rodents, suggesting a therapeutic potential of T(regs) for GVHD in humans. However, the clinical application of T(reg)-based therapy is hampered by the low frequency of human T(regs) and the lack of a reliable model to test their therapeutic effects in vivo. Recently, we successfully generated human alloantigen-specific CD8(hi) T(regs) in a large scale from antigenically naïve precursors ex vivo using allogeneic CD40-activated B cells as stimulators. We report a human allogeneic GVHD model established in humanized mice to mimic GVHD after BMT in humans. We demonstrate that ex vivo-induced CD8(hi) T(regs) controlled GVHD in an allospecific manner by reducing alloreactive T cell proliferation as well as decreasing inflammatory cytokine and chemokine secretion within target organs through a CTLA-4-dependent mechanism in humanized mice. These CD8(hi) T(regs) induced long-term tolerance effectively without compromising general immunity and graft-versus-tumor activity. Our results support testing of human CD8(hi) T(regs) in GVHD in clinical trials.
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Affiliation(s)
- Jian Zheng
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 000000, China
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Lewis DB, Barclay CJ. Efficiency and cross-bridge work output of skeletal muscle is decreased at low levels of activation. Pflugers Arch 2013; 466:599-609. [PMID: 24013759 DOI: 10.1007/s00424-013-1344-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 11/30/2022]
Abstract
The purpose of this study was to determine how the mechanical efficiency of skeletal muscle is affected by level of activation. Experiments were performed in vitro (35 °C) using bundles of fibres from fast-twitch extensor digitorum longus (EDL) and slow-twitch soleus muscles of mice. Measurements were made of the total work and heat produced in response to 10 brief contractions. Mechanical efficiency was the ratio of total work performed to (total heat produced + work performed). Level of activation was varied by altering stimulation frequency between 40 and 160 Hz. Efficiency did not differ significantly between the two muscle types but was significantly lower using 40 Hz stimulation (mean efficiency ± SEM, 0.092 ± 0.012, n = 12, averaged across EDL and soleus) than at any of the other frequencies (160 Hz: 0.147 ± 0.007, n = 12). Measurements of the partitioning of energy output between force-dependent and force-independent components enabled calculation of the amount of Ca(2+) released and number of cross-bridge cycles performed during the contractions. At 40 Hz stimulation frequency, less Ca(2+) was released than at higher frequencies and fewer cross-bridge cycles were performed. Furthermore, less work was performed in each cross-bridge cycle. It is concluded that skeletal muscles are less efficient at low levels of activation than when fully activated and this indicates that level of activation affects not only the number of cycling cross-bridges but also the ability of individual cross-bridges to perform work.
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Affiliation(s)
- D B Lewis
- School of Rehabilitation Sciences, Griffith University, Gold Coast, Queensland, Australia, 4222
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Palin AC, Ramachandran V, Acharya S, Lewis DB. Human neonatal naive CD4+ T cells have enhanced activation-dependent signaling regulated by the microRNA miR-181a. J Immunol 2013; 190:2682-91. [PMID: 23408835 DOI: 10.4049/jimmunol.1202534] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Compared with older children and adults, human neonates have reduced and delayed CD4(+) T cell immunity to certain pathogens, but the mechanisms for these developmental differences in immune function remain poorly understood. We investigated the hypothesis that impaired human neonatal CD4(+) T cell immunity was due to reduced signaling by naive CD4(+) T cells following engagement of the αβ-TCR/CD3 complex and CD28. Surprisingly, calcium flux following engagement of CD3 was significantly higher in neonatal naive CD4(+) T cells from umbilical cord blood (CB) compared with naive CD4(+) T cells from adult peripheral blood. Enhanced calcium flux was also observed in adult CD4(+) recent thymic emigrants. Neonatal naive CD4(+) T cells also had higher activation-induced Erk phosphorylation. The microRNA miR-181a, which enhances activation-induced calcium flux in murine thymocytes, was expressed at significantly higher levels in CB naive CD4(+) T cells compared with adult cells. Overexpression of miR-181a in adult naive CD4(+) T cells increased activation-induced calcium flux, implying that the increased miR-181a levels of CB naive CD4(+) T cells contributed to their enhanced signaling. In contrast, AP-1-dependent transcription, which is downstream of Erk and required for full T cell activation, was decreased in CB naive CD4(+) T cells compared with adult cells. Thus, CB naive CD4(+) T cells have enhanced activation-dependent calcium flux, indicative of the retention of a thymocyte-like phenotype. Enhanced calcium signaling and Erk phosphorylation are decoupled from downstream AP-1-dependent transcription, which is reduced and likely contributes to limitations of human fetal and neonatal CD4(+) T cell immunity.
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Affiliation(s)
- Amy C Palin
- Department of Pediatrics, Program in Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
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Bhaumik S, Giffon T, Bolinger D, Kirkman R, Lewis DB, Weaver CT, Randolph DA. Retinoic acid hypersensitivity promotes peripheral tolerance in recent thymic emigrants. J Immunol 2013; 190:2603-13. [PMID: 23401586 DOI: 10.4049/jimmunol.1200852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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
Whereas thymic education eliminates most self-reactive T cells, additional mechanisms to promote tolerance in the periphery are critical to prevent excessive immune responses against benign environmental Ags and some self-Ags. In this study we show that murine CD4(+) recent thymic emigrants (RTEs) are programmed to facilitate tolerance in the periphery. Both in vitro and in vivo, naive RTEs more readily upregulate Foxp3 than do mature naive cells after stimulation under tolerogenic conditions. In RTEs, a relatively high sensitivity to retinoic acid contributes to decreased IFN-γ production, permitting the expression of Foxp3. Conversely, mature naive CD4 cells have a lower sensitivity to retinoic acid, resulting in increased IFN-γ production and subsequent IFN-γ-mediated silencing of Foxp3 expression. Enhanced retinoic acid signaling and Foxp3 induction in RTEs upon Ag encounter in the periphery may serve as form of secondary education that complements thymic education and helps avoid inappropriate immune responses. This mechanism for tolerance may be particularly important in settings where RTEs comprise a large fraction of the peripheral T cell pool, such as in newborns or after umbilical cord blood transplant.
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Affiliation(s)
- Suniti Bhaumik
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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Abraham RS, Albanesi C, Alevizos I, Anguita J, Anstead GM, Aranow C, Austin HA, Babu S, Ballow MC, Balow JE, Barnidge DR, Belmont JW, Belz GT, Ben-Yehuda D, Berek C, Beukelman T, Bieber T, Bijlsma JW, Bleesing JJ, Blutt SE, Bohle B, Borzova E, Boyaka PN, Knut B, Bustamante J, Buttgereit F, Byrne M, Calder VL, Carneiro-Sampaio M, Carotta S, Casanova JL, Cavacini LA, Chan ES, Chinen J, Chitnis T, Cho M, Christopher-Stine L, Cope AP, Corry DB, Cottrell T, Coutinho A, Craveiro M, Cron RQ, Cuellar-Rodriguez J, Dalakas MC, de Barros SC, Devlin BH, Diamond B, Dispenzieri A, Du Clos TW, Dupuis-Boisson S, Eagar TN, Edhegard KD, Eisenbarth GS, Elmets CA, Erkan D, Feinberg MB, Fikrig E, Fleisher TA, Fontenot AP, Franco LM, Freeman AF, Frew AJ, Friedman T, Fujihashi K, Gadina M, Galli SJ, Gaspar HB, Gatt ME, Gershwin ME, Ghoreschi K, Gillespie SL, Goronzy JJ, Grattan CE, Greenspan NS, Grunebaum E, Haeberli G, Hall RP, Hamilton RG, Harriman GR, Hasni SA, Helbling A, Hingorani M, Holland SM, Hruz PL, Illei G, Imboden JB, Izraeli S, Jaffe ES, Jagobi C, Jalkanen S, Jetanalin P, Jouanguy E, June CH, Kallies A, Kaufmann SH, Kavanaugh A, Khan S, Kheradmand F, Khoury SJ, Koretzky GA, Korngold R, Kovalszki A, Kuhns DB, Kyle RA, Lanza IR, Laurence A, Lee SJ, Lenardo MJ, Levinson AI, Levy O, Lewis DB, Lewis DE, Lightman SL, Lockshin MD, Lotze MT, Luong A, Mackay M, Malo JL, Maltzman JS, Mannon PJ, Manns MP, Markert ML, McCarthy EA, McDonald DR, McGhee JR, Melby PC, Metcalfe DD, Metz M, Miller SD, Mitchell AL, Mittal S, Miyara M, Mold C, Moller DR, Mueller SN, Müller UR, Murphy PM, Noel P, Notarangelo L, Nutman TB, Nutt SL, Oliveira JB, Olson CM, O'Shea JJ, Pai SY, Pandit L, Paul ME, Pearce SH, Peterson EJ, Picard C, Pichler WJ, Pittaluga S, Puel A, Radbruch A, Reece ST, Reveille JD, Rich RR, Rivat C, Robinson BW, Rodgers JR, Roifman CM, Rosen A, Rosenbaum JT, Rouse BT, Rowley SD, Sakaguchi S, Salmi M, Schroeder HW, Seibel MJ, Selmi C, Shafer WM, Shah PK, Shankar S, Shaw AR, Shearer WT, Sheikh J, Siegel R, Simon A, Simonian PL, Smith GP, Smith JR, Snow AL, Stephens DS, Stone JH, Straumann A, Su HC, Swainson L, Szymanska-Mroczek E, Taylor N, Thrasher AJ, Timares L, Torres RM, Uzel G, van der Meer JW, van der Hilst JC, Varga J, Waldman M, Weiser P, Weller PF, Weyand CM, Whiteside TL, Wigley FM, Winchester RJ, Wing K, Wood K, Xu H, Zhang SY, Zimmermann VS. List of contributors. Clin Immunol 2013. [DOI: 10.1016/b978-0-7234-3691-1.09995-5] [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: 10/23/2022]
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Morimoto M, Kérourédan O, Gendronneau M, Shuen C, Baradaran-Heravi A, Asakura Y, Basiratnia M, Bogdanovic R, Bonneau D, Buck A, Charrow J, Cochat P, Dehaai KA, Fenkçi MS, Frange P, Fründ S, Fryssira H, Keller K, Kirmani S, Kobelka C, Kohler K, Lewis DB, Massella L, McLeod DR, Milford DV, Nobili F, Olney AH, Semerci CN, Stajic N, Stein A, Taque S, Zonana J, Lücke T, Hendson G, Bonnaure-Mallet M, Boerkoel CF. Dental abnormalities in Schimke immuno-osseous dysplasia. J Dent Res 2012; 91:29S-37S. [PMID: 22699664 DOI: 10.1177/0022034512450299] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Described for the first time in 1971, Schimke immuno-osseous dysplasia (SIOD) is an autosomal-recessive multisystem disorder that is caused by bi-allelic mutations of SMARCAL1, which encodes a DNA annealing helicase. To define better the dental anomalies of SIOD, we reviewed the records from SIOD patients with identified bi-allelic SMARCAL1 mutations, and we found that 66.0% had microdontia, hypodontia, or malformed deciduous and permanent molars. Immunohistochemical analyses showed expression of SMARCAL1 in all developing teeth, raising the possibility that the malformations are cell-autonomous consequences of SMARCAL1 deficiency. We also found that stimulation of cultured skin fibroblasts from SIOD patients with the tooth morphogens WNT3A, BMP4, and TGFβ1 identified altered transcriptional responses, raising the hypothesis that the dental malformations arise in part from altered responses to developmental morphogens. To the best of our knowledge, this is the first systematic study of the dental anomalies associated with SIOD.
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Affiliation(s)
- M Morimoto
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
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Morimoto M, Yu Z, Stenzel P, Clewing JM, Najafian B, Mayfield C, Hendson G, Weinkauf JG, Gormley AK, Parham DM, Ponniah U, André JL, Asakura Y, Basiratnia M, Bogdanović R, Bokenkamp A, Bonneau D, Buck A, Charrow J, Cochat P, Cordeiro I, Deschenes G, Fenkçi MS, Frange P, Fründ S, Fryssira H, Guillen-Navarro E, Keller K, Kirmani S, Kobelka C, Lamfers P, Levtchenko E, Lewis DB, Massella L, McLeod DR, Milford DV, Nobili F, Saraiva JM, Semerci CN, Shoemaker L, Stajić N, Stein A, Taha D, Wand D, Zonana J, Lücke T, Boerkoel CF. Reduced elastogenesis: a clue to the arteriosclerosis and emphysematous changes in Schimke immuno-osseous dysplasia? Orphanet J Rare Dis 2012; 7:70. [PMID: 22998683 PMCID: PMC3568709 DOI: 10.1186/1750-1172-7-70] [Citation(s) in RCA: 22] [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] [Received: 03/15/2012] [Accepted: 09/14/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arteriosclerosis and emphysema develop in individuals with Schimke immuno-osseous dysplasia (SIOD), a multisystem disorder caused by biallelic mutations in SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1). However, the mechanism by which the vascular and pulmonary disease arises in SIOD remains unknown. METHODS We reviewed the records of 65 patients with SMARCAL1 mutations. Molecular and immunohistochemical analyses were conducted on autopsy tissue from 4 SIOD patients. RESULTS Thirty-two of 63 patients had signs of arteriosclerosis and 3 of 51 had signs of emphysema. The arteriosclerosis was characterized by intimal and medial hyperplasia, smooth muscle cell hyperplasia and fragmented and disorganized elastin fibers, and the pulmonary disease was characterized by panlobular enlargement of air spaces. Consistent with a cell autonomous disorder, SMARCAL1 was expressed in arterial and lung tissue, and both the aorta and lung of SIOD patients had reduced expression of elastin and alterations in the expression of regulators of elastin gene expression. CONCLUSIONS This first comprehensive study of the vascular and pulmonary complications of SIOD shows that these commonly cause morbidity and mortality and might arise from impaired elastogenesis. Additionally, the effect of SMARCAL1 deficiency on elastin expression provides a model for understanding other features of SIOD.
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Affiliation(s)
- Marie Morimoto
- Provincial Medical Genetics Program, Department of Medical Genetics, Children's and Women's Health Centre of BC, 4500 Oak Street, Room C234, Vancouver, BC, V6H 3N1, Canada
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Baradaran-Heravi A, Cho KS, Tolhuis B, Sanyal M, Morozova O, Morimoto M, Elizondo LI, Bridgewater D, Lubieniecka J, Beirnes K, Myung C, Leung D, Fam HK, Choi K, Huang Y, Dionis KY, Zonana J, Keller K, Stenzel P, Mayfield C, Lücke T, Bokenkamp A, Marra MA, van Lohuizen M, Lewis DB, Shaw C, Boerkoel CF. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. Hum Mol Genet 2012; 21:2572-87. [PMID: 22378147 DOI: 10.1093/hmg/dds083] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biallelic mutations of the DNA annealing helicase SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) cause Schimke immuno-osseous dysplasia (SIOD, MIM 242900), an incompletely penetrant autosomal recessive disorder. Using human, Drosophila and mouse models, we show that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin and modulate gene expression. We also show that, as found in SIOD patients, deficiency of the SMARCAL1 orthologs alone is insufficient to cause disease in fruit flies and mice, although such deficiency causes modest diffuse alterations in gene expression. Rather, disease manifests when SMARCAL1 deficiency interacts with genetic and environmental factors that further alter gene expression. We conclude that the SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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