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Fu Q, Vegesna M, Sundararaman N, Damoc E, Arrey TN, Pashkova A, Mengesha E, Debbas P, Joung S, Li D, Cheng S, Braun J, McGovern DPB, Murray C, Xuan Y, Eyk JEV. Paradigm shift in biomarker translation: a pipeline to generate clinical grade biomarker candidates from DIA-MS discovery. bioRxiv 2024:2024.03.20.586018. [PMID: 38562888 PMCID: PMC10983901 DOI: 10.1101/2024.03.20.586018] [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] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package. This innovative tool uses the discovery cohort analysis to select precursors, peptides, and proteins that adhere to established targeted assay criteria. TEAQ was applied to Data-Independent Acquisition MS data from plasma samples acquired on an Orbitrap™ Astral™ MS. Identified precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra-protein correlation from 11-point loading curves under three throughputs, to develop a resource for clinical-grade targeted assays. From a clinical cohort of individuals with inflammatory bowel disease (n=492), TEAQ successfully identified 1116 signature peptides for 327 quantifiable proteins from 1180 identified proteins. Embedding stringent selection criteria adaptable to targeted assay development into the analysis of discovery data will streamline the transition to validation and clinical studies.
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Khrom M, Long M, Dube S, Robbins L, Botwin GJ, Yang S, Mengesha E, Li D, Naito T, Bonthala NN, Ha C, Melmed G, Rabizadeh S, Syal G, Vasiliauskas E, Ziring D, Brant SR, Cho J, Duerr RH, Rioux J, Schumm P, Silverberg M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Xavier RJ, Kugathasan S, Hercules D, Targan SR, Sartor RB, Haritunians T, McGovern DPB. Comprehensive Association Analyses of Extraintestinal Manifestations in Inflammatory Bowel Disease. Gastroenterology 2024:S0016-5085(24)00232-4. [PMID: 38490347 DOI: 10.1053/j.gastro.2024.02.026] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel disease (IBD) frequently develop extraintestinal manifestations (EIMs) that contribute substantially to morbidity. We assembled the largest multicohort data set to date to investigate the clinical, serologic, and genetic factors associated with EIM complications in IBD. METHODS Data were available in 12,083 unrelated European ancestry IBD cases with presence or absence of EIMs (eg, ankylosing spondylitis [ankylosing spondylitis and sacroiliitis], primary sclerosing cholangitis [PSC], peripheral arthritis, and skin and ocular manifestations) across 4 cohorts (Cedars-Sinai Medical Center, National Institute for Diabetes and Digestive and Kidney Diseases IBD Genetics Consortium, Sinai Helmsley Alliance for Research Excellence Consortium, and Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn's Disease cohort). Clinical and serologic parameters were analyzed by means of univariable and multivariable regression analyses using a mixed-effects model. Within-case logistic regression was performed to assess genetic associations. RESULTS Most EIMs occurred more commonly in female subjects (overall EIM: P = 9.0E-05, odds ratio [OR], 1.2; 95% CI, 1.1-1.4), with CD (especially colonic disease location; P = 9.8E-09, OR, 1.7; 95% CI, 1.4-2.0), and in subjects who required surgery (both CD and UC; P = 3.6E-19, OR, 1.7; 95% CI, 1.5-1.9). Smoking increased risk of EIMs except for PSC, where there was a "protective" effect. Multiple serologic associations were observed, including with PSC (IgG and IgA, perinuclear anti-nuclear cytoplasmic antibody; anti-Saccharomyces cerevisiae antibodies; and anti-flagellin) and any EIM (IgG and IgA, perinuclear anti-nuclear cytoplasmic antibody; anti-Saccharomyces cerevisiae antibodies; and anti-Pseudomonas fluorescens-associated sequence). We identified genome-wide significant associations within major histocompatibility complex (ankylosing spondylitis and sacroiliitis, P = 1.4E-15; OR, 2.5; 95% CI, 2.0-3.1; PSC, P = 2.7E-10; OR, 2.8; 95% CI, 2.0-3.8; ocular, P = 2E-08, OR, 3.6; 95% CI, 2.3-5.6; and overall EIM, P = 8.4E-09; OR, 2.2; 95% CI, 1.7-2.9) and CPEB4 (skin, P = 2.7E-08; OR, 1.5; 95% CI, 1.3-1.8). Genetic associations implicated tumor necrosis factor, JAK-STAT, and IL6 as potential targets for EIMs. Contrary to previous reports, only 2% of our subjects had multiple EIMs and most co-occurrences were negatively correlated. CONCLUSIONS We have identified demographic, clinical, and genetic associations with EIMs that revealed underlying mechanisms and implicated novel and existing drug targets-important steps toward a more personalized approach to IBD management.
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Millie Long
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Lori Robbins
- Palmetto Digestive Health Specialists, Charleston, South Carolina
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christina Ha
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gil Melmed
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shervin Rabizadeh
- Department of Pediatrics, Pediatric Inflammatory Bowel Disease Program, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gaurav Syal
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Eric Vasiliauskas
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Ziring
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, New York
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John Rioux
- Department of Medicine, Université de Montréal and Research Center, Montreal Heart Institute, Montréal, Québec, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Mark Silverberg
- University of Toronto, Samuel Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Bana Jabri
- University of Chicago, Pritzker School of Medicine, Chicago, Illinois
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Subra Kugathasan
- Children's Healthcare of Atlanta Combined Center for Pediatric Inflammatory Bowel Disease, Atlanta, Georgia; Emory School of Medicine, Atlanta, Georgia
| | | | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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Gu P, Mendonca O, Carter D, Dube S, Wang P, Huang X, Li D, Moore JH, McGovern DPB. AI-luminating Artificial Intelligence in Inflammatory Bowel Diseases: A Narrative Review on the Role of AI in Endoscopy, Histology, and Imaging for IBD. Inflamm Bowel Dis 2024:izae030. [PMID: 38452040 DOI: 10.1093/ibd/izae030] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Endoscopy, histology, and cross-sectional imaging serve as fundamental pillars in the detection, monitoring, and prognostication of inflammatory bowel disease (IBD). However, interpretation of these studies often relies on subjective human judgment, which can lead to delays, intra- and interobserver variability, and potential diagnostic discrepancies. With the rising incidence of IBD globally coupled with the exponential digitization of these data, there is a growing demand for innovative approaches to streamline diagnosis and elevate clinical decision-making. In this context, artificial intelligence (AI) technologies emerge as a timely solution to address the evolving challenges in IBD. Early studies using deep learning and radiomics approaches for endoscopy, histology, and imaging in IBD have demonstrated promising results for using AI to detect, diagnose, characterize, phenotype, and prognosticate IBD. Nonetheless, the available literature has inherent limitations and knowledge gaps that need to be addressed before AI can transition into a mainstream clinical tool for IBD. To better understand the potential value of integrating AI in IBD, we review the available literature to summarize our current understanding and identify gaps in knowledge to inform future investigations.
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Affiliation(s)
- Phillip Gu
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Dan Carter
- Department of Gastroenterology, Sheba Medical Center, Tel Aviv, Israel
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul Wang
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiuzhen Huang
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Debiao Li
- Biomedical Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Sebastian S, Siegmund B, Teferra F, McGovern DPB, Queiroz NSF, van der Woude CJ, Sharma V. Promoting equity in inflammatory bowel disease: a global approach to care. Lancet Gastroenterol Hepatol 2024; 9:192-194. [PMID: 38219765 DOI: 10.1016/s2468-1253(23)00368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 01/16/2024]
Affiliation(s)
- Shaji Sebastian
- IBD Unit, Department of Gastroenterology, Hull University Teaching Hospitals, Hull HU3 2JZ, UK; Hull York Medical School, Hull, UK.
| | - Britta Siegmund
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany; Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Dermot P B McGovern
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Vishal Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Spencer EA, Dubinsky MC, Kamm MA, Chaparro M, Gionchetti P, Rizzello F, Gisbert JP, Wright EK, Schulberg JD, Hamilton AL, McGovern DPB, Dervieux T. Corrigendum: Poor prognostic factors of pharmacokinetic origin predict outcomes in inflammatory bowel disease patients treated with anti-tumor necrosis factor-α. Front Immunol 2024; 15:1383704. [PMID: 38476224 PMCID: PMC10929709 DOI: 10.3389/fimmu.2024.1383704] [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: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2024.1342477.].
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Affiliation(s)
- Elizabeth A. Spencer
- Division of Gastroenterology, Icahn School of Medicine Mount Sinai, New York, NY, United States
| | - Marla C. Dubinsky
- Division of Gastroenterology, Icahn School of Medicine Mount Sinai, New York, NY, United States
| | - Michael A. Kamm
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Paolo Gionchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Italy, Bologna, Italy
- DIMEC University of Bologna-Italy, Bologna, Italy
| | - Fernando Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Italy, Bologna, Italy
- DIMEC University of Bologna-Italy, Bologna, Italy
| | - Javier P. Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Emily K. Wright
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Julien D. Schulberg
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Amy L. Hamilton
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Dermot P. B. McGovern
- F. Widjaja Inflammatory Bowel Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Thierry Dervieux
- Research and Development, Prometheus Laboratories, San Diego, CA, United States
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Spencer EA, Dubinsky MC, Kamm MA, Chaparro M, Gionchetti P, Rizzello F, Gisbert JP, Wright EK, Schulberg JD, Hamilton AL, McGovern DPB, Dervieux T. Poor prognostic factors of pharmacokinetic origin predict outcomes in inflammatory bowel disease patients treated with anti-tumor necrosis factor-α. Front Immunol 2024; 15:1342477. [PMID: 38476237 PMCID: PMC10929708 DOI: 10.3389/fimmu.2024.1342477] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction We evaluated baseline Clearance of anti-tumor necrosis factors and human leukocyte antigen variant (HLA DQA1*05) in combination as poor prognostic factors (PPF) of pharmacokinetic (PK) origin impacting immune response (formation of antidrug antibodies) and disease control of inflammatory bowel disease (IBD) patients treated with infliximab or adalimumab. Methods Baseline Clearance was estimated in IBD patients before starting treatment using weight and serum albumin concentrations. HLA DQA1*05 carrier status (rs2097432 A/G or G/G variant) was measured using real time polymerase chain reaction. The outcomes consisted of immune response, clinical and biochemical remission (C-reactive protein<3 mg/L in the absence of symptoms), and endoscopic remission (SES-CD<3). Statistical analysis consisted of logistic regression and nonlinear mixed effect models. Results and discussion In 415 patients enrolled from 4 different cohorts (median age 27 [IQR: 15-43] years, 46% females), Clearance>0.326 L/day and HLA DQA1*05 carrier status were 2-fold more likely to have antidrug antibodies (OR=2.3, 95%CI: 1.7-3.4; p<0.001, and OR=1.9, 95%CI: 1.4-2.8; p<0.001, respectively). Overall, each incremental PPF of PK origin resulted in a 2-fold (OR=2.16, 95%CI: 1.7-2.7; p<0.11) [corrected] higher likelihood of antidrug antibody formation. The presence of both PPF of PK origin resulted in higher rates of antidrug antibodies (p<0.01) and lower clinical and biochemical remission (p<0.01). Each incremental increase in PPF of PK origin associated with lower likelihood of endoscopic remission (OR=0.4, 95%CI: 0.2-0.7; p<0.001). Prior biologic experience heightened the negative impact of PPF of PK origin on clinical and biochemical remission (p<0.01). Implementation of proactive therapeutic drug monitoring reduced it, particularly during maintenance and in the presence of higher drug concentrations (p<0.001). We conclude that PPF of PK origin, including both higher Clearance and carriage of HLA DQA1*05, impact outcomes in patients with IBD.
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Affiliation(s)
- Elizabeth A. Spencer
- Division of Gastroenterology, Icahn School of Medicine Mount Sinai, New York, NY, United States
| | - Marla C. Dubinsky
- Division of Gastroenterology, Icahn School of Medicine Mount Sinai, New York, NY, United States
| | - Michael A. Kamm
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Paolo Gionchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Italy, Bologna, Italy
- DIMEC University of Bologna-Italy , Bologna, Italy
| | - Fernando Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Italy, Bologna, Italy
- DIMEC University of Bologna-Italy , Bologna, Italy
| | - Javier P. Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM) and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Emily K. Wright
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Julien D. Schulberg
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Amy L. Hamilton
- St Vincent’s Hospital and The University of Melbourne, Melbourne, VIC, Australia
| | - Dermot P. B. McGovern
- F. Widjaja Inflammatory Bowel Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Thierry Dervieux
- Research and Development, Prometheus Laboratories, San Diego, CA, United States
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Malique A, Sun S, Chandwe K, Amadi B, Haritunians T, Jain U, Muegge BD, Frein J, Sasaki Y, Foster A, Storer CE, Mengesha E, Kern J, McGovern DPB, Head RD, Kelly P, Liu TC. NAD + precursors and bile acid sequestration treat preclinical refractory environmental enteric dysfunction. Sci Transl Med 2024; 16:eabq4145. [PMID: 38170788 DOI: 10.1126/scitranslmed.abq4145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/07/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Environmental enteric dysfunction (EED) is a diffuse small bowel disorder associated with poor growth, inadequate responses to oral vaccines, and nutrient malabsorption in millions of children worldwide. We identify loss of the small intestinal Paneth and goblet cells that are critical for innate immunity, reduced villous height, increased bile acids, and dysregulated nicotinamide adenine dinucleotide (NAD+) synthesis signaling as potential mechanisms underlying EED and which also correlated with diminished length-for-age z score. Isocaloric low-protein diet (LPD) consumption in mice recapitulated EED histopathology and transcriptomic changes in a microbiota-independent manner, as well as increases in serum and fecal bile acids. Children with refractory EED harbor single-nucleotide polymorphisms in key enzymes involved in NAD+ synthesis. In mice, deletion of Nampt, the gene encoding the rate-limiting enzyme in the NAD+ salvage pathway, from intestinal epithelium also reduced Paneth cell function, a deficiency that was further aggravated by LPD. Separate supplementation with NAD+ precursors or bile acid sequestrant partially restored LPD-associated Paneth cell defects and, when combined, fully restored all histopathology defects in LPD-fed mice. Therapeutic regimens that increase protein and NAD+ contents while reducing excessive bile acids may benefit children with refractory EED.
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Affiliation(s)
- Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shengxiang Sun
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Brian D Muegge
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer Frein
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amanda Foster
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad E Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Justin Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition Group, Department of Medicine, University of Zambia School of Medicine, P.O. Box 50398, Lusaka, Zambia
- Blizard Institute, Barts & the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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8
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Gu P, Dube S, Lee Y, Yang S, Li D, Haritunians T, Vasiliauskas E, Bonthala N, Syal G, Yarur A, Ziring D, Targan S, Rabizadeh S, Melmed GY, Fleshner P, McGovern DPB. Comparative Persistence of Non-tumor Necrosis Factor (TNF) vs. TNF Antagonists for Post-operative Prophylaxis in Crohn's Disease (CD). Dig Dis Sci 2024; 69:235-245. [PMID: 38015321 PMCID: PMC10787872 DOI: 10.1007/s10620-023-08192-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND The comparative safety and effectiveness of available biologics for post-operative prophylaxis in Crohn's disease (CD) is uncertain. Drug persistence may serve as a real-world proxy for tolerability and effectiveness. We evaluated the comparative persistence of non-TNF and TNF antagonists for post-operative prophylaxis and their comparative effectiveness for preventing early endoscopic post-operative recurrence (POR). METHODS We conducted a single-center, retrospective study of surgically naïve CD subjects undergoing ileocecal or small bowel resection between 1/1/2000 and 12/31/2021 and prescribed a biologic for post-operative prophylaxis. We compared the risk of prophylaxis failure (requiring recurrent surgery or discontinuation of therapy due to persistent POR despite optimized drug level or dose escalation, immunogenicity, and/or adverse event) and early endoscopic POR (Rutgeert's score ≥ i2 within 15 months postoperatively) between non-TNF and TNF antagonist prophylaxis using Cox proportional hazard and logistic regression, respectively, adjusting for demographic and disease characteristics. RESULTS The study included 291 subjects (81% TNF antagonists). After multivariable adjustment, non-TNF antagonist prophylaxis was associated with a significantly lower risk of prophylaxis failure than TNF antagonists (hazard ratio 0.26; 95% confidence interval (CI) [0.13-0.53]). Prophylaxis with non-TNF and TNF antagonists had similar risk of early endoscopic POR (odds ratio 0.66; 95% CI [0.32-1.36]). Stratifying the non-TNF antagonists by anti-integrin and anti-IL12/23 yielded similar results. CONCLUSION In a cohort of surgically naïve CD subjects prescribed a biologic for post-operative prophylaxis, non-TNF antagonists had greater persistence than TNF antagonists with similar risk for early endoscopic POR. If confirmed by large, prospective studies, these findings can inform post-operative management strategies in CD.
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Affiliation(s)
- Phillip Gu
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA.
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - YooJin Lee
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Eric Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Niru Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Gaurav Syal
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Andres Yarur
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - David Ziring
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Stephan Targan
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Shervin Rabizadeh
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Phillip Fleshner
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, 8730 Alden Drive, Thalians Bldg, #E222, Los Angeles, CA, 90048, USA
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9
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Uhlig HH, Booth C, Cho J, Dubinsky M, Griffiths AM, Grimbacher B, Hambleton S, Huang Y, Jones K, Kammermeier J, Kanegane H, Koletzko S, Kotlarz D, Klein C, Lenardo MJ, Lo B, McGovern DPB, Özen A, de Ridder L, Ruemmele F, Shouval DS, Snapper SB, Travis SP, Turner D, Wilson DC, Muise AM. Precision medicine in monogenic inflammatory bowel disease: proposed mIBD REPORT standards. Nat Rev Gastroenterol Hepatol 2023; 20:810-828. [PMID: 37789059 DOI: 10.1038/s41575-023-00838-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 10/05/2023]
Abstract
Owing to advances in genomics that enable differentiation of molecular aetiologies, patients with monogenic inflammatory bowel disease (mIBD) potentially have access to genotype-guided precision medicine. In this Expert Recommendation, we review the therapeutic research landscape of mIBD, the reported response to therapies, the medication-related risks and systematic bias in reporting. The mIBD field is characterized by the absence of randomized controlled trials and is dominated by retrospective observational data based on case series and case reports. More than 25 off-label therapeutics (including small-molecule inhibitors and biologics) as well as cellular therapies (including haematopoietic stem cell transplantation and gene therapy) have been reported. Heterogeneous reporting of outcomes impedes the generation of robust therapeutic evidence as the basis for clinical decision making in mIBD. We discuss therapeutic goals in mIBD and recommend standardized reporting (mIBD REPORT (monogenic Inflammatory Bowel Disease Report Extended Phenotype and Outcome of Treatments) standards) to stratify patients according to a genetic diagnosis and phenotype, to assess treatment effects and to record safety signals. Implementation of these pragmatic standards should help clinicians to assess the therapy responses of individual patients in clinical practice and improve comparability between observational retrospective studies and controlled prospective trials, supporting future meta-analysis.
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Affiliation(s)
- Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Claire Booth
- UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Paediatric Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Judy Cho
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- Department of Paediatric Gastroenterology, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne M Griffiths
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, Toronto, Canada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Toronto, Canada
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert Ludwig University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center, Faculty of Medicine, Albert Ludwig University of Freiburg, Freiburg, Germany
- Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Ying Huang
- Department of Gastroenterology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kelsey Jones
- Paediatric Gastroenterology, Great Ormond Street Hospital, London, UK
- Kennedy Institute, University of Oxford, Oxford, UK
| | - Jochen Kammermeier
- Gastroenterology Department, Evelina London Children's Hospital, London, UK
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sibylle Koletzko
- Dr. von Hauner Children's Hospital, Department of Paediatrics, University Hospital, LMU Munich, Munich, Germany
- Department of Paediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Daniel Kotlarz
- Dr. von Hauner Children's Hospital, Department of Paediatrics, University Hospital, LMU Munich, Munich, Germany
- German Center for Child and Adolescent Health, Munich, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Paediatrics, University Hospital, LMU Munich, Munich, Germany
- German Center for Child and Adolescent Health, Munich, Germany
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Dermot P B McGovern
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ahmet Özen
- Marmara University Division of Allergy and Immunology, Istanbul, Turkey
| | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus University Medical Center Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Ruemmele
- Université Paris Cité, APHP, Hôpital Necker Enfants Malades, Service de Gastroentérologie pédiatrique, Paris, France
| | - Dror S Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Scott B Snapper
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Department of Paediatrics and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Simon P Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
- Kennedy Institute, University of Oxford, Oxford, UK
| | - Dan Turner
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David C Wilson
- Child Life and Health, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- Department of Paediatric Gastroenterology, The Royal Hospital for Children, and Young People, Edinburgh, UK
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, Toronto, Canada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Toronto, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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10
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Cristian HR, Walshe M, Birch S, Sabic K, Korie U, Chasteau C, Miladinova VM, Sabol WB, Mengesha E, Hanna M, Pozdnyakova V, Datta L, Kohen R, Milgrom R, Stempak JM, Bitton A, Brant SR, Rioux JD, McGovern DPB, Duerr RH, Cho JH, Schumm PL, Silverberg MS, Lazarev M. Clinical predictors of early and late endoscopic recurrence following ileocolonic resection in Crohn's disease. J Crohns Colitis 2023:jjad186. [PMID: 37976264 DOI: 10.1093/ecco-jcc/jjad186] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIM Multiple factors are suggested to place Crohn's disease patients at risk of recurrence after ileocolic resection with conflicting associations. We aimed to identify clinical predictors of recurrence at first (early) and further (late) postoperative colonoscopy. METHODS Crohn's disease patients undergoing ileocolic resection were prospectively recruited at six North American centers. Clinical data was collected and endoscopic recurrence was defined as Rutgeerts score ≥i2. A multivariable model was fitted to analyze variables independently associated with recurrence. RESULTS A total of 365 patients undergoing 674 postoperative colonoscopies were included with a median age of 32 years, 189 (51.8%) were male and 37 (10.1%) non-Whites. Postoperatively, 133 (36.4%) used anti-TNF and 30 (8.2%) were smokers. At first colonoscopy, 109 (29.9%) had recurrence. Male gender (OR = 1.95, 95% CI 1.12 - 3.40), non-White ethnicity (OR = 2.48, 95% CI 1.09 - 5.63), longer interval between surgery and colonoscopy (OR = 1.09, 95% CI 1.002 - 1.18), and postoperative smoking (OR = 2.78, 95% CI 1.16 - 6.67) were associated with recurrence, while prophylactic anti-TNF reduced the risk (OR = 0.28, 95% CI 0.14 - 0.55). Postoperative anti-TNF prophylaxis had a protective effect on anti-TNF experienced patients but not on anti-TNF naïve patients. Among patients without recurrence at first colonoscopy, Rutgeerts score i1 was associated with subsequent recurrence (OR = 4.43, 95% CI 1.73 - 11.35). CONCLUSIONS We identified independent clinical predictors of early and late Crohn's disease postoperative endoscopic recurrence. Clinical factors traditionally used for risk stratification failed to predict recurrence and need to be revised.
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Affiliation(s)
- Hernandez-Rocha Cristian
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Sondra Birch
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ujunwa Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Colleen Chasteau
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vessela M Miladinova
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - William B Sabol
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Mary Hanna
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Lisa Datta
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
| | - Rita Kohen
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Raquel Milgrom
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Joanne M Stempak
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Alain Bitton
- Inflammatory Bowel Disease Centre, Division of Gastroenterology, McGill University Health Centre, Montréal, Quebec, Canada
| | - Steven R Brant
- Crohn's and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Phil L Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Mark Lazarev
- Department of Gastroenterology, The John Hopkins Medical Institutions, Baltimore, MD, USA
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11
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Astore C, Sharma S, Nagpal S, Cutler DJ, Rioux JD, Cho JH, McGovern DPB, Brant SR, Kugathasan S, Jordan IK, Gibson G. The role of admixture in the rare variant contribution to inflammatory bowel disease. Genome Med 2023; 15:97. [PMID: 37968638 PMCID: PMC10647102 DOI: 10.1186/s13073-023-01244-w] [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: 04/05/2023] [Accepted: 10/10/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Identification of rare variants involved in complex, polygenic diseases like Crohn's disease (CD) has accelerated with the introduction of whole exome/genome sequencing association studies. Rare variants can be used in both diagnostic and therapeutic assessments; however, since they are likely to be restricted to specific ancestry groups, their contributions to risk assessment need to be evaluated outside the discovery population. Prior studies implied that the three known rare variants in NOD2 are absent in West African and Asian populations and only contribute in African Americans via admixture. METHODS Whole genome sequencing (WGS) data from 3418 African American individuals, 1774 inflammatory bowel disease (IBD) cases, and 1644 controls were used to assess odds ratios and allele frequencies (AF), as well as haplotype-specific ancestral origins of European-derived CD variants discovered in a large exome-wide association study. Local and global ancestry was performed to assess the contribution of admixture to IBD contrasting European and African American cohorts. RESULTS Twenty-five rare variants associated with CD in European discovery cohorts are typically five-fold lower frequency in African Americans. Correspondingly, where comparisons could be made, the rare variants were found to have a predicted four-fold reduced burden for IBD in African Americans, when compared to European individuals. Almost all of the rare CD European variants were found on European haplotypes in the African American cohort, implying that they contribute to disease risk in African Americans primarily due to recent admixture. In addition, proportion of European ancestry correlates the number of rare CD European variants each African American individual carry, as well as their polygenic risk of disease. Similar findings were observed for 23 mutations affecting 10 other common complex diseases for which the rare variants were discovered in European cohorts. CONCLUSIONS European-derived Crohn's disease rare variants are even more rare in African Americans and contribute to disease risk mainly due to admixture, which needs to be accounted for when performing cross-ancestry genetic assessments.
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Affiliation(s)
- Courtney Astore
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Shivam Sharma
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Sini Nagpal
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, QC, H1Y3N1, Canada
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dermot P B McGovern
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08554, USA
- Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, 21287, USA
| | - Steven R Brant
- Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - I King Jordan
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Greg Gibson
- Center for Integrative Genomics and School of Biological Sciences, Georgia Institute of Technology, Krone EBB1 Building, 950 Atlantic Drive, Atlanta, GA, 30332, USA.
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12
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Akhlaghpour M, Haritunians T, More SK, Thomas LS, Stamps DT, Dube S, Li D, Yang S, Landers CJ, Mengesha E, Hamade H, Murali R, Potdar AA, Wolf AJ, Botwin GJ, Khrom M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Sartor RB, Xavier RJ, Brant SR, Cho JH, Duerr RH, Lazarev MG, Rioux JD, Schumm LP, Silverberg MS, Zaghiyan K, Fleshner P, Melmed GY, Vasiliauskas EA, Ha C, Rabizadeh S, Syal G, Bonthala NN, Ziring DA, Targan SR, Long MD, McGovern DPB, Michelsen KS. Genetic coding variant in complement factor B (CFB) is associated with increased risk for perianal Crohn's disease and leads to impaired CFB cleavage and phagocytosis. Gut 2023; 72:2068-2080. [PMID: 37080587 DOI: 10.1136/gutjnl-2023-329689] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 04/22/2023]
Abstract
OBJECTIVE Perianal Crohn's disease (pCD) occurs in up to 40% of patients with CD and is associated with poor quality of life, limited treatment responses and poorly understood aetiology. We performed a genetic association study comparing CD subjects with and without perianal disease and subsequently performed functional follow-up studies for a pCD associated SNP in Complement Factor B (CFB). DESIGN Immunochip-based meta-analysis on 4056 pCD and 11 088 patients with CD from three independent cohorts was performed. Serological and clinical variables were analysed by regression analyses. Risk allele of rs4151651 was introduced into human CFB plasmid by site-directed mutagenesis. Binding of recombinant G252 or S252 CFB to C3b and its cleavage was determined in cell-free assays. Macrophage phagocytosis in presence of recombinant CFB or serum from CFB risk, or protective CD or healthy subjects was assessed by flow cytometry. RESULTS Perianal complications were associated with colonic involvement, OmpC and ASCA serology, and serology quartile sum score. We identified a genetic association for pCD (rs4151651), a non-synonymous SNP (G252S) in CFB, in all three cohorts. Recombinant S252 CFB had reduced binding to C3b, its cleavage was impaired, and complement-driven phagocytosis and cytokine secretion were reduced compared with G252 CFB. Serine 252 generates a de novo glycosylation site in CFB. Serum from homozygous risk patients displayed significantly decreased macrophage phagocytosis compared with non-risk serum. CONCLUSION pCD-associated rs4151651 in CFB is a loss-of-function mutation that impairs its cleavage, activation of alternative complement pathway, and pathogen phagocytosis thus implicating the alternative complement pathway and CFB in pCD aetiology.
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Affiliation(s)
- Marzieh Akhlaghpour
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shyam K More
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa S Thomas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalton T Stamps
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carol J Landers
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Hussein Hamade
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Andrea J Wolf
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | | | - Bana Jabri
- Biological Sciences Division, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
| | - Sergio A Lira
- Immunology Institute, Mount Sinai Medical Center, New York, New York, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Washington Univ. Sch. of Medicine, Saint Louis, Missouri, USA
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Steven R Brant
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Judy H Cho
- Genetics and Genomics Sciences, Mt Sinai School of Medicine, New York, New York, USA
| | - Richard H Duerr
- Departments of Medicine and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark G Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Rioux
- Faculty of Medicine, Universite de Montreal, Montreal, Québec, Canada
| | - L Philip Schumm
- Dept of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Karen Zaghiyan
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eric A Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christina Ha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gaurav Syal
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David A Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Millie D Long
- Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathrin S Michelsen
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Solitano V, Facciorusso A, McGovern DPB, Nguyen T, Colman RJ, Zou L, Boland BS, Syversen SW, Jørgensen KK, Ma C, Armuzzi A, Wilson A, Jairath V, Singh S. HLA-DQA1∗05 Genotype and Immunogenicity to Tumor Necrosis Factor-α Antagonists: A Systematic Review and Meta-analysis. Clin Gastroenterol Hepatol 2023; 21:3019-3029.e5. [PMID: 37061107 DOI: 10.1016/j.cgh.2023.03.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND & AIMS Identifying patients at high risk of immunogenicity is important when selecting tumor necrosis factor (TNF)-α antagonists in patients with immune-mediated inflammatory diseases (IMIDs). We evaluated the association HLA-DQA1∗05 genotype and risk of immunogenicity with TNF-α antagonists. METHODS Through a systematic review through July 14, 2022, we identified studies in patients with IMIDs treated with TNF-α antagonists, which reported the risk of immunogenicity and/or secondary loss of response in patients with HLA-DQA1∗05 variants. Primary outcome was risk of immunogenicity. We performed random effects meta-analysis and used GRADE to appraise certainty of evidence. RESULTS On meta-analysis of 13 studies (3756 patients; median follow-up, 12 months; 41% with variants), HLA-DQA1∗05 variants were associated with 75% higher risk of immunogenicity compared with non-carriers (relative risk, 1.75; 95% confidence interval, 1.37-2.25) with considerable heterogeneity (I2 = 62%) (low certainty evidence). Positive and negative predictive values of HLA-DQA1∗05 variants for predicting immunogenicity were 30% and 80%, respectively. Proactive therapeutic drug monitoring, but not concomitant use of IMMs, IMIDs, and TNF-α antagonist-type, modified this association. Patients with HLA-DQA1∗05 variants experienced 2.2-fold higher risk of secondary loss of response (6 cohorts; relative risk, 2.24; 95% confidence interval, 1.67-3.00; I2 = 0%) (moderate certainty evidence). CONCLUSION Variants in HLA-DQA1∗05 are associated with an increased risk in immunogenicity and secondary loss of response in patients with IMIDs treated with TNF-α antagonists. However, the positive and negative predictive value is moderate, and decisions on concomitant use of IMMs to prevent immunogenicity should be individualized based on all factors that influence drug clearance.
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Affiliation(s)
- Virginia Solitano
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, Canada; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical System, Los Angeles, California
| | - Tran Nguyen
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, Canada
| | - Ruben J Colman
- Division of Paediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Lily Zou
- Department of Statistics and Actuarial Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Brigid S Boland
- Department of Statistics and Actuarial Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Silje W Syversen
- Center for Treatment of Rheumatic and Musculoskeletal Diseases (REMEDY), Diakonhjemmet Hospital, Oslo, Norway
| | | | - Christopher Ma
- Division of Gastroenterology and Hepatology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Alessandro Armuzzi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Aze Wilson
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, Canada; Division of Clinical Pharmacology, Department of Medicine, Western University, London, Ontario, Canada; Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
| | - Vipul Jairath
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, Canada; Department of Epidemiology and Biostatistics, Western University, London, Ontario, Canada
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California.
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14
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Khrom M, Li D, Naito T, Lee HS, Botwin GJ, Potdar AA, Boucher G, Yang S, Mengesha E, Dube S, Song K, McGovern DPB, Haritunians T. Sex-Dimorphic Analyses Identify Novel and Sex-Specific Genetic Associations in Inflammatory Bowel Disease. Inflamm Bowel Dis 2023; 29:1622-1632. [PMID: 37262302 PMCID: PMC10547236 DOI: 10.1093/ibd/izad089] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Sex is an integral variable often overlooked in complex disease genetics. Differences between sexes have been reported in natural history, disease complications, and age of onset in inflammatory bowel disease (IBD). While association studies have identified >230 IBD loci, there have been a limited number of studies investigating sex differences underlying these genetic associations. METHODS We report the first investigation of sex-dimorphic associations via meta-analysis of a sex-stratified association study (34 579 IBD cases, 39 125 controls). In addition, we performed chromosome (chr) X-specific analyses, considering models of X inactivation (XCI) and XCI escape. Demographic and clinical characteristics were also compared between sexes. RESULTS We identified significant differences between sexes for disease location and perianal complication in Crohn's disease and disease extent in ulcerative colitis. We observed genome-wide-significant sex-dimorphic associations (P < 5 × 10-8) at loci not previously reported in large-scale IBD genetic studies, including at chr9q22, CARMIL1, and UBASH3A. We identified variants in known IBD loci, including in chr2p15 and within the major histocompatibility complex on chr6, exhibiting sex-specific patterns of association (P < 5 × 10-7 in one sex only). We identified 3 chrX associations with IBD, including a novel Crohn's disease susceptibility locus at Xp22. CONCLUSIONS These analyses identified novel IBD loci, in addition to characterizing sex-specific patterns of associations underlying sex-dimorphic associations. By elucidating the role of sex in IBD genetics, our study will help enhance our understanding of the differences between the sexes in IBD biology and underscores a need to move beyond conventional sex-combined analyses to appreciate the genetic architecture of IBD more comprehensively.
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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15
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Lee YJ, Li D, Mujukian A, Debbas P, Hampton M, Mengesha E, Cheng S, Ebinger JE, Chiorean M, Lum D, Damas OM, Braun J, McGovern DPB, Melmed GY. Postvaccination Symptoms After a Fourth Dose of mRNA SARS-CoV-2 Vaccination in Patients With Inflammatory Bowel Disease. Inflamm Bowel Dis 2023:izad198. [PMID: 37773982 DOI: 10.1093/ibd/izad198] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 10/01/2023]
Abstract
Overall, 1933 participants with IBD completed at least 1 questionnaire regarding postvaccination symptoms after administration of each of the 4 mRNA SARS-CoV-2 vaccine doses. Symptoms after a fourth mRNA vaccine are less frequent and generally milder than after previous doses.
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Affiliation(s)
- Yoo Jin Lee
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philip Debbas
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Melissa Hampton
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Cheng
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph E Ebinger
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Donald Lum
- The Oregon Clinic, Portland, Oregon, USA
| | - Oriana M Damas
- Division of Gastroenterology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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16
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Li D, Pavlovitch-Bedzyk AJ, Ebinger JE, Khan A, Hamideh M, Merchant A, Figueiredo JC, Cheng S, Davis MM, McGovern DPB, Melmed GY, Xu AM, Braun J. A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination. Int J Mol Sci 2023; 24:14223. [PMID: 37762524 PMCID: PMC10531868 DOI: 10.3390/ijms241814223] [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: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Quantitative metrics for vaccine-induced T-cell responses are an important need for developing correlates of protection and their use in vaccine-based medical management and population health. Molecular TCR analysis is an appealing strategy but currently requires a targeted methodology involving complex integration of ex vivo data (antigen-specific functional T-cell cytokine responses and TCR molecular responses) that uncover only public antigen-specific metrics. Here, we describe an untargeted private TCR method that measures breadth and depth metrics of the T-cell response to vaccine challenge using a simple pre- and post-vaccine subject sampling, TCR immunoseq analysis, and a bioinformatic approach using self-organizing maps and GLIPH2. Among 515 subjects undergoing SARS-CoV-2 mRNA vaccination, we found that breadth and depth metrics were moderately correlated between the targeted public TCR response and untargeted private TCR response methods. The untargeted private TCR method was sufficiently sensitive to distinguish subgroups of potential clinical significance also observed using public TCR methods (the reduced T-cell vaccine response with age and the paradoxically elevated T-cell vaccine response of patients on anti-TNF immunotherapy). These observations suggest the promise of this untargeted private TCR method to produce T-cell vaccine-response metrics in an antigen-agnostic and individual-autonomous context.
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Affiliation(s)
- Dalin Li
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Ana Jimena Pavlovitch-Bedzyk
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Abdul Khan
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Mohamed Hamideh
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Akil Merchant
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jane C. Figueiredo
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Mark M. Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dermot P. B. McGovern
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Gil Y. Melmed
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Alexander M. Xu
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jonathan Braun
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
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17
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Ferru-Clément R, Boucher G, Forest A, Bouchard B, Bitton A, Lesage S, Schumm P, Lazarev M, Brant S, Duerr RH, McGovern DPB, Silverberg M, Cho JH, Ananthakrishnan A, Xavier RJ, Rioux JD, Des Rosiers C. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease. Inflamm Bowel Dis 2023; 29:1024-1037. [PMID: 36662167 PMCID: PMC10320374 DOI: 10.1093/ibd/izac281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation. METHODS We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients. RESULTS We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location. CONCLUSIONS Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.
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Affiliation(s)
- Romain Ferru-Clément
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Laboratoire Histocompatibilité et Immunogénétique, Établissement français du sang–Nouvelle-Aquitaine, site de Poitiers, Poitiers, France
| | | | - Anik Forest
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Alain Bitton
- Division of Gastroenterology, McGill University Health Centre, Montreal, QC, Canada
| | - Sylvie Lesage
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, IL, USA
| | - Mark Lazarev
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steve Brant
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pennsylvania, PA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Silverberg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Judy H Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ashwin Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médicine, Université de Montréal, Montreal, QC, Canada
| | - Christine Des Rosiers
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Nutrition, Université de Montréal, Montreal, QC, Canada
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18
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Li D, Debbas P, Mujukian A, Cheng S, Braun J, McGovern DPB, Melmed GY. Postvaccination Symptoms After a Third Dose of mRNA SARS-CoV-2 Vaccination in Patients With Inflammatory Bowel Disease: Results From CORALE-IBD. Inflamm Bowel Dis 2023; 29:883-887. [PMID: 35998072 PMCID: PMC9452161 DOI: 10.1093/ibd/izac174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND The safety of a third dose of SARS-CoV-2 mRNA vaccination in patients with inflammatory bowel disease is unknown. METHODS We compared symptoms following a third SARS-CoV-2 mRNA vaccine dose with symptoms after the second dose in IBD. RESULTS The study group included 594 patients (70% female, 58% BNT162b2). Overall, 41% reported symptoms after a third dose. Symptom frequency and severity were lower after the third dose relative to the second dose for every organ system, except for gastrointestinal symptoms which were marginally worse. CONCLUSION The frequency and severity of symptoms after a third mRNA vaccine dose are generally similar or milder than after a second dose for most organ systems.
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Affiliation(s)
- Dalin Li
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philip Debbas
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Cheng
- Smidt Heart Institute, Department of Medicine, Cedars-Sinai, Los Angeles, CA, USA
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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19
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Liu Z, Liu R, Gao H, Jung S, Gao X, Sun R, Liu X, Kim Y, Lee HS, Kawai Y, Nagasaki M, Umeno J, Tokunaga K, Kinouchi Y, Masamune A, Shi W, Shen C, Guo Z, Yuan K, Zhu S, Li D, Liu J, Ge T, Cho J, Daly MJ, McGovern DPB, Ye BD, Song K, Kakuta Y, Li M, Huang H. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat Genet 2023; 55:796-806. [PMID: 37156999 PMCID: PMC10290755 DOI: 10.1038/s41588-023-01384-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 06/14/2022] [Accepted: 03/27/2023] [Indexed: 05/10/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic disorders of the gastrointestinal tract with the following two subtypes: Crohn's disease (CD) and ulcerative colitis (UC). To date, most IBD genetic associations were derived from individuals of European (EUR) ancestries. Here we report the largest IBD study of individuals of East Asian (EAS) ancestries, including 14,393 cases and 15,456 controls. We found 80 IBD loci in EAS alone and 320 when meta-analyzed with ~370,000 EUR individuals (~30,000 cases), among which 81 are new. EAS-enriched coding variants implicate many new IBD genes, including ADAP1 and GIT2. Although IBD genetic effects are generally consistent across ancestries, genetics underlying CD appears more ancestry dependent than UC, driven by allele frequency (NOD2) and effect (TNFSF15). We extended the IBD polygenic risk score (PRS) by incorporating both ancestries, greatly improving its accuracy and highlighting the importance of diversity for the equitable deployment of PRS.
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Affiliation(s)
- Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Han Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Xiang Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruicong Sun
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Liu
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongjae Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshitaka Kinouchi
- Student Healthcare Center, Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Wenzhao Shi
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Chengguo Shen
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kai Yuan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhu
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Dalin Li
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dermot P B McGovern
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea.
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Mingsong Li
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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20
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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 2023; 14:2256. [PMID: 37080976 PMCID: PMC10119186 DOI: 10.1038/s41467-023-37849-3] [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: 09/06/2021] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.
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Affiliation(s)
- Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kyle Gettler
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalin Li
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Maffucci
- Immunology Institute, Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ksenija Sabic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Adam P Levine
- Division of Medicine, University College London (UCL), London, UK
- Research Department of Pathology, University College London (UCL), London, UK
| | - Elena R Schiff
- Division of Medicine, University College London (UCL), London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony W Segal
- Division of Medicine, University College London (UCL), London, UK
| | | | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Oncology Boston Children's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Mark S Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Steven R Brant
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dermot P B McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Ebinger JE, Joung SY, Wang M, Liu Y, Prostko JC, Frias EC, Stewart JL, Braun J, McGovern DPB, Melmed GY, Jordan SC, Claggett BL, Sobhani K, Cheng S. Long-term durability of antibody responses after SARS-CoV-2 vaccination and influencing factors. J Intern Med 2023; 293:520-523. [PMID: 36625223 PMCID: PMC10714121 DOI: 10.1111/joim.13601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Sandy Y. Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Minhao Wang
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Yunxian Liu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dermot P. B. McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Gil Y. Melmed
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stanley C. Jordan
- Comprehensive Transplant Center, Department of Medicine, Division of Nephrology, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
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22
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Gu P, Dube S, McGovern DPB. Medical and Surgical Implications of Mesenteric Adipose Tissue in Crohn's Disease: A Review of the Literature. Inflamm Bowel Dis 2023; 29:458-469. [PMID: 35731568 DOI: 10.1093/ibd/izac120] [Citation(s) in RCA: 4] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 12/09/2022]
Abstract
Mesenteric adipose tissue (MAT) has gained substantial attention as an active player in Crohn's disease (CD), but its clinical significance is poorly understood and likely reflects, in part, difficulties assessing MAT noninvasively. Recent radiologic studies have identified candidate surrogate markers that may reflect inflammatory alterations of MAT in CD and have found that certain features including visceral adipose tissue may inform risk of complicated disease behavior, risk for surgery, and postoperative outcomes. Additionally, emerging surgical data have suggested MAT may even be a therapeutic target to mitigate postoperative recurrence of CD. However, the current studies have variable results, reduced sample sizes, and methodological limitations that preclude incorporating the radiologic and surgical findings into clinical practice. Nonetheless, the results are promising and potentially have important implications for the medical and surgical management of CD, which merits that additional studies are warranted. Thus, we have reviewed the available literature on the medical and surgical implications of MAT in CD to summarize our current understanding and identify gaps in knowledge to inform future investigations.
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Affiliation(s)
- Phillip Gu
- Karsh Division of Gastroenterology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shishir Dube
- Karsh Division of Gastroenterology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- Karsh Division of Gastroenterology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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23
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Kakuta Y, Shirai T, McGovern DPB, Braun J, Fujii H, Masamune A. Novel Diagnostic Autoantibodies Against Endothelial Protein C Receptor in Patients With Ulcerative Colitis. Clin Gastroenterol Hepatol 2023; 21:844-846. [PMID: 34971808 DOI: 10.1016/j.cgh.2021.12.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 02/07/2023]
Abstract
There have been many reports on serologic autoantibodies in inflammatory bowel diseases (IBD),1 consisting of ulcerative colitis (UC) and Crohn's disease (CD), and recently Kuwada et al2 reported a new autoantibody against integrin αvβ6 with high sensitivity and specificity for UC. Concurrently, we had discovered autoantibodies against endothelial protein C receptor (EPCR) in Takayasu arteritis (TAK), which is sometimes complicated by UC.3 Interestingly, this autoantibody was found in most patients with TAK associated with UC, and we found that the positivity rate in patients with UC without TAK was also high, suggesting that anti-EPCR antibody is a candidate autoantibody useful for the diagnosis of UC.4 To clarify the diagnostic usefulness of anti-EPCR antibodies in patients with IBD and their relationship to several disease subphenotypes and their disease activities, we analyzed the serum samples from patients with IBD and non-IBD control subjects in Japan and the United States.
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Affiliation(s)
- Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Tsuyoshi Shirai
- Department of Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Dermot P B McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hiroshi Fujii
- Department of Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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24
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Cordero RY, Cordero JB, Stiemke AB, Datta LW, Buyske S, Kugathasan S, McGovern DPB, Brant SR, Simpson CL. Trans-ancestry, Bayesian meta-analysis discovers 20 novel risk loci for inflammatory bowel disease in an African American, East Asian and European cohort. Hum Mol Genet 2023; 32:873-882. [PMID: 36308435 PMCID: PMC9941836 DOI: 10.1093/hmg/ddac269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated chronic intestinal disorder with major phenotypes: ulcerative colitis (UC) and Crohn's disease (CD). Multiple studies have identified over 240 IBD susceptibility loci. However, most studies have centered on European (EUR) and East Asian (EAS) populations. The prevalence of IBD in non-EUR, including African Americans (AAs), has risen in recent years. Here we present the first attempt to identify loci in AAs using a trans-ancestry Bayesian approach (MANTRA) accounting for heterogeneity between diverse ancestries while allowing for the similarity between closely related populations. We meta-analyzed genome-wide association studies (GWAS) and Immunochip data from a 2015 EUR meta-analysis of 38 155 IBD cases and 48 485 controls and EAS Immunochip study of 2824 IBD cases and 3719 controls, and our recent AA IBD GWAS of 2345 cases and 5002 controls. Across the major IBD phenotypes, we found significant evidence for 92% of 205 loci lead SNPs from the 2015 meta-analysis, but also for three IBD loci only established in latter studies. We detected 20 novel loci, all containing immunity-related genes or genes with other evidence for IBD or immune-mediated disease relevance: PLEKHG5;TNFSFR25 (encoding death receptor 3, receptor for TNFSF15 gene product TL1A), XKR6, ELMO1, BC021024;PI4KB;PSMD4 and APLP1 for IBD; AUTS2, XKR6, OSER1, TET2;AK094561, BCAP29 and APLP1 for CD; and GABBR1;MOG, DQ570892, SPDEF;ILRUN, SMARCE1;CCR7;KRT222;KRT24;KRT25, ANKS1A;TCP11, IL7, LRRC18;WDFY4, XKR6 and TNFSF4 for UC. Our study highlights the value of combining low-powered genomic studies from understudied populations of diverse ancestral backgrounds together with a high-powered study to enable novel locus discovery, including potentially important therapeutic IBD gene targets.
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Affiliation(s)
- Roberto Y Cordero
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jennifer B Cordero
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew B Stiemke
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ 08854, USA
| | - Subra Kugathasan
- Department of Pediatrics and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
- Rutgers Crohn’s and Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Human Genetics Institute of New Jersey and Department of Genetics, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claire L Simpson
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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25
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Liu JJ, Abraham BP, Adamson P, Barnes EL, Brister KA, Damas OM, Glover SC, Hooks K, Ingram A, Kaplan GG, Loftus EV, McGovern DPB, Narain-Blackwell M, Odufalu FD, Quezada S, Reeves V, Shen B, Stappenbeck TS, Ward L. The Current State of Care for Black and Hispanic Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2023; 29:297-307. [PMID: 35816130 DOI: 10.1093/ibd/izac124] [Citation(s) in RCA: 3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 02/03/2023]
Abstract
Research on the care of inflammatory bowel disease (IBD) patients has been primarily in populations of European ancestry. However, the incidence of IBD, which comprises Crohn's disease and ulcerative colitis, is increasing in different populations around the world. In this comprehensive review, we examine the epidemiology, clinical presentations, disease phenotypes, treatment outcomes, social determinants of health, and genetic and environmental factors in the pathogenesis of IBD in Black and Hispanic patients in the United States. To improve health equity of underserved minorities with IBD, we identified the following priority areas: access to care, accurate assessment of treatment outcomes, incorporation of Black and Hispanic patients in therapeutic clinical trials, and investigation of environmental factors that lead to the increase in disease incidence.
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Affiliation(s)
- Julia J Liu
- Division of Gastroenterology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Bincy P Abraham
- Division of Gastroenterology and Hepatology, Houston Methodist Academic Institute, Houston, TX, USA
| | - Paula Adamson
- Division of Gastroenterology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Edward L Barnes
- Division of Gastroenterology and Hepatology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Kelly A Brister
- Department of Surgery, University of Mississippi Medical Center, Jackson, MS, USA
| | - Oriana M Damas
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sarah C Glover
- Division of Gastroenterology and Hepatology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kimberly Hooks
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
| | - Ana Ingram
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
| | - Gilaad G Kaplan
- Division of Gastroenterology and Hepatology, Department of Medicine and Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Edward V Loftus
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Florence-Damilola Odufalu
- Division of Gastroenterology and Liver Diseases, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Sandra Quezada
- Division of Gastroenterology and Hepatology, University of Maryland, College Park, College Park, MD, USA
| | - Vonda Reeves
- GI Associates and Endoscopy Center, Jackson, MS, USA
| | - Bo Shen
- Inflammatory Bowel Disease Center, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, NY, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Latonia Ward
- Color of Crohn's and Chronic Illness, Glenarden, MD, USA
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26
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Wang L, Yang JD, Yoo CC, Lai KKY, Braun J, McGovern DPB, Xie Y, Pandol SJ, Lu SC, Li D. Magnetic resonance imaging for characterization of hepatocellular carcinoma metabolism. Front Physiol 2022; 13:1056511. [PMID: 36589457 PMCID: PMC9800006 DOI: 10.3389/fphys.2022.1056511] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
With a better understanding of the pathophysiological and metabolic changes in hepatocellular carcinoma (HCC), multiparametric and novel functional magnetic resonance (MR) and positron emission tomography (PET) techniques have received wide interest and are increasingly being applied in preclinical and clinical research. These techniques not only allow for non-invasive detection of structural, functional, and metabolic changes in malignant tumor cells but also characterize the tumor microenvironment (TME) and the interactions of malignant tumor cells with the TME, which has hypoxia and low pH, resulting from the Warburg effect and accumulation of metabolites produced by tumor cells and other cellular components. The heterogeneity and complexity of the TME require a combination of images with various parameters and modalities to characterize tumors and guide therapy. This review focuses on the value of multiparametric magnetic resonance imaging and PET/MR in evaluating the structural and functional changes of HCC and in detecting metabolites formed owing to HCC and the TME.
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Affiliation(s)
- Lixia Wang
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ju Dong Yang
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States,Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States,Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Charles C. Yoo
- Office of the Medical Director 1st MRI, Los Angeles, CA, United States
| | - Keane K. Y. Lai
- Department of Molecular Medicine, Beckman Research Institute of City of Hope and City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel Disease Institute, Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dermot P. B. McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Yibin Xie
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Stephen J. Pandol
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Shelly C. Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Debiao Li
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States,Department of Bioengineering, University of California, Los Angeles, CA, United States,*Correspondence: Debiao Li,
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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet 2022; 54:1275-1283. [PMID: 36038634 PMCID: PMC9700438 DOI: 10.1038/s41588-022-01156-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [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: 07/01/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.
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Affiliation(s)
- Aleksejs Sazonovs
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christine R Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kai Yuan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandon Avila
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Abreu
- Crohn's and Colitis Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Matthieu Allez
- Hopital Saint-Louis, APHP, Universite de Paris, INSERM U1160, Paris, France
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Crohn's and Colitis Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gil Atzmon
- Department for Human Biology, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- The Institute for Aging Research, The Nathan Shock Center of Excellence in the Basic Biology of Aging and the Paul F. Glenn Center for the Biology of Human Aging Research at Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Laurent Beaugerie
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Alain Bitton
- McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Bernd Bokemeyer
- Department of Internal Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Jacques Cosnes
- Professeur Chef de Service chez APHP and Universite Paris-6, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Allan Daly
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noor Dawany
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
- University of Rome Sapienza, Rome, Italy
- IRGB - CNR, Cagliari, Italy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eva Ellinghaus
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Laura Fachal
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kyle Gettler
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Philippe Goyette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Daniel Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marc Hoeppner
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Peter Irving
- Department of Gastroenterology, Guys and Saint Thomas Hospital, London, UK
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Vivek Iyer
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Chaim Jalas
- Director of Genetic Resources and Services, Center for Rare Jewish Genetic Disorders, Bonei Olam, Brooklyn, NY, USA
| | - Judith Kelsen
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Barbara S Kirschner
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Kimmo Kontula
- Department of Medicine, Helsinki University Hospital, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Subra Kugathasan
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Chloé Lévesque
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - James D Lewis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Crohn's and Colitis Foundation, New York, NY, USA
| | | | - Britt-Sabina Loescher
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - John Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra May
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Myriam Mni
- University of Liège, ULG, Liège, Belgium
| | | | | | | | | | - David T Okou
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
- Institut National de Sante Publique (INSP), Abidjan, Côte d'Ivoire
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jean Paquette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Joel Pekow
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Natalie Prescott
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel L Rice
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Bruce Sands
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Stefan Schreiber
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Philippe Seksik
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Rasha Shawky
- IBD BioResource, NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Alison Simmons
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skeiceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Matthew Solomonson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hari Somineni
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Turner
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
- Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Andrea E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Séverine Vermeire
- University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Andre Franke
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Crohn's Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Kurt Isselbacher Professor of Medicine at Harvard Medical School, Cambridge, MA, USA
- Core Institute Member, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Immunology Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John D Rioux
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Mark J Daly
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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Jacobs JP, Goudarzi M, Lagishetty V, Li D, Mak T, Tong M, Ruegger P, Haritunians T, Landers C, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih D, Targan S, Borneman J, Fornace AJ, McGovern DPB, Braun J. Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome. Genome Med 2022; 14:91. [PMID: 35971134 PMCID: PMC9377146 DOI: 10.1186/s13073-022-01099-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/13/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Crohn's disease (CD) patients demonstrate distinct intestinal microbial compositions and metabolic characteristics compared to unaffected controls. However, the impact of inflammation and underlying genetic risk on these microbial profiles and their relationship to disease phenotype are unclear. We used lavage sampling to characterize the colonic mucosal-luminal interface (MLI) microbiome of CD patients in endoscopic remission and unaffected controls relative to obesity, disease genetics, and phenotype. METHODS Cecum and sigmoid colon were sampled from 110 non-CD controls undergoing screening colonoscopy who were stratified by body mass index and 88 CD patients in endoscopic remission (396 total samples). CD polygenic risk score (GRS) was calculated using 186 known CD variants. MLI pellets were analyzed by 16S ribosomal RNA gene sequencing, and supernatants by untargeted liquid chromatography-mass spectrometry. RESULTS CD and obesity were each associated with decreased cecal and sigmoid MLI bacterial diversity and distinct bacterial composition compared to controls, including expansion of Escherichia/Shigella. Cecal and sigmoid dysbiosis indices for CD were significantly greater in obese controls than non-overweight controls. CD, but not obesity, was characterized by altered biogeographic relationship between the sigmoid and cecum. GRS was associated with select taxonomic shifts that overlapped with changes seen in CD compared to controls including Fusobacterium enrichment. Stricturing or penetrating Crohn's disease behavior was characterized by lower MLI bacterial diversity and altered composition, including reduced Faecalibacterium, compared to uncomplicated CD. Taxonomic profiles including reduced Parasutterella were associated with clinical disease progression over a mean follow-up of 3.7 years. Random forest classifiers using MLI bacterial abundances could distinguish disease state (area under the curve (AUC) 0.93), stricturing or penetrating Crohn's disease behavior (AUC 0.82), and future clinical disease progression (AUC 0.74). CD patients showed alterations in the MLI metabolome including increased cholate:deoxycholate ratio compared to controls. CONCLUSIONS Obesity, CD in endoscopic remission, and high CD genetic risk have overlapping colonic mucosal-luminal interface (MLI) microbiome features, suggesting a shared microbiome contribution to CD and obesity which may be influenced by genetic factors. Microbial profiling during endoscopic remission predicted Crohn's disease behavior and progression, supporting that MLI sampling could offer unique insight into CD pathogenesis and provide novel prognostic biomarkers.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
| | | | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Tytus Mak
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Maomeng Tong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Paul Ruegger
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Philip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Eric Vasiliauskas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Andrew Ippoliti
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, USA
| | - Gil Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - David Shih
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
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29
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Ricciuto A, Rauter I, McGovern DPB, Mader RM, Reinisch W. Precision Medicine in Inflammatory Bowel Diseases: Challenges and Considerations for the Path Forward. Gastroenterology 2022; 162:1815-1821. [PMID: 35278416 DOI: 10.1053/j.gastro.2022.02.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/18/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Amanda Ricciuto
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Robert M Mader
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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30
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Ebinger JE, Joung S, Liu Y, Wu M, Weber B, Claggett B, Botting PG, Sun N, Driver M, Kao YH, Khuu B, Wynter T, Nguyen TT, Alotaibi M, Prostko JC, Frias EC, Stewart JL, Goodridge HS, Chen P, Jordan SC, Jain M, Sharma S, Fert-Bober J, Van Eyk JE, Minissian MB, Arditi M, Melmed GY, Braun JG, McGovern DPB, Cheng S, Sobhani K. Demographic and clinical characteristics associated with variations in antibody response to BNT162b2 COVID-19 vaccination among healthcare workers at an academic medical centre: a longitudinal cohort analysis. BMJ Open 2022; 12:e059994. [PMID: 35613792 PMCID: PMC9130668 DOI: 10.1136/bmjopen-2021-059994] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/11/2022] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES We sought to understand the demographic and clinical factors associated with variations in longitudinal antibody response following completion of two-dose regiment of BNT162b2 vaccination. DESIGN This study is a 10-month longitudinal cohort study of healthcare workers and serially measured anti-spike protein IgG (IgG-S) antibody levels using mixed linear models to examine their associations with participant characteristics. SETTING A large, multisite academic medical centre in Southern California, USA. PARTICIPANTS A total of 843 healthcare workers met inclusion criteria including completion of an initial two-dose course of BNT162b2 vaccination, complete clinical history and at least two blood samples for analysis. Patients had an average age of 45±13 years, were 70% female and 7% with prior SARS-CoV-2 infection. RESULTS Vaccine-induced IgG-S levels remained in the positive range for 99.6% of individuals up to 10 months after initial two-dose vaccination. Prior SARS-CoV-2 infection was the primary correlate of sustained higher postvaccination IgG-S levels (partial R2=0.133), with a 1.74±0.11 SD higher IgG-S response (p<0.001). Female sex (beta 0.27±0.06, p<0.001), younger age (0.01±0.00, p<0.001) and absence of hypertension (0.17±0.08, p=0.003) were also associated with persistently higher IgG-S responses. Notably, prior SARS-CoV-2 infection augmented the associations of sex (-0.42 for male sex, p=0.08) and modified the associations of hypertension (1.17, p=0.001), such that infection-naïve individuals with hypertension had persistently lower IgG-S levels whereas prior infected individuals with hypertension exhibited higher IgG-S levels that remained augmented over time. CONCLUSIONS While the IgG-S antibody response remains in the positive range for up to 10 months following initial mRNA vaccination in most adults, determinants of sustained higher antibody levels include prior SARS-CoV-2 infection, female sex, younger age and absence of hypertension. Certain determinants of the longitudinal antibody response appear significantly modified by prior infection status. These findings offer insights regarding factors that may influence the 'hybrid' immunity conferred by natural infection combined with vaccination.
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Affiliation(s)
- Joseph E Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Yunxian Liu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Min Wu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Brittany Weber
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Brian Claggett
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Patrick G Botting
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nancy Sun
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Matthew Driver
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Yu Hung Kao
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Briana Khuu
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Timothy Wynter
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Trevor-Trung Nguyen
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mona Alotaibi
- Division of Pulmonary and Critical Care Medicine, University of California San Diego, San Diego, California, USA
| | - John C Prostko
- Applied Research and Technology, Abbott Laboratories, Abbott Park, Illinois, USA
| | - Edwin C Frias
- Applied Research and Technology, Abbott Laboratories, Abbott Park, Illinois, USA
| | - James L Stewart
- Applied Research and Technology, Abbott Laboratories, Abbott Park, Illinois, USA
| | - Helen S Goodridge
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Peter Chen
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stanley C Jordan
- Transplant Immunology Laboratory and Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mohit Jain
- Department of Medicine, School of Medicine, University of California, San Diego, San Diego, California, USA
| | - Sonia Sharma
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Justyna Fert-Bober
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jennifer E Van Eyk
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Margo B Minissian
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Moshe Arditi
- Smidt Heart Institute; Department of Pediatrics, Division of Infectious Diseases and Immunology; Infectious and Immunologic Diseases Research Center (IIDRC); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan G Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
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31
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Li D, Xu A, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Prostko JC, Frias EC, Stewart JL, Pozdnyakova V, Debbas P, Mujukian A, Horizon AA, Merin N, Joung S, Botwin GJ, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. The T-Cell Response to SARS-CoV-2 Vaccination in Inflammatory Bowel Disease is Augmented with Anti-TNF Therapy. Inflamm Bowel Dis 2022; 28:1130-1133. [PMID: 35397000 PMCID: PMC9047232 DOI: 10.1093/ibd/izac071] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 12/12/2022]
Abstract
Lay Summary
T-cell and antibody responses to severe acute respiratory syndrome coronavirus 2 vaccination in inflammatory bowel disease patients are poorly correlated. T-cell responses are preserved by most biologic therapies, but augmented by anti-tumor necrosis factor (anti-TNF) treatment. While anti-TNF therapy blunts the antibody response, cellular immunity after vaccination is robust.
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Affiliation(s)
- Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexander Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - John C Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Edwin C Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - James L Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gregory J Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jane C Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ian M Kaplan
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- Address correspondence to: Jonathan Braun, MD, PhD, Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA ()
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32
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Xu AM, Li D, Ebinger JE, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Joung S, Botwin GJ, Pozdnyakova V, Debbas P, Mujukian A, Prostko JC, Frias EC, Stewart JL, Horizon AA, Merin N, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease. Front Immunol 2022; 13:880190. [PMID: 35464463 PMCID: PMC9024211 DOI: 10.3389/fimmu.2022.880190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022] Open
Abstract
T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust immune responses after infection or vaccination. For patients with inflammatory bowel disease (IBD), a spectrum of chronic intestinal inflammatory diseases usually requiring immunomodulatory treatment, the T-cell response has not been well characterized. Understanding the patient factors that result in strong vaccination responses is critical to guiding vaccination schedules and identifying mechanisms of T-cell responses in IBD and other immune-mediated conditions. Here we used T-cell receptor sequencing to show that T-cell responses in an IBD cohort were influenced by demographic and immune factors, relative to a control cohort of health care workers (HCWs). Subjects were sampled at the time of SARS-CoV-2 vaccination, and longitudinally afterwards; TCR Vβ gene repertoires were sequenced and analyzed for COVID-19-specific clones. We observed significant differences in the overall strength of the T-cell response by age and vaccine type. We further stratified the T-cell response into Class-I- and Class-II-specific responses, showing that Ad26.COV2.S vector vaccine induced Class-I-biased T-cell responses, whereas mRNA vaccine types led to different responses, with mRNA-1273 vaccine inducing a more Class-I-deficient T-cell response compared to BNT162b2. Finally, we showed that these T-cell patterns were consistent with antibody levels from the same patients. Our results account for the surprising success of vaccination in nominally immuno-compromised IBD patients, while suggesting that a subset of IBD patients prone to deficiencies in T-cell response may warrant enhanced booster protocols.
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Affiliation(s)
- Alexander M. Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | | | - Heidi Chapman
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gregory J. Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Arash A. Horizon
- Center for Rheumatology Medical Group, Los Angeles, CA, United States
| | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane C. Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ian M. Kaplan
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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33
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Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M, Cho J, Shouval DS, Kammermeier J, Koletzko S, Bagalopal K, Capitani M, Cavounidis A, Pires E, Weidinger C, McCullagh J, Arkwright PD, Haller W, Siegmund B, Peters L, Jostins L, Travis SPL, Anderson CA, Snapper S, Klein C, Schadt E, Zilbauer M, Xavier R, Teichmann S, Muise AM, Regev A, Uhlig HH. An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease. Gastroenterology 2022; 162:859-876. [PMID: 34780721 DOI: 10.1053/j.gastro.2021.11.014] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/18/2021] [Accepted: 11/08/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Monogenic forms of inflammatory bowel disease (IBD) illustrate the essential roles of individual genes in pathways and networks safeguarding immune tolerance and gut homeostasis. METHODS To build a taxonomy model, we assessed 165 disorders. Genes were prioritized based on penetrance of IBD and disease phenotypes were integrated with multi-omics datasets. Monogenic IBD genes were classified by (1) overlapping syndromic features, (2) response to hematopoietic stem cell transplantation, (3) bulk RNA-sequencing of 32 tissues, (4) single-cell RNA-sequencing of >50 cell subsets from the intestine of healthy individuals and patients with IBD (pediatric and adult), and (5) proteomes of 43 immune subsets. The model was validated by addition of newly identified monogenic IBD defects. As a proof-of-concept, we explore the intersection between immunometabolism and antimicrobial activity for a group of disorders (G6PC3/SLC37A4). RESULTS Our quantitative integrated taxonomy defines the cellular landscape of monogenic IBD gene expression across 102 genes with high and moderate penetrance (81 in the model set and 21 genes in the validation set). We illustrate distinct cellular networks, highlight expression profiles across understudied cell types (e.g., CD8+ T cells, neutrophils, epithelial subsets, and endothelial cells) and define genotype-phenotype associations (perianal disease and defective antimicrobial activity). We illustrate processes and pathways shared across cellular compartments and phenotypic groups and highlight cellular immunometabolism with mammalian target of rapamycin activation as one of the converging pathways. There is an overlap of genes and enriched cell-specific expression between monogenic and polygenic IBD. CONCLUSION Our taxonomy integrates genetic, clinical and multi-omic data; providing a basis for genomic diagnostics and testable hypotheses for disease functions and treatment responses.
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Affiliation(s)
- Chrissy Bolton
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; Institute of Child Health, University College London, London, UK
| | - Christopher S Smillie
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sumeet Pandey
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, Australia
| | - Dermot P B McGovern
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marina Macchi
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dror S Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah-Tiqva, Israel, affiliated with Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jochen Kammermeier
- Gastroenterology Department, Evelina London Children's Hospital, London, UK
| | - Sibylle Koletzko
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany; Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | | | - Melania Capitani
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Athena Cavounidis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Carl Weidinger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health Department of Gastroenterology, Rheumatology and Infectious Disease, Campus Benjamin Franklin, Berlin, Germany
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Peter D Arkwright
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Wolfram Haller
- Department of Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
| | - Britta Siegmund
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health Department of Gastroenterology, Rheumatology and Infectious Disease, Campus Benjamin Franklin, Berlin, Germany
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luke Jostins
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Simon P L Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; Biomedical Research Center, University of Oxford, Oxford, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Scott Snapper
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthias Zilbauer
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK; Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Ramnik Xavier
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton UK
| | - Aleixo M Muise
- Gastroenterology Division, The Hospital for Sick Children, Toronto, Ontario, Canada; SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK; The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, United Kingdom.
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34
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Suzuki K, Kakuta Y, Naito T, Takagawa T, Hanai H, Araki H, Sasaki Y, Sakuraba H, Sasaki M, Hisamatsu T, Motoya S, Matsumoto T, Onodera M, Ishiguro Y, Nakase H, Andoh A, Hiraoka S, Shinozaki M, Fujii T, Katsurada T, Kobayashi T, Fujiya M, Otsuka T, Oshima N, Suzuki Y, Sato Y, Hokari R, Noguchi M, Ohta Y, Matsuura M, Kawai Y, Tokunaga K, Nagasaki M, Kudo H, Minegishi N, Okamoto D, Shimoyama Y, Moroi R, Kuroha M, Shiga H, Li D, McGovern DPB, Kinouchi Y, Masamune A. Genetic Background of Mesalamine-induced Fever and Diarrhea in Japanese Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:21-31. [PMID: 33501934 DOI: 10.1093/ibd/izab004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 12/23/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Some patients with inflammatory bowel disease (IBD) who were under mesalamine treatment develop adverse reactions called "mesalamine allergy," which includes high fever and worsening diarrhea. Currently, there is no method to predict mesalamine allergy. Pharmacogenomic approaches may help identify these patients. Here we analyzed the genetic background of mesalamine intolerance in the first genome-wide association study of Japanese patients with IBD. METHODS Two independent pharmacogenetic IBD cohorts were analyzed: the MENDEL (n = 1523; as a discovery set) and the Tohoku (n = 788; as a replication set) cohorts. Genome-wide association studies were performed in each population, followed by a meta-analysis. In addition, we constructed a polygenic risk score model and combined genetic and clinical factors to model mesalamine intolerance. RESULTS In the combined cohort, mesalamine-induced fever and/or diarrhea was significantly more frequent in ulcerative colitis vs Crohn's disease. The genome-wide association studies and meta-analysis identified one significant association between rs144384547 (upstream of RGS17) and mesalamine-induced fever and diarrhea (P = 7.21e-09; odds ratio = 11.2). The estimated heritability of mesalamine allergy was 25.4%, suggesting a significant correlation with the genetic background. Furthermore, a polygenic risk score model was built to predict mesalamine allergy (P = 2.95e-2). The combined genetic/clinical prediction model yielded a higher area under the curve than did the polygenic risk score or clinical model alone (area under the curve, 0.89; sensitivity, 71.4%; specificity, 90.8%). CONCLUSIONS Mesalamine allergy was more common in ulcerative colitis than in Crohn's disease. We identified a novel genetic association with and developed a combined clinical/genetic model for this adverse event.
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Affiliation(s)
- Kaoru Suzuki
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.,F. Widjaja Foundation Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tetsuya Takagawa
- Center for Inflammatory Bowel Disease, Division of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | | | - Hiroshi Araki
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yu Sasaki
- Department of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Hirotake Sakuraba
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Makoto Sasaki
- Division of Gastroenterology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Tadakazu Hisamatsu
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Mitaka, Japan
| | - Satoshi Motoya
- IBD Center, Sapporo-Kosei General Hospital, Sapporo, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Motoyuki Onodera
- Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Iwate, Japan
| | - Yoh Ishiguro
- Department of Gastroenterology and Hematology, Hirosaki National Hospital, Hirosaki, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Akira Andoh
- Department of Gastroenterology, Shiga University of Medical Science, Otsu, Japan
| | - Sakiko Hiraoka
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Masaru Shinozaki
- Department of Surgery, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Toshimitsu Fujii
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takehiko Katsurada
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Taku Kobayashi
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Mikihiro Fujiya
- Department of Medicine, Division of Gastroenterology and Hematology/Oncology, Asahikawa Medical University, Asahikawa, Japan
| | - Takafumi Otsuka
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Naoki Oshima
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Shimane, Japan
| | - Yasuo Suzuki
- Department of Internal Medicine, Toho University Sakura Medical Center, Sakura, Japan
| | - Yuichirou Sato
- Department of Gastroenterology, Osaki Citizen Hospital, Osaki, Japan
| | - Ryota Hokari
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Japan
| | | | - Yuki Ohta
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Minoru Matsuura
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Mitaka, Japan.,Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Hisaaki Kudo
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Daisuke Okamoto
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yusuke Shimoyama
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Gastroenterology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yoshitaka Kinouchi
- Health Administration Center, Center for the Advancement of Higher Education, Tohoku University, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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35
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Cavounidis A, Pandey S, Capitani M, Friedrich M, Cross A, Gartner L, Aschenbrenner D, Kim-Schulze S, Lam YK, Berridge G, McGovern DPB, Kessler B, Fischer R, Klenerman P, Hester J, Issa F, Torres EA, Powrie F, Gochuico BR, Gahl WA, Cohen L, Uhlig HH. Hermansky-Pudlak syndrome type 1 causes impaired anti-microbial immunity and inflammation due to dysregulated immunometabolism. Mucosal Immunol 2022; 15:1431-1446. [PMID: 36302964 PMCID: PMC9607658 DOI: 10.1038/s41385-022-00572-1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 02/04/2023]
Abstract
Hermansky-Pudlak syndrome (HPS) types 1 and 4 are caused by defective vesicle trafficking. The mechanism for Crohn's disease-like inflammation, lung fibrosis, and macrophage lipid accumulation in these patients remains enigmatic. The aim of this study is to understand the cellular basis of inflammation in HPS-1. We performed mass cytometry, proteomic and transcriptomic analyses to investigate peripheral blood cells and serum of HPS-1 patients. Using spatial transcriptomics, granuloma-associated signatures in the tissue of an HPS-1 patient with granulomatous colitis were dissected. In vitro studies were conducted to investigate anti-microbial responses of HPS-1 patient macrophages and cell lines. Monocytes of HPS-1 patients exhibit an inflammatory phenotype associated with dysregulated TNF, IL-1α, OSM in serum, and monocyte-derived macrophages. Inflammatory macrophages accumulate in the intestine and granuloma-associated macrophages in HPS-1 show transcriptional signatures suggestive of a lipid storage and metabolic defect. We show that HPS1 deficiency leads to an altered metabolic program and Rab32-dependent amplified mTOR signaling, facilitated by the accumulation of mTOR on lysosomes. This pathogenic mechanism translates into aberrant bacterial clearance, which can be rescued with mTORC1 inhibition. Rab32-mediated mTOR signaling acts as an immuno-metabolic checkpoint, adding to the evidence that defective bioenergetics can drive hampered anti-microbial activity and contribute to inflammation.
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Affiliation(s)
- Athena Cavounidis
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.425090.a0000 0004 0468 9597Present Address: GSK, Wavre, Belgium
| | - Sumeet Pandey
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,Present Address: GSK Immunology Network, GSK Medicines Research Center, Stevenage, UK
| | - Melania Capitani
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,Present Address: SenTcell Ltd, London, UK
| | - Matthias Friedrich
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Amy Cross
- grid.4991.50000 0004 1936 8948Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Lisa Gartner
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dominik Aschenbrenner
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.419481.10000 0001 1515 9979Present Address: Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Seunghee Kim-Schulze
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ying Ka Lam
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Georgina Berridge
- grid.4991.50000 0004 1936 8948Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dermot P. B. McGovern
- grid.50956.3f0000 0001 2152 9905F. Widjaja Foundation Inflammatory Bowel and Immunobiology Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Benedikt Kessler
- grid.4991.50000 0004 1936 8948Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- grid.4991.50000 0004 1936 8948Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joanna Hester
- grid.4991.50000 0004 1936 8948Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Fadi Issa
- grid.4991.50000 0004 1936 8948Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Esther A. Torres
- grid.267033.30000 0004 0462 1680University of Puerto Rico School of Medicine, Puerto Rico, USA
| | - Fiona Powrie
- grid.4991.50000 0004 1936 8948Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Bernadette R. Gochuico
- grid.94365.3d0000 0001 2297 5165Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Louis Cohen
- grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Holm H. Uhlig
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.4991.50000 0004 1936 8948Department of Paediatrics, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
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36
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Figueiredo JC, Merin NM, Hamid O, Choi SY, Lemos T, Cozen W, Nguyen N, Finster LJ, Foley J, Darrah J, Gong J, Paquette R, Mita AC, Vescio R, Mehmi I, Basho R, Tourtellotte WG, Huynh CA, Melmed GY, Braun J, McGovern DPB, Mengesha E, Botwin G, Prostko JC, Frias EC, Stewart JL, Joung S, Van Eyk J, Ebinger JE, Cheng S, Sobhani K, Reckamp KL, Merchant A. Longitudinal SARS-CoV-2 mRNA Vaccine-Induced Humoral Immune Responses in Patients with Cancer. Cancer Res 2021; 81:6273-6280. [PMID: 34759001 PMCID: PMC9060668 DOI: 10.1158/0008-5472.can-21-3554] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 10/19/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
Longitudinal studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine-induced immune responses in patients with cancer are needed to optimize clinical care. In a prospective cohort study of 366 (291 vaccinated) patients, we measured antibody levels [anti-spike (IgG-(S-RBD) and anti-nucleocapsid immunoglobulin] at three time points. Antibody level trajectories and frequency of breakthrough infections were evaluated by tumor type and timing of treatment relative to vaccination. IgG-(S-RBD) at peak response (median = 42 days after dose 2) was higher (P = 0.002) and remained higher after 4 to 6 months (P = 0.003) in patients receiving mRNA-1273 compared with BNT162b2. Patients with solid tumors attained higher peak levels (P = 0.001) and sustained levels after 4 to 6 months (P < 0.001) compared with those with hematologic malignancies. B-cell targeted treatment reduced peak (P = 0.001) and sustained antibody responses (P = 0.003). Solid tumor patients receiving immune checkpoint inhibitors before vaccination had lower sustained antibody levels than those who received treatment after vaccination (P = 0.043). Two (0.69%) vaccinated and one (1.9%) unvaccinated patient had severe COVID-19 illness during follow-up. Our study shows variation in sustained antibody responses across cancer populations receiving various therapeutic modalities, with important implications for vaccine booster timing and patient selection. SIGNIFICANCE: Long-term studies of immunogenicity of SARS-CoV-2 vaccines in patients with cancer are needed to inform evidence-based guidelines for booster vaccinations and to tailor sequence and timing of vaccinations to elicit improved humoral responses.
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Affiliation(s)
- Jane C Figueiredo
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Noah M Merin
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Omid Hamid
- The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, California
| | - So Yung Choi
- Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Tucker Lemos
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Wendy Cozen
- Division of Hematology/Oncology, Department of Medicine, Department of Pathology, School of Medicine, University of California Irvine, Orange, California
| | - Nathalie Nguyen
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Laurel J Finster
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Joslyn Foley
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Justin Darrah
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jun Gong
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ronald Paquette
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Alain C Mita
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Robert Vescio
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Inderjit Mehmi
- The Angeles Clinic and Research Institute, A Cedars-Sinai Affiliate, Los Angeles, California
| | - Reva Basho
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Warren G Tourtellotte
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Carissa A Huynh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California
| | - Greg Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California
| | | | | | | | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jennifer Van Eyk
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Joseph E Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Karen L Reckamp
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Akil Merchant
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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37
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Ebinger JE, Lan R, Sun N, Wu M, Joung S, Botwin GJ, Botting P, Al-Amili D, Aronow H, Beekley J, Coleman B, Contreras S, Cozen W, Davis J, Debbas P, Diaz J, Driver M, Fert-Bober J, Gu Q, Heath M, Herrera E, Hoang A, Hussain SK, Huynh C, Kim L, Kittleson M, Liu Y, Lloyd J, Luong E, Malladi B, Merchant A, Merin N, Mujukian A, Nguyen N, Nguyen TT, Pozdnyakova V, Rashid M, Raedschelders K, Reckamp KL, Rhoades K, Sternbach S, Vallejo R, White S, Tompkins R, Wong M, Arditi M, Figueiredo JC, Van Eyk JE, Miles PB, Chavira C, Shane R, Sobhani K, Melmed GY, McGovern DPB, Braun JG, Cheng S, Minissian MB. Symptomology following mRNA vaccination against SARS-CoV-2. Prev Med 2021; 153:106860. [PMID: 34687733 PMCID: PMC8527734 DOI: 10.1016/j.ypmed.2021.106860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 01/08/2023]
Abstract
Despite demonstrated efficacy of vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease-2019 (COVID-19), widespread hesitancy to vaccination persists. Improved knowledge regarding frequency, severity, and duration of vaccine-associated symptoms may help reduce hesitancy. In this prospective observational study, we studied 1032 healthcare workers who received both doses of the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine and completed post-vaccine symptom surveys both after dose 1 and after dose 2. We defined appreciable post-vaccine symptoms as those of at least moderate severity and lasting at least 2 days. We found that symptoms were more frequent following the second vaccine dose than the first (74% vs. 60%, P < 0.001), with >80% of all symptoms resolving within 2 days. The most common symptom was injection site pain, followed by fatigue and malaise. Overall, 20% of participants experienced appreciable symptoms after dose 1 and 30% after dose 2. In multivariable analyses, female sex was associated with greater odds of appreciable symptoms after both dose 1 (OR, 95% CI 1.73, 1.19-2.51) and dose 2 (1.76, 1.28-2.42). Prior COVID-19 was also associated with appreciable symptoms following dose 1, while younger age and history of hypertension were associated with appreciable symptoms after dose 2. We conclude that most post-vaccine symptoms are reportedly mild and last <2 days. Appreciable post-vaccine symptoms are associated with female sex, prior COVID-19, younger age, and hypertension. This information can aid clinicians in advising patients on the safety and expected symptomatology associated with vaccination.
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Affiliation(s)
- Joseph E Ebinger
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Roy Lan
- College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nancy Sun
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Min Wu
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandy Joung
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gregory J Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Patrick Botting
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniah Al-Amili
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Centre, Los Angeles, CA, USA
| | - Harriet Aronow
- Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - James Beekley
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bernice Coleman
- Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandra Contreras
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wendy Cozen
- Division of Hematology/Oncology, Department of Medicine, School of Medicine at UCI, Irvine, CA, USA; Department of Pathology, School of Medicine at UCI, Irvine, CA, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Jennifer Davis
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Jacqueline Diaz
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew Driver
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Justyna Fert-Bober
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Quanquan Gu
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Mallory Heath
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ergueen Herrera
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amy Hoang
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shehnaz K Hussain
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Carissa Huynh
- Biobank & Translational Research Core Laboratory, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Linda Kim
- Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michelle Kittleson
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yunxian Liu
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - John Lloyd
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eric Luong
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bhavya Malladi
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Noah Merin
- Department of Internal Medicine, Division of Hematology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Nathalie Nguyen
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Trevor-Trung Nguyen
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Mohamad Rashid
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Koen Raedschelders
- Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L Reckamp
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kylie Rhoades
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sarah Sternbach
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rocío Vallejo
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shane White
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Rose Tompkins
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Melissa Wong
- Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Moshe Arditi
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious, Immunologic Diseases Research Center (IIDRC), Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer E Van Eyk
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Peggy B Miles
- Employee Health Services, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cynthia Chavira
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rita Shane
- Department of Pharmacy, Cedar-Sinai Medical Center, Los Angeles, CA, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA
| | - Jonathan G Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA..
| | - Susan Cheng
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Margo B Minissian
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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38
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Melmed GY, Botwin GJ, Sobhani K, Li D, Prostko J, Figueiredo J, Cheng S, Braun J, McGovern DPB. Antibody Responses After SARS-CoV-2 mRNA Vaccination in Adults With Inflammatory Bowel Disease. Ann Intern Med 2021; 174:1768-1770. [PMID: 34633830 PMCID: PMC8513793 DOI: 10.7326/m21-2483] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Gil Y Melmed
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gregory J Botwin
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, Illinois
| | - Jane Figueiredo
- Department of Medicine and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Susan Cheng
- Departments of Medicine, Cardiology, and Biomedical Sciences and Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of eMedicine, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of eMedicine, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
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Ouahed J, Kelsen JR, Spessott WA, Kooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton KE, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Anyane-Yeboa K, Wou K, Jain P, Field M, Tollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes J, Horwitz BH, Kotlarz D, Klein C, Evans J, Dorsey J, Warner N, Elkadri A, Muise AM, Goldsmith J, Thompson B, Engelhardt KR, Cant AJ, Hambleton S, Barclay A, Toth-Petroczy A, Vuzman D, Carmichael N, Bodea C, Cassa CA, Devoto M, Maas RL, Behrens EM, Giraudo CG, Snapper SB. Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. J Crohns Colitis 2021; 15:1908-1919. [PMID: 33891011 PMCID: PMC8575043 DOI: 10.1093/ecco-jcc/jjab077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS Very early onset inflammatory bowel disease [VEOIBD] is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic aetiologies of VEOIBD have been identified, many characterized by highly penetrant recessive or dominant variants in underlying immune and/or epithelial pathways. We sought to identify the genetic cause of VEOIBD in a subset of patients with a unique clinical presentation. METHODS Whole exome sequencing was performed on five families with ten patients who presented with a similar constellation of symptoms including medically refractory infantile-onset IBD, bilateral sensorineural hearing loss and, in the majority, recurrent infections. Genetic aetiologies of VEOIBD were assessed and Sanger sequencing was performed to confirm novel genetic findings. Western analysis on peripheral blood mononuclear cells and functional studies with epithelial cell lines were employed. RESULTS In each of the ten patients, we identified damaging heterozygous or biallelic variants in the Syntaxin-Binding Protein 3 gene [STXBP3], a protein known to regulate intracellular vesicular trafficking in the syntaxin-binding protein family of molecules, but not associated to date with either VEOIBD or sensorineural hearing loss. These mutations interfere with either intron splicing or protein stability and lead to reduced STXBP3 protein expression. Knock-down of STXBP3 in CaCo2 cells resulted in defects in cell polarity. CONCLUSION Overall, we describe a novel genetic syndrome and identify a critical role for STXBP3 in VEOIBD, sensorineural hearing loss and immune dysregulation.
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Affiliation(s)
- Jodie Ouahed
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Judith R Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Waldo A Spessott
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Kameron Kooshesh
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Maria L Sanmillan
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Noor Dawany
- Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Voytek Slowik
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergey Nejentsev
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - João Farela Neves
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, the Netherlands.,Primary Immunodeficiencies Unit; Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Helena Flores
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Lisbon, 1150, Portugal
| | - Wendy K Chung
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Ashley Wilson
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Kwame Anyane-Yeboa
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Karen Wou
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Preti Jain
- Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.,Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Sophia Tollefson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Maiah H Dent
- Department of Genetics, Yale University, New Haven, CT, 06510, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Andrew C Kwong
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Faith Taliaferro
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Bruce H Horwitz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Division of Emergency Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Kotlarz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, 80337, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, 80337, Germany
| | - Jonathan Evans
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL 32207, USA
| | - Jill Dorsey
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL 32207, USA
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Abdul Elkadri
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Jeffrey Goldsmith
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin Thompson
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK
| | - Karin R Engelhardt
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK
| | - Andrew J Cant
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK.,Children's Immunology Service, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Sophie Hambleton
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK.,Children's Immunology Service, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Andrew Barclay
- Department of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Agnes Toth-Petroczy
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dana Vuzman
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Nikkola Carmichael
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Corneliu Bodea
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher A Cassa
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Translational and Precision Medicine, University Sapienza, Rome 00185, Italy.,CNR-IRGB, Cagliari 09042, Italy
| | - Richard L Maas
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Edward M Behrens
- Division of Rheumatology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Claudio G Giraudo
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
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Siegel CA, Siegel LS, Dubinsky MC, Targan S, Braun J, Landers C, Bilsborough J, Princen F, Lasch K, Candela N, McGovern DPB, Dervieux T. Performance Characteristics of a Clinical Decision Support Tool for Disease Complications in Crohn's Disease. Crohns Colitis 360 2021; 3:otab074. [PMID: 36777269 PMCID: PMC9802159 DOI: 10.1093/crocol/otab074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 11/14/2022] Open
Abstract
Background Patients with Crohn's disease (CD) are at risk of complications. Performance characteristics of a decision support tool assessing the risk of CD complications were evaluated. Methods CDPATH (formerly called the Personalized Risk and Outcome Prediction Tool [PROSPECT]) was calibrated and validated in 2 cohorts. Tool prediction of disease characteristics was assessed using Cox regression and Harrell's C-statistic. Results All associations of CD complications and CDPATH components were significant except perianal location. There was a significant association between individualized risk assessment scores and CD complications in both cohorts. Conclusion CDPATH is validated as a clinical decision support tool for assessing the risk of CD complications.
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Affiliation(s)
- Corey A Siegel
- Dartmouth–Hitchcock Inflammatory Bowel Disease Center, Dartmouth–Hitchcock Medical Center, Lebanon, New Hampshire, USA,MiTest Health, LLC, Hanover, New Hampshire, USA,Address correspondence to: Corey A. Siegel, MD, MS, Section of Gastroenterology and Hepatology, Dartmouth–Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA ()
| | | | - Marla C Dubinsky
- MiTest Health, LLC, Hanover, New Hampshire, USA,Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Braun
- Prometheus Laboratories, Inc., San Diego, California, USA
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Fred Princen
- Prometheus Laboratories, Inc., San Diego, California, USA
| | - Karen Lasch
- Takeda Pharmaceuticals U.S.A., Inc., Lexington, Massachusetts, USA
| | - Ninfa Candela
- Takeda Pharmaceuticals U.S.A., Inc., Lexington, Massachusetts, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Walshe M, Nayeri S, Ji J, Hernandez-Rocha C, Sabic K, Hu L, Giri M, Nayar S, Brant S, McGovern DPB, Rioux JD, Duerr RH, Cho JH, Schumm PL, Lazarev M, Silverberg MS. A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence. J Crohns Colitis 2021; 16:900-910. [PMID: 34698823 PMCID: PMC9282882 DOI: 10.1093/ecco-jcc/jjab186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] recurrence following ileocolic resection [ICR] is common. We sought to identify blood-based biomarkers associated with CD recurrence. METHODS CD patients undergoing ICR were recruited across six centres. Serum samples were obtained at post-operative colonoscopy. A multiplex immunoassay was used to analyse 92 inflammation-related proteins [Olink Proteomics]. Bayesian analysis was used to identify proteins associated with increasing Rutgeerts score. Identified proteins were used in receiver operating characteristic [ROC] analysis to examine the ability to identify CD recurrence [Rutgeerts score ≥i2]. Existing single cell data were interrogated to further elucidate the role of the identified proteins. RESULTS Data from 276 colonoscopies in 213 patients were available. Median time from surgery to first and second colonoscopy was 7 (interquartile range [IQR] 6-9) and 19 [IQR 16-23] months, respectively. Disease recurrence was evident at 60 [30%] first and 36 [49%] second colonoscopies. Of 14 proteins significantly associated with Rutgeerts score, the strongest signal was seen for CXCL9 and MMP1. Among patients on anti-tumour necrosis factor drugs, CXCL9 and CXCL11 were most strongly associated with Rutgeerts score. Both are CXCR3 ligands. Incorporation of identified proteins into ROC analysis improved the ability to identify disease recurrence as compared to C-reactive protein alone: area under the curve [AUC] 0.75 (95% confidence interval [CI]: 0.66-0.82] vs 0.64 [95% CI 0.56-0.72], p = 0.012. Single cell transcriptomic data provide evidence that innate immune cells are the primary source of the identified proteins. CONCLUSIONS CXCR3 ligands are associated with CD recurrence following ICR. Incorporation of novel blood-based candidate biomarkers may aid in identification of CD recurrence.
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Affiliation(s)
- Margaret Walshe
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Shadi Nayeri
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cristian Hernandez-Rocha
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada,Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Canada
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liangyuan Hu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Brant
- Crohn’s and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John D Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada,Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA,USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Phil L Schumm
- Department of Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Mark S Silverberg
- Corresponding author: Dr Mark Silverberg, MD, PhD, FRCPC, University of Toronto, Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, 441–600 University Avenue, Toronto, Ontario, M5G1X5, Canada. Tel: +1-416-586-4800 ext 8236; Fax: +1-416-619-5524;
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Parrish AB, Lopez NE, Truong A, Zaghiyan K, Melmed GY, McGovern DPB, Ha C, Syal G, Bonthala N, Jain A, Landers CJ, Targan SR, Fleshner P. Preoperative Serum Vedolizumab Levels Do Not Impact Postoperative Outcomes in Inflammatory Bowel Disease. Dis Colon Rectum 2021; 64:1259-1266. [PMID: 34516445 DOI: 10.1097/dcr.0000000000001920] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Vedolizumab has been proposed to lead to fewer postoperative complications because of its gut specificity. Studies, however, suggest an increased risk of surgical site infections, yet the data are conflicting. OBJECTIVE This study aimed to assess the effect of vedolizumab drug levels on postoperative outcomes in patients undergoing major abdominal surgery for IBD. DESIGN This was a retrospective study of a prospectively maintained database. SETTING Patients were operated on by a single surgeon at an academic medical center. PATIENTS A total of 72 patients with IBD undergoing major abdominal surgery were included. INTERVENTIONS Patients were exposed preoperatively to vedolizumab. MAIN OUTCOME MEASURES The primary outcome measured was the postoperative morbidity in patients who had IBD with detectable vs undetectable vedolizumab levels. RESULTS A total of 72 patients were included in the study. Thirty-eight patients had detectable vedolizumab levels (>1.6 μg/mL), and 34 had undetectable vedolizumab levels. The overall rate of complications was 39%, and ileus was the most common complication. There were no significant differences in clinical variables between the detectable and undetectable vedolizumab level patient groups except for the time between the last dose and surgery (p < 0.01). There were 42 patients in the ulcerative colitis cohort; 48% had an undetectable vedolizumab level and 52% had a detectable vedolizumab level. There were no differences in any postoperative morbidity between ulcerative colitis groups. The Crohn's cohort had 27 patients; 48% had an undetectable vedolizumab levels and 52% had a detectable vedolizumab level. There was a significantly lower incidence of postoperative ileus in patients who had Crohn's disease with detectable vedolizumab levels compared with patients with an undetectable vedolizumab level (p < 0.04). LIMITATIONS Limitations include a low overall patient population and a high rate of stoma formation. CONCLUSIONS Serum vedolizumab levels do not influence postoperative morbidity in IBD. Vedolizumab may reduce the incidence of postoperative ileus in patients with Crohn's disease. See Video Abstract at http://links.lww.com/DCR/B574. LOS NIVELES DE VEDOLIZUMAB EN SUERO PREOPERATORIO, NO AFECTAN LOS RESULTADOS POSTOPERATORIOS EN LA ENFERMEDAD INFLAMATORIA INTESTINAL ANTECEDENTES:Se ha propuesto que el vedolizumab presenta menos complicaciones postoperatorias debido a su especificidad intestinal. Sin embargo, estudios sugieren un mayor riesgo de infecciones en el sitio quirúrgico, aunque los datos son contradictorios.OBJETIVO:Evaluar el efecto en los niveles del fármaco vedolizumab, en resultados postoperatorios de pacientes sometidos a cirugía mayor abdominal, por enfermedad inflamatoria intestinal.DISEÑO:Estudio retrospectivo de una base de datos mantenida prospectivamente.ENTORNO CLÍNICO:Pacientes intervenidos por un solo cirujano en un centro médico académico.PACIENTES:Un total de 72 pacientes con enfermedad inflamatoria intestinal sometidos a cirugía mayor abdominal.INTERVENCIONES:Exposición preoperatoria a vedolizumab.PRINCIPALES MEDIDAS DE VALORACIÓN:Morbilidad postoperatoria en pacientes con enfermedad inflamatoria intestinal, con niveles detectables versus no detectables de vedolizumab.RESULTADOS:Se incluyó en el estudio a un total de 72 pacientes. Treinta y ocho pacientes tuvieron niveles detectables de vedolizumab (> 1,6 mcg / ml) y 34 con niveles no detectables de vedolizumab. La tasa global de complicaciones fue del 39% y el íleo fue la complicación más común. No hubo diferencias significativas en las variables clínicas entre los grupos de pacientes con niveles detectables y no detectables de vedolizumab, excepto por el intervalo de tiempo entre la última dosis y la cirugía (p <.01). La cohorte de colitis ulcerosa tuvo 42 pacientes, el 48% con un nivel no detectable de vedolizumab y el 52% un nivel detectable de vedolizumab. No hubo diferencias en ninguna morbilidad postoperatoria entre los grupos de colitis ulcerosa. La cohorte de Crohn tuvo 27 pacientes, 48% con niveles no detectables de vedolizumab y el 52% con niveles detectables de vedolizumab. Hubo una incidencia significativamente menor de íleo postoperatorio en pacientes de Crohn con niveles detectables de vedolizumab, comparados con los pacientes con un nivel no detectable de vedolizumab (p <0,04).LIMITACIONES:Las limitaciones incluyen una baja población general de pacientes y una alta tasa de formación de estomas.CONCLUSIONES:Los niveles séricos de vedolizumab no influyen en la morbilidad postoperatoria de la enfermedad inflamatoria intestinal. Vedolizumab puede reducir la incidencia de íleo postoperatorio en pacientes de Crohn. Consulte Video Resumen en http://links.lww.com/DCR/B574.
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MESH Headings
- Adult
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/therapeutic use
- Colitis, Ulcerative/blood
- Colitis, Ulcerative/epidemiology
- Colitis, Ulcerative/surgery
- Crohn Disease/blood
- Crohn Disease/epidemiology
- Crohn Disease/surgery
- Female
- Gastrointestinal Agents/adverse effects
- Gastrointestinal Agents/metabolism
- Gastrointestinal Agents/therapeutic use
- Humans
- Ileus/epidemiology
- Incidence
- Inflammatory Bowel Diseases/blood
- Inflammatory Bowel Diseases/surgery
- Male
- Middle Aged
- Morbidity
- Outcome Assessment, Health Care
- Postoperative Complications/epidemiology
- Postoperative Period
- Preoperative Period
- Retrospective Studies
- Surgical Stomas
- Surgical Wound Infection/chemically induced
- Surgical Wound Infection/epidemiology
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Affiliation(s)
- Aaron B Parrish
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Nicole E Lopez
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Adam Truong
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Karen Zaghiyan
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Gil Y Melmed
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Dermot P B McGovern
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Christina Ha
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Gaurav Syal
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Nirupama Bonthala
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Anjali Jain
- Prometheus Laboratories, San Diego, California
| | - Carol J Landers
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Stephan R Targan
- Department of Gastroenterology, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
| | - Phillip Fleshner
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles California
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Shiao SL, Kershaw KM, Limon JJ, You S, Yoon J, Ko EY, Guarnerio J, Potdar AA, McGovern DPB, Bose S, Dar TB, Noe P, Lee J, Kubota Y, Maymi VI, Davis MJ, Henson RM, Choi RY, Yang W, Tang J, Gargus M, Prince AD, Zumsteg ZS, Underhill DM. Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy. Cancer Cell 2021; 39:1202-1213.e6. [PMID: 34329585 PMCID: PMC8830498 DOI: 10.1016/j.ccell.2021.07.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/28/2020] [Accepted: 07/01/2021] [Indexed: 12/20/2022]
Abstract
Studies suggest that the efficacy of cancer chemotherapy and immunotherapy is influenced by intestinal bacteria. However, the influence of the microbiome on radiation therapy is not as well understood, and the microbiome comprises more than bacteria. Here, we find that intestinal fungi regulate antitumor immune responses following radiation in mouse models of breast cancer and melanoma and that fungi and bacteria have opposite influences on these responses. Antibiotic-mediated depletion or gnotobiotic exclusion of fungi enhances responsiveness to radiation, whereas antibiotic-mediated depletion of bacteria reduces responsiveness and is associated with overgrowth of commensal fungi. Further, elevated intratumoral expression of Dectin-1, a primary innate sensor of fungi, is negatively associated with survival in patients with breast cancer and is required for the effects of commensal fungi in mouse models of radiation therapy.
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Affiliation(s)
- Stephen L Shiao
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Kathleen M Kershaw
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sungyong You
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Junhee Yoon
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Emily Y Ko
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jlenia Guarnerio
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shikha Bose
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tahir B Dar
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Paul Noe
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jung Lee
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Yuzu Kubota
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Viviana I Maymi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Madison J Davis
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Regina M Henson
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Rachel Y Choi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Wensha Yang
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Gargus
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alexander D Prince
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - David M Underhill
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Mo A, Nagpal S, Gettler K, Haritunians T, Giri M, Haberman Y, Karns R, Prince J, Arafat D, Hsu NY, Chuang LS, Argmann C, Kasarskis A, Suarez-Farinas M, Gotman N, Mengesha E, Venkateswaran S, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, LeLeiko NS, Heyman MB, Griffiths AM, Patel AS, Noe JD, Davis Thomas S, Aronow BJ, Walters TD, McGovern DPB, Hyams JS, Kugathasan S, Cho JH, Denson LA, Gibson G. Stratification of risk of progression to colectomy in ulcerative colitis via measured and predicted gene expression. Am J Hum Genet 2021; 108:1765-1779. [PMID: 34450030 DOI: 10.1016/j.ajhg.2021.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful prediction of this adverse status. By contrast, in Crohn disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a transcriptional risk score (TRS). Here, we demonstrate that a measured TRS based on bulk rectal gene expression in the PROTECT inception cohort study has a positive predictive value approaching 50% for colectomy. Single-cell profiling demonstrates that the genes are active in multiple diverse cell types from both the epithelial and immune compartments. Expression quantitative trait locus (QTL) analysis identifies genes with differential effects at baseline and week 52 follow-up, but for the most part, differential expression associated with colectomy risk is independent of local genetic regulation. Nevertheless, a predicted polygenic transcriptional risk score (PPTRS) derived by summation of transcriptome-wide association study (TWAS) effects identifies UC-affected individuals at 5-fold elevated risk of colectomy with data from the UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with TWASs for stratification of risk of disease complications.
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Affiliation(s)
- Angela Mo
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sini Nagpal
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kyle Gettler
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mamta Giri
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yael Haberman
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Sheba Medical Center, Tel Hashomer, Tel Aviv University, Tel Aviv 5265601, Israel
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dalia Arafat
- Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nai-Yun Hsu
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Data Science and Genomic Technology, and Department of Population Health Science and Policy, Mount Sinai School of Medicine, New York City, NY 10029, USA
| | - Nathan Gotman
- University of North Carolina, Chapel Hill, NC 27516, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Paul A Rufo
- Harvard University-Children's Hospital Boston, Boston, MA 02115, USA
| | - Susan S Baker
- Women & Children's Hospital of Buffalo, Buffalo, NY 14222, USA
| | | | - James Markowitz
- Cohen Children's Medical Center of New York, New Hyde Park, NY 11040, USA
| | | | - Joel R Rosh
- Goryeb Children's Hospital-Atlantic Health, Morristown, NJ 07960, USA
| | | | - David R Mack
- Children's Hospital of East Ontario, Ottawa, ON K1P 1J1, Canada
| | | | - Sapana Shah
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University, New York City, NY 10032, USA
| | - Melvin B Heyman
- University of California at San Francisco, San Francisco, CA 94143, USA
| | | | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Bruce J Aronow
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | | | - Judy H Cho
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Greg Gibson
- Georgia Institute of Technology, Atlanta, GA 30332, USA.
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45
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Liu TC, Kern JT, Jain U, Sonnek NM, Xiong S, Simpson KF, VanDussen KL, Winkler ES, Haritunians T, Malique A, Lu Q, Sasaki Y, Storer C, Diamond MS, Head RD, McGovern DPB, Stappenbeck TS. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host Microbe 2021; 29:988-1001.e6. [PMID: 34010595 DOI: 10.1016/j.chom.2021.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 05/18/2020] [Revised: 12/22/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Intestinal Paneth cells modulate innate immunity and infection. In Crohn's disease, genetic mutations together with environmental triggers can disable Paneth cell function. Here, we find that a western diet (WD) similarly leads to Paneth cell dysfunction through mechanisms dependent on the microbiome and farnesoid X receptor (FXR) and type I interferon (IFN) signaling. Analysis of multiple human cohorts suggests that obesity is associated with Paneth cell dysfunction. In mouse models, consumption of a WD for as little as 4 weeks led to Paneth cell dysfunction. WD consumption in conjunction with Clostridium spp. increased the secondary bile acid deoxycholic acid levels in the ileum, which in turn inhibited Paneth cell function. The process required excess signaling of both FXR and IFN within intestinal epithelial cells. Our findings provide a mechanistic link between poor diet and inhibition of gut innate immunity and uncover an effect of FXR activation in gut inflammation.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Naomi M Sonnek
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katherine F Simpson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Talin Haritunians
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Atika Malique
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Qiuhe Lu
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chad Storer
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Richard D Head
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles 90048, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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46
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Botwin GJ, Li D, Figueiredo J, Cheng S, Braun J, McGovern DPB, Melmed GY. Adverse Events Following SARS-CoV-2 mRNA Vaccination Among Patients with Inflammatory Bowel Disease. medRxiv 2021:2021.03.30.21254607. [PMID: 33821287 PMCID: PMC8020989 DOI: 10.1101/2021.03.30.21254607] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Patients with immune-mediated inflammatory diseases (IMID) such as inflammatory bowel disease (IBD) on immunosuppressive and biologic therapies were largely excluded from SARS-CoV-2 mRNA vaccine trials. We thus evaluated post-mRNA vaccination adverse events (AE) in 246 vaccinated adults with IBD participating in a longitudinal vaccine registry. In general, AE frequency was similar to that reported in the general population. As in the general population, AE were more common among younger patients, and those with prior COVID-19. We additionally found that AE were less common in individuals receiving biologic therapy. Those with IBD and other IMID on these commonly prescribed therapies can be reassured that the AE risk is likely not increased, and may be reduced, while on biologics.
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47
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Jain U, Ver Heul AM, Xiong S, Gregory MH, Demers EG, Kern JT, Lai CW, Muegge BD, Barisas DAG, Leal-Ekman JS, Deepak P, Ciorba MA, Liu TC, Hogan DA, Debbas P, Braun J, McGovern DPB, Underhill DM, Stappenbeck TS. Debaryomyces is enriched in Crohn's disease intestinal tissue and impairs healing in mice. Science 2021; 371:1154-1159. [PMID: 33707263 PMCID: PMC10114606 DOI: 10.1126/science.abd0919] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/15/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Alterations of the mycobiota composition associated with Crohn's disease (CD) are challenging to link to defining elements of pathophysiology, such as poor injury repair. Using culture-dependent and -independent methods, we discovered that Debaryomyces hansenii preferentially localized to and was abundant within incompletely healed intestinal wounds of mice and inflamed mucosal tissues of CD human subjects. D. hansenii cultures from injured mice and inflamed CD tissues impaired colonic healing when introduced into injured conventionally raised or gnotobiotic mice. We reisolated D. hansenii from injured areas of these mice, fulfilling Koch's postulates. Mechanistically, D. hansenii impaired mucosal healing through the myeloid cell-specific type 1 interferon-CCL5 axis. Taken together, we have identified a fungus that inhabits inflamed CD tissue and can lead to dysregulated mucosal healing.
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Affiliation(s)
- Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aaron M Ver Heul
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shanshan Xiong
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin H Gregory
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elora G Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Justin T Kern
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Medicine, VA Medical Center, St. Louis, MO 63106, USA
| | - Derek A G Barisas
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - J Steven Leal-Ekman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Parakkal Deepak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew A Ciorba
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Philip Debbas
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
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48
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Ebinger JE, Botwin GJ, Albert CM, Alotaibi M, Arditi M, Berg AH, Binek A, Botting P, Fert-Bober J, Figueiredo JC, Grein JD, Hasan W, Henglin M, Hussain SK, Jain M, Joung S, Karin M, Kim EH, Li D, Liu Y, Luong E, McGovern DPB, Merchant A, Merin N, Miles PB, Minissian M, Nguyen TT, Raedschelders K, Rashid MA, Riera CE, Riggs RV, Sharma S, Sternbach S, Sun N, Tourtellotte WG, Van Eyk JE, Sobhani K, Braun JG, Cheng S. Seroprevalence of antibodies to SARS-CoV-2 in healthcare workers: a cross-sectional study. BMJ Open 2021; 11:e043584. [PMID: 33579769 PMCID: PMC7883610 DOI: 10.1136/bmjopen-2020-043584] [Citation(s) in RCA: 24] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/30/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE We sought to determine the extent of SARS-CoV-2 seroprevalence and the factors associated with seroprevalence across a diverse cohort of healthcare workers. DESIGN Observational cohort study of healthcare workers, including SARS-CoV-2 serology testing and participant questionnaires. SETTINGS A multisite healthcare delivery system located in Los Angeles County. PARTICIPANTS A diverse and unselected population of adults (n=6062) employed in a multisite healthcare delivery system located in Los Angeles County, including individuals with direct patient contact and others with non-patient-oriented work functions. MAIN OUTCOMES Using Bayesian and multivariate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody levels, including pre-existing demographic and clinical characteristics; potential COVID-19 illness-related exposures; and symptoms consistent with COVID-19 infection. RESULTS We observed a seroprevalence rate of 4.1%, with anosmia as the most prominently associated self-reported symptom (OR 11.04, p<0.001) in addition to fever (OR 2.02, p=0.002) and myalgias (OR 1.65, p=0.035). After adjusting for potential confounders, seroprevalence was also associated with Hispanic ethnicity (OR 1.98, p=0.001) and African-American race (OR 2.02, p=0.027) as well as contact with a COVID-19-diagnosed individual in the household (OR 5.73, p<0.001) or clinical work setting (OR 1.76, p=0.002). Importantly, African-American race and Hispanic ethnicity were associated with antibody positivity even after adjusting for personal COVID-19 diagnosis status, suggesting the contribution of unmeasured structural or societal factors. CONCLUSION AND RELEVANCE The demographic factors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace. The size and diversity of our study population, combined with robust survey and modelling techniques, provide a vibrant picture of the demographic factors, exposures and symptoms that can identify individuals with susceptibility as well as potential to mount an immune response to COVID-19.
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Affiliation(s)
- Joseph E Ebinger
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory J Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christine M Albert
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mona Alotaibi
- Division of Pulmonary and Critical Care Medicine, University of California, San Diego, La Jolla, California, USA
| | - Moshe Arditi
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Anders H Berg
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Aleksandra Binek
- Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Patrick Botting
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Justyna Fert-Bober
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jane C Figueiredo
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan D Grein
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Epidemiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Wohaib Hasan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Biobank & Translational Research Core Laboratory, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mir Henglin
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shehnaz K Hussain
- Department of Public Health Sciences and Comprehensive Cancer Center, University of California, Davis, Davis, California, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Sandy Joung
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michael Karin
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Elizabeth H Kim
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Yunxian Liu
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eric Luong
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Akil Merchant
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Noah Merin
- Department of Internal Medicine, Division of Hematology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Peggy B Miles
- Employee Health Services, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Margo Minissian
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Brawerman Nursing Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Trevor Trung Nguyen
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Koen Raedschelders
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mohamad A Rashid
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Celine E Riera
- Center for Neural Science and Medicine, Department of Biomedical Sciences, Board of Governors Regenerative Medicine Institute, Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Richard V Riggs
- Chief Medical Officer, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sonia Sharma
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Sarah Sternbach
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nancy Sun
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Warren G Tourtellotte
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Biobank & Translational Research Core Laboratory, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jennifer E Van Eyk
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Advanced Clinical Biosystems Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Barbra Streisand Women's Heart Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan G Braun
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Susan Cheng
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Barbra Streisand Women's Heart Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
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49
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Degenhardt F, Mayr G, Wendorff M, Boucher G, Ellinghaus E, Ellinghaus D, ElAbd H, Rosati E, Hübenthal M, Juzenas S, Abedian S, Vahedi H, Thelma BK, Yang SK, Ye BD, Cheon JH, Datta LW, Daryani NE, Ellul P, Esaki M, Fuyuno Y, McGovern DPB, Haritunians T, Hong M, Juyal G, Jung ES, Kubo M, Kugathasan S, Lenz TL, Leslie S, Malekzadeh R, Midha V, Motyer A, Ng SC, Okou DT, Raychaudhuri S, Schembri J, Schreiber S, Song K, Sood A, Takahashi A, Torres EA, Umeno J, Alizadeh BZ, Weersma RK, Wong SH, Yamazaki K, Karlsen TH, Rioux JD, Brant SR, Franke A. Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations. Hum Mol Genet 2021; 30:356-369. [PMID: 33555323 PMCID: PMC8098114 DOI: 10.1093/hmg/ddab017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabrielle Boucher
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Dermatology, Venerology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Homayon Vahedi
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi 110021, India
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naser Ebrahim Daryani
- Department of Gastroenterology, Emam Hospital, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Myhunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 351-0198, Japan
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Pediatric Institute, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Stephen Leslie
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Vandana Midha
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Allan Motyer
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - David T Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Centre for Genetics and Genomics Versus Arthritis, Division of Musculosceletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - John Schembri
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Ajit Sood
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, Riken, Yokohama, 230-0045, Japan
| | - Esther A Torres
- Department of Medicine, University of Puerto Rico Center for IBD, University of Puerto Rico School of Medicine, Rio Piedras, San Juan, PR 00936-5067, USA
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700 AB Groningen, The Netherlands
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway.,Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, 0372 Oslo, Norway
| | - John D Rioux
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Medicine, Rutgers Robert Wood Johnson School of Medicine and Department of Genetics, Rutgers University Brunswick and Piscataway, NJ 08903-0019, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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50
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Naito T, Botwin GJ, Haritunians T, Li D, Yang S, Khrom M, Braun J, Abbou L, Mengesha E, Stevens C, Masamune A, Daly M, McGovern DPB. Prevalence and Effect of Genetic Risk of Thromboembolic Disease in Inflammatory Bowel Disease. Gastroenterology 2021; 160:771-780.e4. [PMID: 33098885 DOI: 10.1053/j.gastro.2020.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/29/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS The largest cause of mortality in patients with inflammatory bowel disease (IBD) remains thromboembolic disease (TED). Recent reports have demonstrated that both monogenic and polygenic factors contribute to TED and 10% of healthy subjects are genetically at high risk for TED. Our aim was to utilize whole-exome sequencing and genome-wide genotyping to determine the proportion of IBD patients genetically at risk for TED and investigate the effect of genetic risk of TED in IBD. METHODS The TED polygenic risk score was calculated from genome-wide genotyping. Thrombophilia pathogenic variants were extracted from whole-exome sequencing. In total, 792 IBD patients had both whole-exome sequencing and genotyping data. We defined patients at genetically high risk for TED if they had a high TED polygenic risk score or carried at least 1 thrombophilia pathogenic variant. RESULTS We identified 122 of 792 IBD patients (15.4%) as genetically high risk for TED. Among 715 of 792 subjects whose documented TED status were available, 63 of the 715 patients (8.8%) had TED events. Genetic TED risk was significantly associated with increased TED event (odds ratio, 2.5; P = .0036). In addition, we confirmed an additive effect of monogenic and polygenic risk on TED (P = .0048). Patients with high TED genetic risk more frequently had thrombosis at multiple sites (78% vs 42%, odds ratio, 3.96; P = .048). CONCLUSIONS Genetic risk (both poly- and monogenic) was significantly associated with TED history. Our results suggest that genetic traits identify approximately 1 in 7 patients with IBD who will experience 2.5-fold or greater risk for TED.
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Affiliation(s)
- Takeo Naito
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California; Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Gregory J Botwin
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michelle Khrom
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan Braun
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Lisa Abbou
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Dermot P B McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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