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Liu H, Guan L, Su X, Zhao L, Shu Q, Zhang J. A broken network of susceptibility genes in the monocytes of Crohn's disease patients. Life Sci Alliance 2024; 7:e202302394. [PMID: 38925865 PMCID: PMC11208737 DOI: 10.26508/lsa.202302394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Su
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lijian Zhao
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Qing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Research, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
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2
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Krishna C, Chiou J, Sakaue S, Kang JB, Christensen SM, Lee I, Aksit MA, Kim HI, von Schack D, Raychaudhuri S, Ziemek D, Hu X. The influence of HLA genetic variation on plasma protein expression. Nat Commun 2024; 15:6469. [PMID: 39085222 PMCID: PMC11291675 DOI: 10.1038/s41467-024-50583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Genetic variation in the human leukocyte antigen (HLA) loci is associated with risk of immune-mediated diseases, but the molecular effects of HLA polymorphism are unclear. Here we examined the effects of HLA genetic variation on the expression of 2940 plasma proteins across 45,330 Europeans in the UK Biobank, with replication analyses across multiple ancestry groups. We detected 504 proteins affected by HLA variants (HLA-pQTL), including widespread trans effects by autoimmune disease risk alleles. More than 80% of the HLA-pQTL fine-mapped to amino acid positions in the peptide binding groove. HLA-I and II affected proteins expressed in similar cell types but in different pathways of both adaptive and innate immunity. Finally, we investigated potential HLA-pQTL effects on disease by integrating HLA-pQTL with fine-mapped HLA-disease signals in the UK Biobank. Our data reveal the diverse effects of HLA genetic variation and aid the interpretation of associations between HLA alleles and immune-mediated diseases.
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Affiliation(s)
- Chirag Krishna
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA.
| | - Joshua Chiou
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Isac Lee
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | | | - Hye In Kim
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - David von Schack
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ziemek
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Xinli Hu
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA.
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3
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Wang W, Zhang Q, Zhao J, Liu T, Yao J, Peng X, Zhi M, Zhang M. HLA-DQA1*05 correlates with increased risk of anti-drug antibody development and reduced response to infliximab in Chinese patients with Crohn's disease. Gastroenterol Rep (Oxf) 2024; 12:goae074. [PMID: 39055374 PMCID: PMC11269678 DOI: 10.1093/gastro/goae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/30/2024] [Accepted: 05/07/2024] [Indexed: 07/27/2024] Open
Abstract
Background The efficacy of anti-TNF therapy in Crohn's disease (CD), such as infliximab, is often compromised by the development of anti-drug antibodies (ADAs). The genetic variation HLA-DQA1*05 has been linked to the immunogenicity of biologics, influencing ADA formation. This study investigates the correlation between HLA-DQA1*05 and ADA formation in CD patients treated with infliximab in a Chinese Han population and assesses clinical outcomes. Methods In this retrospective cohort study, 345 infliximab-exposed CD patients were genotyped for HLADQ A1*05A > G (rs2097432). We evaluated the risk of ADA development, loss of infliximab response, adverse events, and treatment discontinuation among variant and wild-type allele individuals. Results A higher percentage of patients with ADAs formation was observed in HLA-DQA1*05 G variant carriers compared with HLA-DQA1*05 wild-type carriers (58.5% vs 42.9%, P = 0.004). HLA-DQA1*05 carriage significantly increased the risk of ADAs development (adjusted hazard ratio = 1.65, 95% CI 1.18-2.30, P = 0.003) and was associated with a greater likelihood of infliximab response loss (adjusted HR = 2.55, 95% CI 1.78-3.68, P < 0.0001) and treatment discontinuation (adjusted HR = 2.21, 95% CI 1.59-3.06, P < 0.0001). Interestingly, combined therapy with immunomodulators increased the risk of response loss in HLA-DQA1*05 variant carriers. Conclusions HLA-DQA1*05 significantly predicts ADAs formation and impacts treatment outcomes in infliximab-treated CD patients. Pre-treatment screening for this genetic factor could therefore be instrumental in personalizing anti-TNF therapy strategies for these patients.
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Affiliation(s)
- Wei Wang
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Qi Zhang
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Junzhang Zhao
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Tao Liu
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Jiayin Yao
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Xiang Peng
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Min Zhi
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
| | - Min Zhang
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510655, P. R. China
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4
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Chia R, Ray A, Shah Z, Ding J, Ruffo P, Fujita M, Menon V, Saez-Atienzar S, Reho P, Kaivola K, Walton RL, Reynolds RH, Karra R, Sait S, Akcimen F, Diez-Fairen M, Alvarez I, Fanciulli A, Stefanova N, Seppi K, Duerr S, Leys F, Krismer F, Sidoroff V, Zimprich A, Pirker W, Rascol O, Foubert-Samier A, Meissner WG, Tison F, Pavy-Le Traon A, Pellecchia MT, Barone P, Russillo MC, Marín-Lahoz J, Kulisevsky J, Torres S, Mir P, Periñán MT, Proukakis C, Chelban V, Wu L, Goh YY, Parkkinen L, Hu MT, Kobylecki C, Saxon JA, Rollinson S, Garland E, Biaggioni I, Litvan I, Rubio I, Alcalay RN, Kwei KT, Lubbe SJ, Mao Q, Flanagan ME, Castellani RJ, Khurana V, Ndayisaba A, Calvo A, Mora G, Canosa A, Floris G, Bohannan RC, Moore A, Norcliffe-Kaufmann L, Palma JA, Kaufmann H, Kim C, Iba M, Masliah E, Dawson TM, Rosenthal LS, Pantelyat A, Albert MS, Pletnikova O, Troncoso JC, Infante J, Lage C, Sánchez-Juan P, Serrano GE, Beach TG, Pastor P, Morris HR, Albani D, Clarimon J, Wenning GK, Hardy JA, Ryten M, Topol E, Torkamani A, Chiò A, Bennett DA, De Jager PL, Low PA, Singer W, Cheshire WP, Wszolek ZK, Dickson DW, Traynor BJ, Gibbs JR, Dalgard CL, Ross OA, Houlden H, Scholz SW. Genome sequence analyses identify novel risk loci for multiple system atrophy. Neuron 2024; 112:2142-2156.e5. [PMID: 38701790 PMCID: PMC11223971 DOI: 10.1016/j.neuron.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/28/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Multiple system atrophy (MSA) is an adult-onset, sporadic synucleinopathy characterized by parkinsonism, cerebellar ataxia, and dysautonomia. The genetic architecture of MSA is poorly understood, and treatments are limited to supportive measures. Here, we performed a comprehensive analysis of whole genome sequence data from 888 European-ancestry MSA cases and 7,128 controls to systematically investigate the genetic underpinnings of this understudied neurodegenerative disease. We identified four significantly associated risk loci using a genome-wide association study approach. Transcriptome-wide association analyses prioritized USP38-DT, KCTD7, and lnc-KCTD7-2 as novel susceptibility genes for MSA within these loci, and single-nucleus RNA sequence analysis found that the associated variants acted as cis-expression quantitative trait loci for multiple genes across neuronal and glial cell types. In conclusion, this study highlights the role of genetic determinants in the pathogenesis of MSA, and the publicly available data from this study represent a valuable resource for investigating synucleinopathies.
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Affiliation(s)
- Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Anindita Ray
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Zalak Shah
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Paola Ruffo
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA
| | - Sara Saez-Atienzar
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ronald L Walton
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Regina H Reynolds
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK; Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK; Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ramita Karra
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Shaimaa Sait
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Fulya Akcimen
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Monica Diez-Fairen
- Memory and Movement Disorders Units, Department of Neurology, University Hospital Mutua de Terrassa, Barcelona, Spain
| | - Ignacio Alvarez
- Memory and Movement Disorders Units, Department of Neurology, University Hospital Mutua de Terrassa, Barcelona, Spain
| | | | - Nadia Stefanova
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Seppi
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Susanne Duerr
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Fabian Leys
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Krismer
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Victoria Sidoroff
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Walter Pirker
- Department of Neurology, Klinik Ottakring - Wilhelminenspital, Vienna, Austria
| | - Olivier Rascol
- MSA French Reference Center and CIC-1436, Department of Clinical Pharmacology and Neurosciences, University of Toulouse, Toulouse, France
| | - Alexandra Foubert-Samier
- Service de Neurologie des Maladies Neurodégénératives, French Reference Center for MSA, NS-Park/FCRIN Network, CHU Bordeaux, Bordeaux, France
| | - Wassilios G Meissner
- Service de Neurologie des Maladies Neurodégénératives, French Reference Center for MSA, NS-Park/FCRIN Network, CHU Bordeaux, Bordeaux, France; University of Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, France; Department of Medicine, University of Otago, and the New Zealand Brain Research Institute, Christchurch, New Zealand
| | - François Tison
- Service de Neurologie des Maladies Neurodégénératives, French Reference Center for MSA, NS-Park/FCRIN Network, CHU Bordeaux, Bordeaux, France; University of Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, France
| | - Anne Pavy-Le Traon
- French Reference Center for MSA, Department of Neurosciences, Centre d'Investigation Clinique de Toulouse CIC1436, UMR 1048, Institute of Cardiovascular and Metabolic Diseases (I2MC), University Hospital of Toulouse, INSERM, Toulouse, France
| | - Maria Teresa Pellecchia
- Neuroscience Section, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Paolo Barone
- Neuroscience Section, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Maria Claudia Russillo
- Neuroscience Section, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Juan Marín-Lahoz
- Movement Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Institut d'Investigacions Biomèdiques Sant Pau (IIB-Sant Pau), Centro de Investigación en Red Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Barcelona, Spain; Servicio de Neurología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Jaime Kulisevsky
- Movement Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Institut d'Investigacions Biomèdiques Sant Pau (IIB-Sant Pau), Centro de Investigación en Red Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Soraya Torres
- Institut d'Investigacions Biomèdiques Sant Pau (IIB-Sant Pau), Centro de Investigación en Red Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pablo Mir
- Unidad de Trastornos del Movimiento Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Seville, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Madrid, Spain; Departamento de Medicina Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Maria Teresa Periñán
- Unidad de Trastornos del Movimiento Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Seville, Spain; Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University, London, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; The National Hospital for Neurology and Neurosurgery, London, UK
| | - Lesley Wu
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK
| | - Yee Y Goh
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Michele T Hu
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christopher Kobylecki
- Department of Neurology, Northern Care Alliance NHS Foundation Trust, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Jennifer A Saxon
- Cerebral Function Unit, Manchester Centre for Clinical Neurosciences, Salfort, UK; Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Sara Rollinson
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Emily Garland
- Autonomic Dysfunction Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Italo Biaggioni
- Autonomic Dysfunction Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Irene Litvan
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Ileana Rubio
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA; Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Kimberly T Kwei
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qinwen Mao
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Margaret E Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA; Department of Pathology, UT Health San Antonio, San Antonio, TX, USA
| | - Rudolph J Castellani
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Vikram Khurana
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Alain Ndayisaba
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria; Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrea Calvo
- "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy
| | - Gabriele Mora
- Istituti Clinici Scientifici Maugeri, IRCCS, Milan, Italy
| | - Antonio Canosa
- "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy
| | - Gianluca Floris
- Department of Neurology, University Hospital of Cagliari, Cagliari, Italy
| | - Ryan C Bohannan
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Anni Moore
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | | | - Jose-Alberto Palma
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Changyoun Kim
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Michiyo Iba
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Eliezer Masliah
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA; Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA; Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Alexander Pantelyat
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA; Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Jon Infante
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL-UC-CIBERNED, Santander, Spain
| | - Carmen Lage
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL-UC-CIBERNED, Santander, Spain
| | - Pascual Sánchez-Juan
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL-UC-CIBERNED, Santander, Spain; Alzheimer's Centre Reina Sofia-CIEN Foundation-ISCIII, Madrid, Spain
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Pau Pastor
- Genomics and Transcriptomics of Synucleinopathies, Neurosciences, The Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain; Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Huw R Morris
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Jordi Clarimon
- Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain; The Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Gregor K Wenning
- Autonomic Unit - Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - John A Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK; UK Dementia Research Institute of UCL, UCL Institute of Neurology, University College London, London, UK; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Movement Disorders Centre, University College London, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK; Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | - Eric Topol
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Institute of Cognitive Sciences and Technologies, C.N.R., Rome, Italy; Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York, NY, USA
| | - Philip A Low
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA; RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; The National Hospital for Neurology and Neurosurgery, London, UK
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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5
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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; 167:315-332. [PMID: 38490347 PMCID: PMC11193636 DOI: 10.1053/j.gastro.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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 (anti-nuclear cytoplasmic antibody; IgG and IgA, anti-Saccharomyces cerevisiae antibodies; and anti-flagellin) and any EIM (anti-nuclear cytoplasmic antibody; IgG and IgA, 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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MESH Headings
- Humans
- Female
- Male
- Adult
- Cholangitis, Sclerosing/immunology
- Cholangitis, Sclerosing/genetics
- Cholangitis, Sclerosing/diagnosis
- Cholangitis, Sclerosing/complications
- Middle Aged
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/diagnosis
- Crohn Disease/immunology
- Crohn Disease/genetics
- Crohn Disease/diagnosis
- Adolescent
- Risk Factors
- Child
- Spondylitis, Ankylosing/genetics
- Spondylitis, Ankylosing/immunology
- Spondylitis, Ankylosing/diagnosis
- Spondylitis, Ankylosing/complications
- Genetic Predisposition to Disease
- Young Adult
- Sex Factors
- Skin Diseases/etiology
- Skin Diseases/immunology
- Skin Diseases/genetics
- Eye Diseases/etiology
- Eye Diseases/immunology
- Eye Diseases/diagnosis
- Eye Diseases/genetics
- Eye Diseases/epidemiology
- Phenotype
- Inflammatory Bowel Diseases/genetics
- Inflammatory Bowel Diseases/immunology
- Inflammatory Bowel Diseases/diagnosis
- Logistic Models
- Aged
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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, Missouri
| | - 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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6
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Sasaki E, Natori Y, Tokuda E, Kimura-Tsuchiya R, Suga J, Kanazawa K, Koguchi T, Kikuchi N, Okabe N, Murono S, Tachibana K, Soeda S, Shimabukuro M, Saji S. Association between specific human leukocyte antigen alleles and development of thyroid immune-related adverse event. Immunotherapy 2024:1-10. [PMID: 38889451 DOI: 10.1080/1750743x.2024.2353539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/03/2024] [Indexed: 06/20/2024] Open
Abstract
Aim: Inherent variations in human leukocyte antigen (HLA) alleles have been revealed epidemiologically to influence the development of autoimmune diseases. HLA alleles may thus also be associated with the development of immune-related adverse events (irAEs), such as thyroid irAE. Materials & methods: In this case-control study, 71 cancer patients who received immune checkpoint inhibitors were enrolled and HLA-genotyped and the frequency of HLA alleles was compared. Results: A*26:01, DPA1*01:03 and DPB1*02:01 were significantly more frequent in patients with thyroid irAE than in patients without any irAEs (35.0 vs 3.2% [p = 0.004], 80.0 vs 45.2% [p = 0.020] and 55.0 vs 25.8% [p = 0.044], respectively). Conclusion: A*26:01, DPA1*01:03 and DPB1*02:01 appear to be associated with thyroid irAE.
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Affiliation(s)
- Eisaku Sasaki
- Department of Medical Oncology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Yutaka Natori
- Department of Medical Oncology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Emi Tokuda
- Department of Medical Oncology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Reiko Kimura-Tsuchiya
- Department of Medical Oncology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Junko Suga
- Division of Cancer Genome Medicine, Cancer Center, Kyoto University Hospital, Kyoto, 606-8507, Japan
| | - Kenya Kanazawa
- Department of Pulmonary Medicine, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Tomoyuki Koguchi
- Department of Urology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Nobuyuki Kikuchi
- Department of Dermatology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Naoyuki Okabe
- Department of Chest Surgery, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Shigeyuki Murono
- Department of Otorhinolaryngology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Kazunoshin Tachibana
- Department of Breast Surgery, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Shu Soeda
- Department of Obstetrics & Gynecology, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Michio Shimabukuro
- Department of Diabetes, Endocrinology & Metabolism, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Shigehira Saji
- Department of Medical Oncology, Fukushima Medical University, Fukushima, 960-1295, Japan
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7
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Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R, Paul S, Smits G, Wareing S, Kim H, Pomilla C, Chong AY, Brandt DYC, Nielsen R, Neaves S, Timpson N, Crinklaw A, Lindestam Arlehamn CS, Rautanen A, Kizito D, Parks T, Auckland K, Elliott KE, Mills T, Ewer K, Edwards N, Fatumo S, Webb E, Peacock S, Jeffery K, van der Klis FRM, Kaleebu P, Vijayanand P, Peters B, Sette A, Cereb N, Sirima S, Madhi SA, Elliott AM, McVean G, Hill AVS, Sandhu MS. High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response. Nat Med 2024; 30:1384-1394. [PMID: 38740997 PMCID: PMC11108778 DOI: 10.1038/s41591-024-02944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.
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Affiliation(s)
- Alexander J Mentzer
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Alexander T Dilthey
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital of Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | | | | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Clare Cutland
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | | | - Sinu Paul
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Debora Y C Brandt
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Samuel Neaves
- Avon Longitudinal Study of Parents and Children at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicolas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Austin Crinklaw
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Anna Rautanen
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dennison Kizito
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Tom Parks
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Kate E Elliott
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tara Mills
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nick Edwards
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine London, London, UK
| | - Emily Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | - Bjorn Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison M Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
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8
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Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E. Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis. Nat Commun 2024; 15:2568. [PMID: 38531883 PMCID: PMC10966072 DOI: 10.1038/s41467-023-44512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/15/2023] [Indexed: 03/28/2024] Open
Abstract
Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.
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Affiliation(s)
- Pooja Middha
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lydia Yao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zoe Quandt
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Cardenas
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina J Falcon
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew A Gubens
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University of Medicine, Stanford, CA, USA
| | - Khaleeq Khan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Min Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Megan H Murray
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kristin Werking
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luna Jia Zhan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Temerty School of Medicine, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Center for Genes, Environment and Health, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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9
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Ishimoto T, Arakawa Y, Vural S, Stöhr J, Vollmer S, Galinski A, Siewert K, Rühl G, Poluektov Y, Delcommenne M, Horvath O, He M, Summer B, Pohl R, Alharbi R, Dornmair K, Arakawa A, Prinz JC. Multiple environmental antigens may trigger autoimmunity in psoriasis through T-cell receptor polyspecificity. Front Immunol 2024; 15:1374581. [PMID: 38524140 PMCID: PMC10958380 DOI: 10.3389/fimmu.2024.1374581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Psoriasis is a T-cell mediated autoimmune skin disease. HLA-C*06:02 is the main psoriasis-specific risk gene. Using a Vα3S1/Vβ13S1 T-cell receptor (TCR) from a lesional psoriatic CD8+ T-cell clone we had discovered that, as an underlying pathomechanism, HLA-C*06:02 mediates an autoimmune response against melanocytes in psoriasis, and we had identified an epitope from ADAMTS-like protein 5 (ADAMTSL5) as a melanocyte autoantigen. The conditions activating the psoriatic autoimmune response in genetically predisposed individuals throughout life remain incompletely understood. Here, we aimed to identify environmental antigens that might trigger autoimmunity in psoriasis because of TCR polyspecificity. Methods We screened databases with the peptide recognition motif of the Vα3S1/Vβ13S1 TCR for environmental proteins containing peptides activating this TCR. We investigated the immunogenicity of these peptides for psoriasis patients and healthy controls by lymphocyte stimulation experiments and peptide-loaded HLA-C*06:02 tetramers. Results We identified peptides from wheat, Saccharomyces cerevisiae, microbiota, tobacco, and pathogens that activated both the Vα3S1/Vβ13S1 TCR and CD8+ T cells from psoriasis patients. Using fluorescent HLA-C*06:02 tetramers loaded with ADAMTSL5 or wheat peptides, we find that the same CD8+ T cells may recognize both autoantigen and environmental antigens. A wheat-free diet could alleviate psoriasis in several patients. Discussion Our results show that due to TCR polyspecificity, several environmental antigens corresponding to previously suspected psoriasis risk conditions converge in the reactivity of a pathogenic psoriatic TCR and might thus be able to stimulate the psoriatic autoimmune response against melanocytes. Avoiding the corresponding environmental risk factors could contribute to the management of psoriasis.
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Affiliation(s)
- Tatsushi Ishimoto
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Yukiyasu Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Secil Vural
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Julia Stöhr
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Sigrid Vollmer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Katherina Siewert
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Geraldine Rühl
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | | | | | - Orsolya Horvath
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Mengwen He
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Burkhard Summer
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Ralf Pohl
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Rehab Alharbi
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Akiko Arakawa
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Jörg C. Prinz
- Department of Dermatology and Allergy, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
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10
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O'Brien CL, Summers KM, Martin NM, Carter-Cusack D, Yang Y, Barua R, Dixit OVA, Hume DA, Pavli P. The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease. Hum Genet 2024; 143:233-261. [PMID: 38421405 PMCID: PMC11043138 DOI: 10.1007/s00439-024-02642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024]
Abstract
The differentiation of resident intestinal macrophages from blood monocytes depends upon signals from the macrophage colony-stimulating factor receptor (CSF1R). Analysis of genome-wide association studies (GWAS) indicates that dysregulation of macrophage differentiation and response to microorganisms contributes to susceptibility to chronic inflammatory bowel disease (IBD). Here, we analyzed transcriptomic variation in monocyte-derived macrophages (MDM) from affected and unaffected sib pairs/trios from 22 IBD families and 6 healthy controls. Transcriptional network analysis of the data revealed no overall or inter-sib distinction between affected and unaffected individuals in basal gene expression or the temporal response to lipopolysaccharide (LPS). However, the basal or LPS-inducible expression of individual genes varied independently by as much as 100-fold between subjects. Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, variation in early expression of IL1B was significantly associated with local SNV genotype and with subsequent peak expression of target genes including IL23A, CXCL1, CXCL3, CXCL8 and NLRP3. Similarly, variation in early IFNB1 expression was correlated with subsequent expression of IFN target genes. Our results support the view that gene-specific dysregulation in macrophage adaptation to the intestinal milieu is associated with genetic susceptibility to IBD.
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Affiliation(s)
- Claire L O'Brien
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Natalia M Martin
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rasel Barua
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Ojas V A Dixit
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
| | - Paul Pavli
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia.
- School of Medicine and Psychology, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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11
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Qiu X, Teng J, Wang N, Cao L, Cheng C, Su C, Dong Y, Wang F, Chen W. Transcriptomic analysis reveals the potential crosstalk genes and immune relationship between Crohn's disease and atrial fibrillation. J Thorac Dis 2024; 16:1247-1261. [PMID: 38505024 PMCID: PMC10944785 DOI: 10.21037/jtd-23-1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024]
Abstract
Background At present, there is a paucity of research on the link between Crohn's disease (CD) and atrial fibrillation (AF). Nevertheless, both ailments are thought to entail inflammatory and autoimmune processes, and emerging evidence indicates that individuals with CD may face an elevated risk of AF. To shed light on this issue, our study seeks to explore the possibility of shared genes, pathways, and immune cells between these two conditions. Methods We retrieved the gene expression profiles of both CD and AF from the Gene Expression Omnibus (GEO) database and subjected them to analysis. Afterward, we utilized the weighted gene co-expression network analysis (WGCNA) to identify shared genes, which were then subjected to further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Furthermore, we employed a rigorous analytical approach by screening hub genes through both least absolute shrinkage and selection operator (LASSO) regression and support vector machine (SVM), and subsequently constructing a receiver operating characteristic (ROC) curve based on the screening outcomes. Finally, we utilized single-sample gene set enrichment analysis (ssGSEA) to comprehensively evaluate the levels of infiltration of 28 immune cells within the expression profile and their potential association with the shared hub genes. Results Using the WGCNA method, we identified 30 genes that appear to be involved in the pathological progression of both AF and CD. Through GO enrichment analysis on the key gene modules derived from WGCNA, we observed a significant enrichment of pathways related to major histocompatibility complex (MHC) and antigen processing. By leveraging the intersection of LASSO and SVM algorithms, we were able to pinpoint two overlapping genes, namely CXCL16 and HLA-DPB1. Additionally, we evaluated the infiltration of immune cells and observed the upregulation of CD4+ and CD8+ T cells, as well as dendritic cells in patients with AF and CD. Conclusions By employing bioinformatics tools, we conducted an investigation with the objective of elucidating the genetic foundations that connect AF and CD. This study culminated in the identification of CXCL16 and HLA-DPB1 as the most substantial genes implicated in the development of both disorders. Our findings suggest that the immune responses mediated by CD4+ and CD8+ T cells, along with dendritic cells, may hold a crucial role in the intricate interplay between AF and CD.
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Affiliation(s)
- Xiaohan Qiu
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Junlin Teng
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Ning Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Luying Cao
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Congyi Cheng
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Cong Su
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Youran Dong
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Fen Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Wenqiang Chen
- National Key Laboratory for Innovation and Transformation of Luobing Theory, the Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Jinan, China
- Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
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12
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Jia K, Shen J. Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives. Cell Biosci 2024; 14:29. [PMID: 38403629 PMCID: PMC10895848 DOI: 10.1186/s13578-024-01204-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Crohn's disease (CD) is regarded as a lifelong progressive disease affecting all segments of the intestinal tract and multiple organs. Based on genome-wide association studies (GWAS) and gene expression data, transcriptome-wide association studies (TWAS) can help identify susceptibility genes associated with pathogenesis and disease behavior. In this review, we overview seven reported TWASs of CD, summarize their study designs, and discuss the key methods and steps used in TWAS, which affect the prioritization of susceptibility genes. This article summarized the screening of tissue-specific susceptibility genes for CD, and discussed the reported potential pathological mechanisms of overlapping susceptibility genes related to CD in a certain tissue type. We observed that ileal lipid-related metabolism and colonic extracellular vesicles may be involved in the pathogenesis of CD by performing GO pathway enrichment analysis for susceptibility genes. We further pointed the low reproducibility of TWAS associated with CD and discussed the reasons for these issues, strategies for solving them. In the future, more TWAS are needed to be designed into large-scale, unified cohorts, unified analysis pipelines, and fully classified databases of expression trait loci.
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Affiliation(s)
- Keyu Jia
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China
| | - Jun Shen
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Research Center, Ren Ji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China.
- NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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13
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Krishna C, Tervi A, Saffern M, Wilson EA, Yoo SK, Mars N, Roudko V, Cho BA, Jones SE, Vaninov N, Selvan ME, Gümüş ZH, Lenz TL, Merad M, Boffetta P, Martínez-Jiménez F, Ollila HM, Samstein RM, Chowell D. An immunogenetic basis for lung cancer risk. Science 2024; 383:eadi3808. [PMID: 38386728 DOI: 10.1126/science.adi3808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Cancer risk is influenced by inherited mutations, DNA replication errors, and environmental factors. However, the influence of genetic variation in immunosurveillance on cancer risk is not well understood. Leveraging population-level data from the UK Biobank and FinnGen, we show that heterozygosity at the human leukocyte antigen (HLA)-II loci is associated with reduced lung cancer risk in smokers. Fine-mapping implicated amino acid heterozygosity in the HLA-II peptide binding groove in reduced lung cancer risk, and single-cell analyses showed that smoking drives enrichment of proinflammatory lung macrophages and HLA-II+ epithelial cells. In lung cancer, widespread loss of HLA-II heterozygosity (LOH) favored loss of alleles with larger neopeptide repertoires. Thus, our findings nominate genetic variation in immunosurveillance as a critical risk factor for lung cancer.
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Affiliation(s)
- Chirag Krishna
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anniina Tervi
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Miriam Saffern
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Wilson
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nina Mars
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Vladimir Roudko
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Byuri Angela Cho
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel Edward Jones
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Natalie Vaninov
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Miriam Merad
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paolo Boffetta
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy
- Stony Brook Cancer Center, Stony Brook University, New York, NY 11794, USA
| | - Francisco Martínez-Jiménez
- Vall d'Hebron Institute of Oncology, Barcelona 08035, Spain
- Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Hanna M Ollila
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert M Samstein
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Radiation Oncology, Mount Sinai Hospital, New York, NY 10029, USA
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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14
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Kim K, Oh SJ, Lee J, Kwon A, Yu CY, Kim S, Choi CH, Kang SB, Kim TO, Park DI, Lee CK. Regulatory Variants on the Leukocyte Immunoglobulin-Like Receptor Gene Cluster are Associated with Crohn's Disease and Interact with Regulatory Variants for TAP2. J Crohns Colitis 2024; 18:47-53. [PMID: 37523193 DOI: 10.1093/ecco-jcc/jjad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] has a complex polygenic aetiology with high heritability. There is ongoing effort to identify novel variants associated with susceptibility to CD through a genome-wide association study [GWAS] in large Korean populations. METHODS Genome-wide variant data from 902 Korean patients with CD and 72 179 controls were used to assess the genetic associations in a meta-analysis with previous Korean GWAS results from 1621 patients with CD and 4419 controls. Epistatic interactions between CD-risk variants of interest were tested using a multivariate logistic regression model with an interaction term. RESULTS We identified two novel genetic associations with the risk of CD near ZBTB38 and within the leukocyte immunoglobulin-like receptor [LILR] gene cluster [p < 5 × 10-8], with highly consistent effect sizes between the two independent Korean cohorts. CD-risk variants in the LILR locus are known quantitative trait loci [QTL] for multiple LILR genes, of which LILRB2 directly interacts with various ligands including MHC class I molecules. The LILR lead variant exhibited a significant epistatic interaction with CD-associated regulatory variants for TAP2 involved in the antigen presentation of MHC class I molecules [p = 4.11 × 10-4], showing higher CD-risk effects of the TAP2 variant in individuals carrying more risk alleles of the LILR lead variant (odds ratio [OR] = 0.941, p = 0.686 in non-carriers; OR = 1.45, p = 2.51 × 10-4 in single-copy carriers; OR = 2.38, p = 2.76 × 10-6 in two-copy carriers). CONCLUSIONS This study demonstrated that genetic variants at two novel susceptibility loci and the epistatic interaction between variants in LILR and TAP2 loci confer a risk of CD.
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Affiliation(s)
- Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Shin Ju Oh
- Department of Gastroenterology, Center for Crohn's and Colitis, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Junho Lee
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Ayeong Kwon
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Chae-Yeon Yu
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Sangsoo Kim
- Department of Bioinformatics, Soongsil University, Seoul, Republic of Korea
| | - Chang Hwan Choi
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sang-Bum Kang
- Department of Internal Medicine, College of Medicine, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Tae Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Dong Il Park
- Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang Kyun Lee
- Department of Gastroenterology, Center for Crohn's and Colitis, Kyung Hee University College of Medicine, Seoul, Republic of Korea
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15
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ElAbd H, Franke A. Mass Spectrometry-Based Immunopeptidomics of Peptides Presented on Human Leukocyte Antigen Proteins. Methods Mol Biol 2024; 2758:425-443. [PMID: 38549028 DOI: 10.1007/978-1-0716-3646-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Human leukocyte antigen (HLA) proteins are a group of glycoproteins that are expressed at the cell surface, where they present peptides to T cells through physical interactions with T-cell receptors (TCRs). Hence, characterizing the set of peptides presented by HLA proteins, referred to hereafter as the immunopeptidome, is fundamental for neoantigen identification, immunotherapy, and vaccine development. As a result, different methods have been used over the years to identify peptides presented by HLA proteins, including competition assays, peptide microarrays, and yeast display systems. Nonetheless, over the last decade, mass spectrometry-based immunopeptidomics (MS-immunopeptidomics) has emerged as the gold-standard method for identifying peptides presented by HLA proteins. MS-immunopeptidomics enables the direct identification of the immunopeptidome in different tissues and cell types in different physiological and pathological states, for example, solid tumors or virally infected cells. Despite its advantages, it is still an experimentally and computationally challenging technique with different aspects that need to be considered before planning an MS-immunopeptidomics experiment, while conducting the experiment and with analyzing and interpreting the results. Hence, we aim in this chapter to provide an overview of this method and discuss different practical considerations at different stages starting from sample collection until data analysis. These points should aid different groups aiming at utilizing MS-immunopeptidomics, as well as, identifying future research directions to improve the method.
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Affiliation(s)
- Hesham ElAbd
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany.
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16
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Duchniewicz M, Lee JYW, Menon DK, Needham EJ. Candidate Genetic and Molecular Drivers of Dysregulated Adaptive Immune Responses After Traumatic Brain Injury. J Neurotrauma 2024; 41:3-12. [PMID: 37376743 DOI: 10.1089/neu.2023.0187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Abstract Neuroinflammation is a significant and modifiable cause of secondary injury after traumatic brain injury (TBI), driven by both central and peripheral immune responses. A substantial proportion of outcome after TBI is genetically mediated, with an estimated heritability effect of around 26%, but because of the comparatively small datasets currently available, the individual drivers of this genetic effect have not been well delineated. A hypothesis-driven approach to analyzing genome-wide association study (GWAS) datasets reduces the burden of multiplicity testing and allows variants with a high prior biological probability of effect to be identified where sample size is insufficient to withstand data-driven approaches. Adaptive immune responses show substantial genetically mediated heterogeneity and are well established as a genetic source of risk for numerous disease states; importantly, HLA class II has been specifically identified as a locus of interest in the largest TBI GWAS study to date, highlighting the importance of genetic variance in adaptive immune responses after TBI. In this review article we identify and discuss adaptive immune system genes that are known to confer strong risk effects for human disease, with the dual intentions of drawing attention to this area of immunobiology, which, despite its importance to the field, remains under-investigated in TBI and presenting high-yield testable hypotheses for application to TBI GWAS datasets.
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Affiliation(s)
- Michał Duchniewicz
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - John Y W Lee
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David K Menon
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward J Needham
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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17
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Zhang J, Chen L, Xu Q, Zou Y, Sun F, Zhou Q, Luo X, Li Y, Chen C, Zhang S, Xiong F, Yang P, Liu S, Wang CY. Ubc9 regulates the expression of MHC II in dendritic cells to enhance DSS-induced colitis by mediating RBPJ SUMOylation. Cell Death Dis 2023; 14:737. [PMID: 37957143 PMCID: PMC10643556 DOI: 10.1038/s41419-023-06266-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
SUMOylation is an evolutionary conserved regulatory mechanism, in which Ubc9 is the only E2 conjugating enzyme. Previous studies demonstrated that SUMOylation is involved in multiple biological processes, but its role in dendritic cells (DCs) remains to be fully addressed. Herein in this report, we found that DCs deficient in Ubc9 protected mice from dextran sulfate sodium (DSS)-induced colitis, as evidenced by the ameliorated weight loss, colon length, and disrupted colon structure. Mechanistically, Ubc9 mediated SUMOylation of RBPJ, by which it stabilized RBPJ from ubiquitin-mediated degradation to enhance its transcriptional activity, while Ciita, a critical transcription factor, is a direct target downstream of RBPJ, which forms an enhanceosome complex to transcribe the expression of MHC II genes. Therefore, loss of Ubc9 abolished RBPJ SUMOylation, which was coupled with reduced Ciita transcription, thereby attenuating the expression of MHC class II genes. As a consequence of defective MHC II expression, Ubc9-/- DCs were featured by the impaired capability to process antigen and to prime effector CD4+ T cells, thereby protecting mice from DSS-induced colitis. Together, our results shed novel insight into the understanding of SUMOylation in the regulation of DC functions in pathological conditions.
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Affiliation(s)
- Jing Zhang
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Longmin Chen
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Rheumatology and Immunology, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianqian Xu
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Zou
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Sun
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Zhou
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Luo
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cai Chen
- Department of Endocrinology, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Xiong
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Yang
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiwei Liu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, the Key Laboratory of Endocrine and Metabolic Diseases of Shanxi Province, Taiyuan, China.
| | - Cong-Yi Wang
- Department of Respiratory and Critical Care Medicine, the Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, the Key Laboratory of Endocrine and Metabolic Diseases of Shanxi Province, Taiyuan, China.
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18
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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 PMCID: PMC11036449 DOI: 10.1136/gutjnl-2023-329689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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19
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Tsai YY, Qu C, Bonner JD, Sanz-Pamplona R, Lindsey SS, Melas M, McDonnell KJ, Idos GE, Walker CP, Tsang KK, Da Silva DM, Moratalla-Navarro F, Maoz A, Rennert HS, Kast WM, Greenson JK, Moreno V, Rennert G, Gruber SB, Schmit SL. Heterozygote advantage at HLA class I and II loci and reduced risk of colorectal cancer. Front Immunol 2023; 14:1268117. [PMID: 37942321 PMCID: PMC10627840 DOI: 10.3389/fimmu.2023.1268117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023] Open
Abstract
Objective Reduced diversity at Human Leukocyte Antigen (HLA) loci may adversely affect the host's ability to recognize tumor neoantigens and subsequently increase disease burden. We hypothesized that increased heterozygosity at HLA loci is associated with a reduced risk of developing colorectal cancer (CRC). Methods We imputed HLA class I and II four-digit alleles using genotype data from a population-based study of 5,406 cases and 4,635 controls from the Molecular Epidemiology of Colorectal Cancer Study (MECC). Heterozygosity at each HLA locus and the number of heterozygous genotypes at HLA class -I (A, B, and C) and HLA class -II loci (DQB1, DRB1, and DPB1) were quantified. Logistic regression analysis was used to estimate the risk of CRC associated with HLA heterozygosity. Individuals with homozygous genotypes for all loci served as the reference category, and the analyses were adjusted for sex, age, genotyping platform, and ancestry. Further, we investigated associations between HLA diversity and tumor-associated T cell repertoire features, as measured by tumor infiltrating lymphocytes (TILs; N=2,839) and immunosequencing (N=2,357). Results Individuals with all heterozygous genotypes at all three class I genes had a reduced odds of CRC (OR: 0.74; 95% CI: 0.56-0.97, p= 0.031). A similar association was observed for class II loci, with an OR of 0.75 (95% CI: 0.60-0.95, p= 0.016). For class-I and class-II combined, individuals with all heterozygous genotypes had significantly lower odds of developing CRC (OR: 0.66, 95% CI: 0.49-0.87, p= 0.004) than those with 0 or one heterozygous genotype. HLA class I and/or II diversity was associated with higher T cell receptor (TCR) abundance and lower TCR clonality, but results were not statistically significant. Conclusion Our findings support a heterozygote advantage for the HLA class-I and -II loci, indicating an important role for HLA genetic variability in the etiology of CRC.
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Affiliation(s)
- Ya-Yu Tsai
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Chenxu Qu
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Joseph D. Bonner
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Hospital Universitario Lozano Blesa, Aragon Health Research Institute (IISA), ARAID Foundation, Aragon Government, Zaragoza, Spain
| | - Sidney S. Lindsey
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Marilena Melas
- Molecular Diagnostics, New York Genome Center, New York, NY, United States
| | - Kevin J. McDonnell
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Gregory E. Idos
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Christopher P. Walker
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Kevin K. Tsang
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Diane M. Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Ferran Moratalla-Navarro
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Asaf Maoz
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Hedy S. Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - W. Martin Kast
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| | - Joel K. Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Gad Rennert
- B. Rappaport Faculty of Medicine, Technion and the Association for Promotion of Research in Precision Medicine (APRPM), Haifa, Israel
| | - Stephen B. Gruber
- Center for Precision Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Stephanie L. Schmit
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
- Population and Cancer Prevention Program, Case Comprehensive Cancer Center, Cleveland, OH, United States
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20
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Liu R, Li D, Haritunians T, Ruan Y, Daly MJ, Huang H, McGovern DP. Profiling the inflammatory bowel diseases using genetics, serum biomarkers, and smoking information. iScience 2023; 26:108053. [PMID: 37841595 PMCID: PMC10568094 DOI: 10.1016/j.isci.2023.108053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/28/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are two etiologically related yet distinctive subtypes of the inflammatory bowel diseases (IBD). Differentiating CD from UC can be challenging using conventional clinical approaches in a subset of patients. We designed and evaluated a novel molecular-based prediction model aggregating genetics, serum biomarkers, and tobacco smoking information to assist the diagnosis of CD and UC in over 30,000 samples. A joint model combining genetics, serum biomarkers and smoking explains 46% (42-50%, 95% CI) of phenotypic variation. Despite modest overlaps with serum biomarkers, genetics makes unique contributions to distinguishing IBD subtypes. Smoking status only explains 1% (0-6%, 95% CI) of the phenotypic variance suggesting it may not be an effective biomarker. This study reveals that molecular-based models combining genetics, serum biomarkers, and smoking information could complement current diagnostic strategies and help classify patients based on biologic state rather than imperfect clinical parameters.
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Affiliation(s)
- Ruize Liu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yunfeng Ruan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dermot P.B. McGovern
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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21
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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] [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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22
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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23
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Baumdick ME, Niehrs A, Degenhardt F, Schwerk M, Hinrichs O, Jordan-Paiz A, Padoan B, Wegner LHM, Schloer S, Zecher BF, Malsy J, Joshi VR, Illig C, Schröder-Schwarz J, Möller KJ, Martin MP, Yuki Y, Ozawa M, Sauter J, Schmidt AH, Perez D, Giannou AD, Carrington M, Davis RS, Schumacher U, Sauter G, Huber S, Puelles VG, Melling N, Franke A, Altfeld M, Bunders MJ. HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44 + Natural Killer Cells in Ulcerative Colitis. Gastroenterology 2023; 165:946-962.e13. [PMID: 37454979 PMCID: PMC10529779 DOI: 10.1053/j.gastro.2023.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/25/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND & AIMS Ulcerative colitis (UC) is characterized by severe inflammation and destruction of the intestinal epithelium, and is associated with specific risk single nucleotide polymorphisms in HLA class II. Given the recently discovered interactions between subsets of HLA-DP molecules and the activating natural killer (NK) cell receptor NKp44, genetic associations of UC and HLA-DP haplotypes and their functional implications were investigated. METHODS HLA-DP haplotype and UC risk association analyses were performed (UC: n = 13,927; control: n = 26,764). Expression levels of HLA-DP on intestinal epithelial cells (IECs) in individuals with and without UC were quantified. Human intestinal 3-dimensional (3D) organoid cocultures with human NK cells were used to determine functional consequences of interactions between HLA-DP and NKp44. RESULTS These studies identified HLA-DPA1∗01:03-DPB1∗04:01 (HLA-DP401) as a risk haplotype and HLA-DPA1∗01:03-DPB1∗03:01 (HLA-DP301) as a protective haplotype for UC in European populations. HLA-DP expression was significantly higher on IECs of individuals with UC compared with controls. IECs in human intestinal 3D organoids derived from HLA-DP401pos individuals showed significantly stronger binding of NKp44 compared with HLA-DP301pos IECs. HLA-DP401pos IECs in organoids triggered increased degranulation and tumor necrosis factor production by NKp44+ NK cells in cocultures, resulting in enhanced epithelial cell death compared with HLA-DP301pos organoids. Blocking of HLA-DP401-NKp44 interactions (anti-NKp44) abrogated NK cell activity in cocultures. CONCLUSIONS We identified an UC risk HLA-DP haplotype that engages NKp44 and activates NKp44+ NK cells, mediating damage to intestinal epithelial cells in an HLA-DP haplotype-dependent manner. The molecular interaction between NKp44 and HLA-DP401 in UC can be targeted by therapeutic interventions to reduce NKp44+ NK cell-mediated destruction of the intestinal epithelium in UC.
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Affiliation(s)
- Martin E Baumdick
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Annika Niehrs
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Maria Schwerk
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ole Hinrichs
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Ana Jordan-Paiz
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Benedetta Padoan
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Lucy H M Wegner
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Sebastian Schloer
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany; Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation, and Cells in Motion Interfaculty Center, University of Münster, Münster, Germany
| | - Britta F Zecher
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob Malsy
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Vinita R Joshi
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Christin Illig
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Jennifer Schröder-Schwarz
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kimberly J Möller
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | | | | | - Daniel Perez
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anastasios D Giannou
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Randall S Davis
- Departments of Medicine, Microbiology, and Biochemistry and Molecular Genetics, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Kidney Health, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Nathaniel Melling
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Marcus Altfeld
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Madeleine J Bunders
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Section of Regenerative Medicine and Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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24
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Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E. Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.15.23289680. [PMID: 37292751 PMCID: PMC10246037 DOI: 10.1101/2023.05.15.23289680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immune checkpoint inhibitors (ICIs) are a remarkable advancement in cancer therapeutics; however, a substantial proportion of patients develop severe immune-related adverse events (irAEs). Understanding and predicting irAEs is a key to advancing precision immuno-oncology. Immune checkpoint inhibitor-mediated colitis (IMC) is a significant complication from ICI and can have life-threatening consequences. Based on clinical presentation, IMC mimics inflammatory bowel disease, however the link is poorly understood. We hypothesized that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) may predispose to IMC. We developed and validated polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and assessed the role of each of these PRSs on IMC in a cohort of 1,316 patients with non-small cell lung cancer who received ICIs. Prevalence of all-grade IMC in our cohort was 4% (55 cases), and for severe IMC, 2.5% (32 cases). The PRSUC predicted the development of all-grade IMC (HR=1.34 per standard deviation [SD], 95% CI=1.02-1.76, P=0.04) and severe IMC (HR=1.62 per SD, 95% CI=1.12-2.35, P=0.01). PRSCD was not associated with IMC or severe IMC. The association between PRSUC and IMC (all-grade and severe) was consistent in an independent pan-cancer cohort of patients treated with ICIs. Furthermore, PRSUC predicted severe IMC among patients treated with combination ICIs (OR = 2.20 per SD, 95% CI = 1.07-4.53, P=0.03). This is the first study to demonstrate the potential clinical utility of a PRS for ulcerative colitis in identifying patients receiving ICI at high risk of developing IMC, where risk reduction and close monitoring strategies could help improve overall patient outcomes.
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Affiliation(s)
- Pooja Middha
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rohit Thummalapalli
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael J Betti
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lydia Yao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zoe Quandt
- Division of Endocrinology and Metabolism, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eduardo Cardenas
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina J Falcon
- Fiona and Stanley Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew A Gubens
- Medical Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Weill Cornell Medical Center, New York, NY, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University of Medicine, Stanford, CA, USA
| | - Khaleeq Khan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Min Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Megan H Murray
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Kristin Werking
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luna Jia Zhan
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Justin M Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Temerty School of Medicine, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, Center for Genes, Environment and Health and Institute for Human Genetics, University of California San Francisco, San Francisco, California
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25
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Caliendo G, D'Elia G, Makker J, Passariello L, Albanese L, Molinari AM, Vietri MT. Biological, genetic and epigenetic markers in ulcerative colitis. Adv Med Sci 2023; 68:386-395. [PMID: 37813048 DOI: 10.1016/j.advms.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/15/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
In this review, we have summarized the existing knowledge of ulcerative colitis (UC) markers based on current literature, specifically, the roles of potential new biomarkers, such as circulating, fecal, genetic, and epigenetic alterations, in UC onset, disease activity, and in therapy response. UC is a complex multifactorial inflammatory disease. There are many invasive and non-invasive diagnostic methods in UC, including several laboratory markers which are employed in diagnosis and disease assessment; however, colonoscopy remains the most widely used method. Common laboratory abnormalities currently used in the clinical practice include inflammation-induced alterations, serum autoantibodies, and antibodies against bacterial antigens. Other new serum and fecal biomarkers are supportive in diagnosis and monitoring disease activity and therapy response; and potential salivary markers are currently being evaluated as well. Several UC-related genetic and epigenetic alterations are implied in its pathogenesis and therapeutic response. Moreover, the use of artificial intelligence in the integration of laboratory biomarkers and big data could potentially be useful in clinical translation and precision medicine in UC management.
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Affiliation(s)
- Gemma Caliendo
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna D'Elia
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Jasmine Makker
- Department of GKT School of Medical Education, King's College London, London, UK
| | - Luana Passariello
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Luisa Albanese
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Maria Molinari
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Vietri
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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26
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Sakaue S, Gurajala S, Curtis M, Luo Y, Choi W, Ishigaki K, Kang JB, Rumker L, Deutsch AJ, Schönherr S, Forer L, LeFaive J, Fuchsberger C, Han B, Lenz TL, de Bakker PIW, Okada Y, Smith AV, Raychaudhuri S. Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease. Nat Protoc 2023; 18:2625-2641. [PMID: 37495751 PMCID: PMC10786448 DOI: 10.1038/s41596-023-00853-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/27/2023] [Indexed: 07/28/2023]
Abstract
The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software ( https://github.com/immunogenomics/HLA_analyses_tutorial ). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.
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Affiliation(s)
- Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saisriram Gurajala
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle Curtis
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Aaron J Deutsch
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jonathon LeFaive
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Paul I W de Bakker
- Data and Computational Sciences, Vertex Pharmaceuticals, Boston, MA, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Albert V Smith
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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27
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Berner F, Flatz L. Autoimmunity in immune checkpoint inhibitor-induced immune-related adverse events: A focus on autoimmune skin toxicity and pneumonitis. Immunol Rev 2023; 318:37-50. [PMID: 37548043 DOI: 10.1111/imr.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy. However, their use is frequently associated with immune-related adverse events (irAEs) potentially affecting any organ. The mechanisms mediating such irAEs remain poorly understood and biomarkers to predict the development of irAEs are lacking. Growing evidence shows the importance of self-antigens in mediating irAEs during ICI therapy, in particular the well-described melanocyte differentiation antigens in melanoma patients. This review will focus on two novel classes of self-antigens involved in mediating autoimmune skin toxicity and pneumonitis in non-small cell lung cancer patients treated with immunotherapy. T cells specific for these self-antigens are thought to not only mediate irAEs but are thought to simultaneously mediate anti-tumor responses and are therefore associated with both autoimmune toxicity and response to ICI therapy. We further discuss emerging cellular and proteomic immune signatures of irAEs that may serve as biomarkers to help predict which patients are at higher risk of developing these irAEs. The determination of new tumor antigens involved in ICI therapy and the identification of related biomarkers brings us a step forward in the mechanistic understanding of ICIs and will help to monitor patients at higher risk of developing irAEs. Lastly, we discuss the current challenges in collecting research samples for the study of ICI-related mechanisms and in distinguishing between immune signatures of response and those of irAEs.
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Affiliation(s)
- Fiamma Berner
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Dermatology, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
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28
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Akiyama Y, Sonehara K, Maeda D, Katoh H, Naito T, Yamamoto K, Morisaki T, Ishikawa S, Ushiku T, Kume H, Homma Y, Okada Y. Genome-wide association study identifies risk loci within the major histocompatibility complex region for Hunner-type interstitial cystitis. Cell Rep Med 2023; 4:101114. [PMID: 37467720 PMCID: PMC10394254 DOI: 10.1016/j.xcrm.2023.101114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 04/26/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Hunner-type interstitial cystitis (HIC) is a rare, chronic inflammatory disease of the urinary bladder with unknown etiology and genetic background. Here, we conduct a genome-wide association study of 144 patients with HIC and 41,516 controls of Japanese ancestry. The genetic variant, rs1794275, in the major histocompatibility complex (MHC) region (chromosome 6p21.3) is associated with HIC risk (odds ratio [OR] = 2.32; p = 3.4 × 10-9). The association is confirmed in a replication set of 26 cases and 1,026 controls (p = 0.014). Fine mapping demonstrates the contribution to the disease risk of a completely linked haplotype of three human leukocyte antigen HLA-DQβ1 amino acid positions, 71, 74, and 75 (OR = 1.94; p = 5 × 10-8) and of HLA-DPβ1 amino acid position 178, which tags HLA-DPB1∗04:02 (OR = 2.35; p = 7.5 × 10-8). The three HLA-DQβ1 amino acid positions are located together at the peptide binding groove, suggesting their functional importance in antigen presentation. Our study reveals genetic contributions to HIC risk that may be associated with class II MHC molecule antigen presentation.
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Affiliation(s)
- Yoshiyuki Akiyama
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyuto Sonehara
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Daichi Maeda
- Department of Molecular and Cellular Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan; BioBank Japan, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Interstitial Cystitis Medicine, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - Yukinori Okada
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan; The Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
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29
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Teng YS, Yu S. Molecular Mechanisms of Cutaneous Immune-Related Adverse Events (irAEs) Induced by Immune Checkpoint Inhibitors. Curr Oncol 2023; 30:6805-6819. [PMID: 37504358 PMCID: PMC10378098 DOI: 10.3390/curroncol30070498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023] Open
Abstract
Over the past few decades, immune checkpoint inhibitors (ICIs) have emerged as promising therapeutic options for the treatment of various cancers. These novel treatments effectively target key mediators of immune checkpoint pathways. Currently, ICIs primarily consist of monoclonal antibodies that specifically block cytotoxic T-lymphocyte antigen 4 (CTLA-4), programmed cell death 1 (PD-1), programmed cell death-ligand 1 (PD-L1), and lymphocyte activation gene 3 protein (LAG-3). Despite the notable efficacy of ICIs in cancer treatment, they can also trigger immune-related adverse events (irAEs), which present as autoimmune-like or inflammatory conditions. IrAEs have the potential to affect multiple organ systems, with cutaneous toxicities being the most commonly observed. Although cutaneous irAEs are typically of low-grade severity and can usually be managed effectively, there are cases where severe irAEs can become life-threatening. Therefore, early recognition and a comprehensive understanding of the mechanisms underlying cutaneous irAEs are crucial for improving clinical outcomes in cancer patients. However, the precise pathogenesis of cutaneous irAEs remains unclear. This review focuses on the skin manifestations induced by ICIs, the prognosis related to cutaneous irAEs, and the exploration of potential mechanisms involved in cutaneous irAEs.
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Affiliation(s)
- Yi-Shan Teng
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Sebastian Yu
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Department of Dermatology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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30
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Mamootil D. Pediatric Ulcerative Colitis in Siblings. Cureus 2023; 15:e40829. [PMID: 37489193 PMCID: PMC10363254 DOI: 10.7759/cureus.40829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2023] [Indexed: 07/26/2023] Open
Abstract
This case report discusses a nine-year-old female that presented with abdominal pain, diarrhea, and weight loss, suggestive of inflammatory bowel disease (IBD). She had an older brother previously diagnosed with ulcerative colitis (UC), which raised suspicion that she may have the same condition. CT scan of the abdomen/pelvis showed signs of bowel thickening. Stool studies revealed elevated inflammatory markers including lactoferrin and calprotectin, as well as occult blood. She underwent a colonoscopy and rectal biopsy which further confirmed the diagnosis of ulcerative colitis. This article aims to discuss the clinical presentation, role of genetic factors, diagnostic workup, and therapeutic management of ulcerative colitis in the pediatric population.
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Affiliation(s)
- Divya Mamootil
- Internal Medicine, Ascension St. Agnes Hospital, Baltimore, USA
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31
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Xu D, Chen Y, Gao X, Xie W, Wang Y, Shen J, Yang G, Xie B. The genetically predicted causal relationship of inflammatory bowel disease with bone mineral density and osteoporosis: evidence from two-sample Mendelian randomization. Front Immunol 2023; 14:1148107. [PMID: 37275908 PMCID: PMC10233018 DOI: 10.3389/fimmu.2023.1148107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023] Open
Abstract
Background Many existing studies indicated that patients with inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), tend to have the risk of low total body bone mineral density (BMD), and are more likely to have osteoporosis (OS). To determine the causal relationship between IBD and bone metabolic disorders, we herein performed a two-sample Mendelian randomization analysis (TSMR) using publicly available summary statistics. Methods Summary statistics of total body BMD, OS and IBD were downloaded from the Open Genome-Wide Association Study (GWAS), FinnGen consortium and International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). The European and East Asian populations have consisted in this Mendelian Randomization (MR) work. A range of quality control procedures were taken to select eligible instrument SNPs closely associated with total body BMD, OS and IBD. To make the conclusions more reliable, we applied five robust analytical methods, among which the inverse variance weighting (IVW) method acted as the major method. Besides, heterogeneity, pleiotropy and sensitivity were evaluated. Results In the European population, the genetic association of UC on total body BMD (OR=0.97, 95%CI=0.96,0.99, P<0.001) and overall IBD on total body BMD (OR=0.98, 95%CI=0.97,1.00, P=0.013) were significant, while the effect of CD on total body BMD was not significant enough (OR=0.99, 95%CI=0.98,1.00, P=0.085). All of UC, CD and overall IBD can be the genetic risk factor of having OS with pathological fracture (UC: OR=1.13, 95%CI=1.02,1.26, P=0.024, CD: OR=1.14, 95%CI=1.05,1.25, P=0.003, overall IBD: OR=1.13, 95%CI=1.02,1.24, P=0.015). In East Asian groups, only CD had a causal relationship with OS (OR=1.04, 95% CI=1.01,1.07, P=0.019). Conclusion Our study revealed genetically predicted associations between IBD on total body BMD and OS in European and East Asian populations. This work supplemented the results of previous retrospective studies and demonstrated the necessity of BMD monitoring in patients with IBD.
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Affiliation(s)
- Dengyong Xu
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yao Chen
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xing Gao
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Weidong Xie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ya Wang
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou, China
- Department of Hospital Infection-Control, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China
- Department of Hospital Infection-Control, Zhejiang Cancer Hospital, Hangzhou, China
| | - Jiaying Shen
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guang Yang
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Binbin Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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32
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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: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [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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33
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Mortlock S, Lord A, Montgomery G, Zakrzewski M, Simms LA, Krishnaprasad K, Hanigan K, Doecke JD, Walsh A, Lawrance IC, Bampton PA, Andrews JM, Mahy G, Connor SJ, Sparrow MP, Bell S, Florin TH, Begun J, Gearry RB, Radford-Smith GL. An Extremes of Phenotype Approach Confirms Significant Genetic Heterogeneity in Patients with Ulcerative Colitis. J Crohns Colitis 2023; 17:277-288. [PMID: 36111848 PMCID: PMC10024548 DOI: 10.1093/ecco-jcc/jjac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. METHODS We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. RESULTS MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. CONCLUSIONS Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.
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Affiliation(s)
- Sally Mortlock
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anton Lord
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Health Services Research, University of Queensland, Brisbane, QLD, Australia
| | - Grant Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Lisa A Simms
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | - James D Doecke
- Australian eHealth Research Centre, CSIRO, Brisbane, QLD, Australia
| | - Alissa Walsh
- Department of Gastroenterology, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ian C Lawrance
- Centre of Inflammatory Bowel Diseases, Saint John of God Hospital Subiaco, University of Western Australia, WA, Australia
| | | | - Jane M Andrews
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital & University of Adelaide, Adelaide, SA, Australia
| | - Gillian Mahy
- Department of Gastroenterology and Hepatology, Townsville University Hospital, Townsville, QLD, Australia
| | - Susan J Connor
- Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney, NSW, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Miles P Sparrow
- Department of Gastroenterology, Alfred Health, Melbourne, VIC, Australia
| | - Sally Bell
- Department of Gastroenterology and Hepatology, Monash Health, Melbourne, VIC, Australia
| | - Timothy H Florin
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Jakob Begun
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Inflammatory Disease Biology and Therapeutics Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Graham L Radford-Smith
- Corresponding author: Graham Radford-Smith, Gut Health Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. Tel: +617 3362 0499; Fax: +617 3009 0053;
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34
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Fu H, Zheng H, Chen X, Weirauch MT, Muglia LJ, Wang L, Liu Y. NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome Biol 2023; 24:50. [PMID: 36927507 PMCID: PMC10018866 DOI: 10.1186/s13059-023-02889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements' activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single-nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.
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Affiliation(s)
- Hailu Fu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaoting Chen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew T Weirauch
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Present address: Burroughs Wellcome Fund, Research Triangle Park, NC, 27614, USA
| | - Li Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Biology, Xavier University, Cincinnati, OH, 45207, USA.
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45219, USA.
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35
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Tsakok T, Saklatvala J, Rispens T, Loeff FC, de Vries A, Allen MH, Barbosa IA, Baudry D, Dasandi T, Duckworth M, Meynell F, Russell A, Chapman A, McBride S, McKenna K, Perera G, Ramsay H, Ramesh R, Sands K, Shipman A, Burden AD, Griffiths CE, Reynolds NJ, Warren RB, Mahil S, Barker J, Dand N, Smith C, Simpson MA. Development of antidrug antibodies against adalimumab maps to variation within the HLA-DR peptide-binding groove. JCI Insight 2023; 8:e156643. [PMID: 36810251 PMCID: PMC9977494 DOI: 10.1172/jci.insight.156643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/13/2023] [Indexed: 02/23/2023] Open
Abstract
Targeted biologic therapies can elicit an undesirable host immune response characterized by the development of antidrug antibodies (ADA), an important cause of treatment failure. The most widely used biologic across immune-mediated diseases is adalimumab, a tumor necrosis factor inhibitor. This study aimed to identify genetic variants that contribute to the development of ADA against adalimumab, thereby influencing treatment failure. In patients with psoriasis on their first course of adalimumab, in whom serum ADA had been evaluated 6-36 months after starting treatment, we observed a genome-wide association with ADA against adalimumab within the major histocompatibility complex (MHC). The association signal mapped to the presence of tryptophan at position 9 and lysine at position 71 of the HLA-DR peptide-binding groove, with both residues conferring protection against ADA. Underscoring their clinical relevance, these residues were also protective against treatment failure. Our findings highlight antigenic peptide presentation via MHC class II as a critical mechanism in the development of ADA against biologic therapies and downstream treatment response.
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Affiliation(s)
- Teresa Tsakok
- Department of Medical and Molecular Genetics and
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
- St John’s Institute of Dermatology, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom
| | | | - Theo Rispens
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Floris C. Loeff
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
- Biologics Lab, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Annick de Vries
- Biologics Lab, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Michael H. Allen
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Ines A. Barbosa
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - David Baudry
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Tejus Dasandi
- St John’s Institute of Dermatology, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom
| | - Michael Duckworth
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Freya Meynell
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Alice Russell
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Anna Chapman
- Department of Dermatology, Queen Elizabeth Hospital, London, United Kingdom
| | - Sandy McBride
- Department of Dermatology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Kevin McKenna
- Department of Dermatology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Gayathri Perera
- Department of Dermatology, Chelsea and Westminster Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Helen Ramsay
- Department of Dermatology, Sheffield Teaching Hospitals National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Raakhee Ramesh
- Department of Dermatology, Sandwell and West Birmingham National Health Service Trust, Birmingham, United Kingdom
| | - Kathleen Sands
- Department of Dermatology, East Kent Hospitals University National Health Service Foundation Trust, Kent, United Kingdom
| | - Alexa Shipman
- Department of Dermatology, Portsmouth Hospitals National Health Service Trust, Portsmouth, United Kingdom
| | | | - A. David Burden
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Christopher E.M. Griffiths
- Dermatology Centre, Salford Royal National Health Service Foundation Trust, Manchester, United Kingdom
- The University of Manchester, Manchester Academic Health Science Centre, National Institute for Health Research Manchester Biomedical Research Centre, Manchester, United Kingdom
| | - Nick J. Reynolds
- Department of Dermatology, Royal Victoria Infirmary, Newcastle upon Tyne NHS Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
- Institute of Translational and Clinical Medicine, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard B. Warren
- Dermatology Centre, Salford Royal National Health Service Foundation Trust, Manchester, United Kingdom
- The University of Manchester, Manchester Academic Health Science Centre, National Institute for Health Research Manchester Biomedical Research Centre, Manchester, United Kingdom
| | - Satveer Mahil
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
- St John’s Institute of Dermatology, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom
| | - Jonathan Barker
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
- St John’s Institute of Dermatology, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom
| | - Nick Dand
- Department of Medical and Molecular Genetics and
- Health Data Research UK, London, United Kingdom
| | - Catherine Smith
- St John’s Institute of Dermatology, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
- St John’s Institute of Dermatology, Guy’s and St Thomas’ National Health Service Foundation Trust, London, United Kingdom
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Bacos K, Perfilyev A, Karagiannopoulos A, Cowan E, Ofori JK, Bertonnier-Brouty L, Rönn T, Lindqvist A, Luan C, Ruhrmann S, Ngara M, Nilsson Å, Gheibi S, Lyons CL, Lagerstedt JO, Barghouth M, Esguerra JL, Volkov P, Fex M, Mulder H, Wierup N, Krus U, Artner I, Eliasson L, Prasad RB, Cataldo LR, Ling C. Type 2 diabetes candidate genes, including PAX5, cause impaired insulin secretion in human pancreatic islets. J Clin Invest 2023; 133:163612. [PMID: 36656641 PMCID: PMC9927941 DOI: 10.1172/jci163612] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Type 2 diabetes (T2D) is caused by insufficient insulin secretion from pancreatic β cells. To identify candidate genes contributing to T2D pathophysiology, we studied human pancreatic islets from approximately 300 individuals. We found 395 differentially expressed genes (DEGs) in islets from individuals with T2D, including, to our knowledge, novel (OPRD1, PAX5, TET1) and previously identified (CHL1, GLRA1, IAPP) candidates. A third of the identified expression changes in islets may predispose to diabetes, as expression of these genes associated with HbA1c in individuals not previously diagnosed with T2D. Most DEGs were expressed in human β cells, based on single-cell RNA-Seq data. Additionally, DEGs displayed alterations in open chromatin and associated with T2D SNPs. Mouse KO strains demonstrated that the identified T2D-associated candidate genes regulate glucose homeostasis and body composition in vivo. Functional validation showed that mimicking T2D-associated changes for OPRD1, PAX5, and SLC2A2 impaired insulin secretion. Impairments in Pax5-overexpressing β cells were due to severe mitochondrial dysfunction. Finally, we discovered PAX5 as a potential transcriptional regulator of many T2D-associated DEGs in human islets. Overall, we have identified molecular alterations in human pancreatic islets that contribute to β cell dysfunction in T2D pathophysiology.
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Affiliation(s)
- Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | | | - Alexandros Karagiannopoulos
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Elaine Cowan
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Jones K. Ofori
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Ludivine Bertonnier-Brouty
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Andreas Lindqvist
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Cheng Luan
- Unit of Islet Pathophysiology, Department of Clinical Sciences
| | - Sabrina Ruhrmann
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Mtakai Ngara
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Åsa Nilsson
- Human Tissue Lab, Department of Clinical Sciences
| | - Sevda Gheibi
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Claire L. Lyons
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Jens O. Lagerstedt
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | | | - Jonathan L.S. Esguerra
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Malin Fex
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Hindrik Mulder
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Nils Wierup
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Ulrika Krus
- Human Tissue Lab, Department of Clinical Sciences
| | - Isabella Artner
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Lena Eliasson
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Rashmi B. Prasad
- Genomics, Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden.,Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland
| | - Luis Rodrigo Cataldo
- Molecular Metabolism Unit, Department of Clinical Sciences, and,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
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Ali FE, Ibrahim IM, Ghogar OM, Abd-alhameed EK, Althagafy HS, Hassanein EH. Therapeutic interventions target the NLRP3 inflammasome in ulcerative colitis: Comprehensive study. World J Gastroenterol 2023; 29:1026-1053. [PMID: 36844140 PMCID: PMC9950862 DOI: 10.3748/wjg.v29.i6.1026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/29/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
One of the significant health issues in the world is the prevalence of ulcerative colitis (UC). UC is a chronic disorder that mainly affects the colon, beginning with the rectum, and can progress from asymptomatic mild inflammation to extensive inflammation of the entire colon. Understanding the underlying molecular mechanisms of UC pathogenesis emphasizes the need for innovative therapeutic approaches based on identifying molecular targets. Interestingly, in response to cellular injury, the NLR family pyrin domain containing 3 (NLRP3) inflammasome is a crucial part of the inflammation and immunological reaction by promoting caspase-1 activation and the release of interleukin-1β. This review discusses the mechanisms of NLRP3 inflammasome activation by various signals and its regulation and impact on UC.
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Affiliation(s)
- Fares E.M Ali
- Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
| | - Islam M. Ibrahim
- Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
| | - Osama M Ghogar
- Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
| | - Esraa K. Abd-alhameed
- Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 12345, Egypt
| | - Hanan S. Althagafy
- Department of Biochemistry, Faculty of Science, University of Jeddah, Jeddah 12345, Saudi Arabia
| | - Emad H.M. Hassanein
- Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
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38
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Pang X, Song H, Li X, Xu F, Lei B, Wang F, Xu J, Qi L, Wang L, Tan G. Transcriptomic analyses of treatment-naïve pediatric ulcerative colitis patients and exploration of underlying disease pathogenesis. J Transl Med 2023; 21:30. [PMID: 36647141 PMCID: PMC9843999 DOI: 10.1186/s12967-023-03881-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a form of chronic inflammatory bowel disease of nonspecific origin. This study used an RNA-Sequencing (RNA-Seq) approach to evaluate the transcriptomic landscape of a well-stratified treatment-naïve pediatric UC patient population by comparing them with healthy control children. The data were analyzed to evaluate the mechanisms driving UC-related intestinal inflammation and fibrosis. METHODS Intestinal mucosal samples from five pediatric UC patients and five healthy controls were analyzed by RNA-Seq, and results were verified by qPCR. A CRISPR/Cas9 approach was used to knock out the expression of HLA-DRB5, and molecular biology techniques were used for additional mechanistic studies. RESULTS In these analyses, 2290 genes were found to be differentially expressed between the UC and control samples, of which 1258 and 1032 were upregulated and downregulated, respectively. Gene Ontology analysis showed that these genes were enriched in extracellular matrix (ECM)-related processes and that 7 of 8 differentially expressed genes of interest (PIK3CD, IL1β, IL1α, TIMP1, MMP1, MMP12, COL6A3, and HLADRB5) were upregulated and involved in ECM-receptor interaction and inflammatory bowel disease-related pathways. Increased HLA-DRB5 expression driven by intestinal bacteria was found to promote IL-1α secretion, leading to intestinal inflammation and fibrosis, suggesting a possible target for the treatment of UC. CONCLUSION These data suggest that intestinal inflammation is present in pediatric UC patients for extended periods before the onset of symptoms, and intestinal fibrosis begins even during the early stages of UC. Intestinal bacteria were also found to trigger intestinal inflammation and fibrosis, with HLA-DRB5 playing a central role in this process.
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Affiliation(s)
- Xiaoli Pang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Hongxiao Song
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Xiaolu Li
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Fengchao Xu
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Bingxun Lei
- grid.430605.40000 0004 1758 4110Department of Anesthesia, The First Hospital of Jilin University, Changchun, China
| | - Fei Wang
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jing Xu
- grid.430605.40000 0004 1758 4110Health Examination Center, The First Hospital of Jilin University, Changchun, China
| | - Lingli Qi
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Libo Wang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Guangyun Tan
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
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Joustra V, Li Yim AYF, Hageman I, Levin E, Adams A, Satsangi J, de Jonge WJ, Henneman P, D'Haens G. Long-term Temporal Stability of Peripheral Blood DNA Methylation Profiles in Patients With Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 15:869-885. [PMID: 36581079 PMCID: PMC9972576 DOI: 10.1016/j.jcmgh.2022.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS There is great current interest in the potential application of DNA methylation alterations in peripheral blood leukocytes (PBLs) as biomarkers of susceptibility, progression, and treatment response in inflammatory bowel disease (IBD). However, the intra-individual stability of PBL methylation in IBD has not been characterized. Here, we studied the long-term stability of all probes located on the Illumina HumanMethylation EPIC BeadChip array. METHODS We followed a cohort of 46 adult patients with IBD (36 Crohn's disease [CD], 10 ulcerative colitis [UC]; median age, 44 years; interquartile range [IQR] 27-56 years; 50% female) that received standard care follow-up at the Amsterdam University Medical Centers. Paired PBL samples were collected at 2 time points with a median of 7 years (range, 2-9 years) in between. Differential methylation and intra-class correlation (ICC) analyses were used to identify time-associated differences and temporally stable CpGs, respectively. RESULTS Around 60% of all EPIC array loci presented poor intra-individual stability (ICC <0.50); 78.114 (≈9%) showed good (ICC, 0.75-0.89), and 41.274 (≈5%) showed excellent (ICC ≥0.90) stability, between both measured time points. Focusing on previously identified consistently differentially methylated positions indicated that 22 CD-, 11 UC-, and 24 IBD-associated loci demonstrated high stability (ICC ≥0.75) over time; of these, we observed a marked stability of CpG loci associated to the HLA genes. CONCLUSIONS Our data provide insight into the long-term stability of the PBL DNA methylome within an IBD context, facilitating the selection of biologically relevant and robust IBD-associated epigenetic biomarkers with increased potential for independent validation. These data also have potential implications in understanding disease pathogenesis.
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Affiliation(s)
- Vincent Joustra
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew Y F Li Yim
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ishtu Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Horaizon BV, Delft, the Netherlands
| | - Alex Adams
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Jack Satsangi
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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Macleod T, Bridgewood C, McGonagle D. Role of neutrophil interleukin-23 in spondyloarthropathy spectrum disorders. THE LANCET. RHEUMATOLOGY 2023; 5:e47-e57. [PMID: 38251507 DOI: 10.1016/s2665-9913(22)00334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Neutrophilic inflammation is a pervasive characteristic common to spondyloarthropathies and related disorders. This inflammation manifests as Munro's microabscesses of the skin and osteoarticular neutrophilic inflammation in patients with psoriatic arthritis, intestinal crypt abscesses in patients with inflammatory bowel disease, ocular hypopyon in anterior uveitis, and neutrophilic macroscopic and microscopic inflammation in patients with Behçet's disease. Strong MHC class I associations are seen in these diseases, which represent so-called MHC-I-opathies, and these associations indicate an involvement of CD8 T-cell immunopathology that is not yet well understood. In this Personal View, we highlight emerging data suggesting that the T-cell-neutrophil axis involves both a T-cell-mediated and interleukin (IL)-17-mediated (type 17) recruitment and activation of neutrophils, and also a sequestration of activated neutrophils at disease sites that might directly amplify type 17 T-cell responses. This amplification likely involves neutrophilic production of IL-23 and proteases as well as other feedback mechanisms that could be regulated by local microbiota, pathogens, or tissue damage. This crosstalk between innate and adaptive immunity offers a novel explanation for how bacterial and fungal microbes at barrier sites could innately control type 17 T-cell development, with the aim of restoring tissue homoeostasis, and could potentially explain features of clinical disease and treatment response, such as the fast-onset action of the IL-23 pathway blockade in certain patients. This axis could be crucial to understanding non-response to IL-23 inhibitors among patients with ankylosing spondylitis, as the axial skeleton is a site rich in neutrophils and a site of haematopoiesis with myelopoiesis in adults.
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Affiliation(s)
- Tom Macleod
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Charles Bridgewood
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Dennis McGonagle
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK; National Institute for Health Research, Leeds Biomedical Research Centre, Leeds Teaching Hospitals, Leeds, UK.
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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Shih T, Yusung S, Gonsky R, Dutra-Clarke R, Ziring D, Rabizadeh S, Kugathasan S, Denson LA, Li D, Braun J. Environmental Interaction of Resolved Human Cytomegalovirus Infection With Crohn's Disease Location. Inflamm Bowel Dis 2022; 29:328-331. [PMID: 36508344 PMCID: PMC9890217 DOI: 10.1093/ibd/izac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 02/02/2023]
Abstract
Lay Summary
Active cytomegalovirus (CMV) infection complicates management of inflammatory bowel disease, but the relationship of resolved CMV infection to Crohn’s disease (CD) behavior or localization is unknown. This article reports a striking risk (9-fold) of Crohn’s disease localization to the colon with prior CMV infection. It also reports imputed mucosal cellular composition, HLA class 1, and KIR gene variants that delimit prior observations regarding HLA and KIR associations with Crohn’s disease risk and behavior.
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Affiliation(s)
- Terri Shih
- David Geffen UCLA School of Medicine, Los Angeles, CA, 90095, USA
| | - Susy Yusung
- David Geffen UCLA School of Medicine, Los Angeles, CA, 90095, USA
| | - Rivkah Gonsky
- Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - David Ziring
- Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | | | - Lee A Denson
- Cincinnati Children’s Medical Center, Cincinnati, OH, 45229, USA
| | - Dalin Li
- Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan Braun
- Address correspondence to: Jonathan Braun, MD, PhD, F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA, 90048, USA ()
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Berryman MA, Milletich PL, Petrone JR, Roesch LF, Ilonen J, Triplett EW, Ludvigsson J. Autoimmune-associated genetics impact probiotic colonization of the infant gut. J Autoimmun 2022; 133:102943. [PMID: 36356550 DOI: 10.1016/j.jaut.2022.102943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/09/2022]
Abstract
To exemplify autoimmune-associated genetic influence on the colonization of bacteria frequently used in probiotics, microbial composition of stool from 1326 one-year-old infants was analyzed in a prospective general-population cohort, All Babies In Southeast Sweden (ABIS). We show that an individual's HLA haplotype composition has a significant impact on which common Bifidobacterium strains thrive in colonizing the gut. The effect HLA has on the gut microbiome can be more clearly observed when considered in terms of allelic dosage. HLA DR1-DQ5 showed the most significant and most prominent effect on increased Bifidobacterium relative abundance. Therefore, HLA DR1-DQ5 is proposed to act as a protective haplotype in many individuals. Protection-associated HLA haplotypes are more likely to influence the promotion of specific bifidobacteria. In addition, strain-level differences are correlated with colonization proficiency in the gut depending on HLA haplotype makeup. These results demonstrate that HLA genetics should be considered when designing effective probiotics, particularly for those at high genetic risk for autoimmune diseases.
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Affiliation(s)
- Meghan A Berryman
- Triplett Laboratory, Institute of Food and Agriculture, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Patricia L Milletich
- Triplett Laboratory, Institute of Food and Agriculture, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Joseph R Petrone
- Triplett Laboratory, Institute of Food and Agriculture, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Luiz Fw Roesch
- Roesch Laboratory, Institute of Food and Agriculture, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eric W Triplett
- Triplett Laboratory, Institute of Food and Agriculture, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
| | - Johnny Ludvigsson
- Crown Princess Victoria's Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Garcia-Argibay M, Hiyoshi A, Montgomery S. Acute appendicitis and ulcerative colitis: a population-based sibling comparison study. BMJ Open Gastroenterol 2022; 9:bmjgast-2022-001041. [PMID: 36446432 PMCID: PMC9710359 DOI: 10.1136/bmjgast-2022-001041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE To assess the inverse relationship between acute appendicitis and ulcerative colitis (UC) using a sibling comparison design to adjust for unmeasured familial genetic and environmental factors. DESIGN The cohort comprised 3.1 million individuals resident in Sweden between 1984 and 2018 with the linkage of several Swedish national registers. Fitting Cox hazards models, we calculated the risk for developing UC in individuals with and without acute appendicitis by the age 20 years adjusting for several potential confounding factors. Further, we performed sibling-stratified analyses to adjust for shared unmeasured familial confounding factors. RESULTS During 57.7 million person-years of follow-up, 20 848/3 125 232 developed UC among those without appendicitis (3.63 (3.59-3.68) per 10 000 person-years), whereas only 59/35 848 people developed UC among those with appendicitis before age 20 years (1.66 (1.28-2.14) per 10 000 person-years). We found a decreased risk for developing UC in those with acute appendicitis by the age 20 years compared with individuals who did not have appendicitis by this age (HR=0.37 (95% CI 0.29 to 0.48)). When adjusting for shared familial confounders, we observed only a slight attenuation in this association (HR=0.46 (95% CI 0.32 to 0.66)). CONCLUSION Individuals who had acute appendicitis by late adolescence showed a decreased risk for developing UC compared with those who did not. Genetic and shared familial environmental factors seem to potentially play only a small role in this relationship. Our results suggest an independent association of acute appendicitis, or its underlying causes, with UC risk.
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Affiliation(s)
- Miguel Garcia-Argibay
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Faculty of Medicine and Health, Örebro universitet, Örebro, Sweden
| | - Ayako Hiyoshi
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Faculty of Medicine and Health, Örebro universitet, Örebro, Sweden,Department of Public Health Sciences, Stockholm University, Stockholm, Sweden,Department of Epidemiology and Public Health, University College London, London, UK,Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Scott Montgomery
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Faculty of Medicine and Health, Örebro universitet, Örebro, Sweden,Department of Epidemiology and Public Health, University College London, London, UK,Clinical Epidemiology Division, Department of Medicine, Karolinska Institutet, Solna, Sweden
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Sharif K, Ben-Shabat N, Mahagna M, Shani U, Watad A, Cohen AD, Amital H. Inflammatory Bowel Diseases Are Associated with Polymyositis and Dermatomyositis-A Retrospective Cohort Analysis. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121727. [PMID: 36556929 PMCID: PMC9781532 DOI: 10.3390/medicina58121727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/19/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
Background and Objectives: Polymyositis and dermatomyositis (PM/DM) are classified as polygenic autoimmune diseases, whereas inflammatory bowel disease (IBD) is considered a polygenic autoinflammatory disease. In the literature, several cases exist reporting the co-occurrence of both conditions. At the molecular level, PM/DM and IBD share common genetic determinants including interferon regulatory factor and vitamin D receptor susceptibility loci. Accumulating evidence underline several indicators that confer poor prognosis in IBD, including antinuclear antibody positivity and the presence of other autoimmune diseases, therefore the aim of this study is to assess the association between these entities. Materials and Methods: This is a population-based retrospective study using data retrieved from a large electronic medical record in Israel, the Clalit health registry. The sample included PM/DM patients and age- and sex-frequency matched controls. The prevalence of IBD in PM/DM was compared between the two groups and logistic regression was applied to control for confounding variables. Predictors of IBD in patients with PM/DM were also explored. Results: Our study included 12,278 subjects with 2085 PM/DM patients and 10,193 age- and sex- frequency-matched controls. The incidence of IBD in patients with PM/DM was significantly higher even after controlling for various confounding variables (OR of 1.73, 95% CI 1.05-2.86, p-value = 0.033). Anti-nuclear antibodies (ANA) positivity was found to be an independent predictor for IBD diagnosis in patients with PM/DM (OR 3.67, 95% CI 1.01-13.36, p = 0.048). Conclusion: Our analysis reports an association between IBD and PM/DM. Such association could point towards a common pathophysiological background. Further research is needed to further describe the clinical courses and whether a unique therapeutic approach is warranted.
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Affiliation(s)
- Kassem Sharif
- Department of Gastroenterology, Sheba Medical Centre, Tel-Hashomer 5265601, Israel
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
| | - Niv Ben-Shabat
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
| | - Muhammad Mahagna
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
| | - Uria Shani
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
| | - Abdulla Watad
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
- Section of Musculoskeletal Disease, NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Institute of Molecular Medicine, University of Leeds, Chapel Allerton Hospital, Leeds LS7 4SA, UK
| | - Arnon D. Cohen
- Chief Physicians Office, Clalit Health Services, Tel Aviv 6209813, Israel
- Siaal Research Center for Family Medicine and Primary Care, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Howard Amital
- Department of Medicine B, Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer 5262100, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6209813, Israel
- Correspondence: ; Tel.: +972-3-5302661; Fax: +972-3-5304796
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Rosati E, Rios Martini G, Pogorelyy MV, Minervina AA, Degenhardt F, Wendorff M, Sari S, Mayr G, Fazio A, Dowds CM, Hauser C, Tran F, von Schönfels W, Pochhammer J, Salnikova MA, Jaeckel C, Gigla JB, Sabet SS, Hübenthal M, Schiminsky E, Schreiber S, Rosenstiel PC, Scheffold A, Thomas PG, Lieb W, Bokemeyer B, Witte M, Aden K, Hendricks A, Schafmayer C, Egberts JH, Mamedov IZ, Bacher P, Franke A. A novel unconventional T cell population enriched in Crohn's disease. Gut 2022; 71:2194-2204. [PMID: 35264446 PMCID: PMC9554086 DOI: 10.1136/gutjnl-2021-325373] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls. DESIGN We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq. RESULTS We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs. CONCLUSIONS We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriela Rios Martini
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anastasia A Minervina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Soner Sari
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Christel Marie Dowds
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Charlotte Hauser
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Julius Pochhammer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Maria A Salnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Charlot Jaeckel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Johannes Boy Gigla
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernd Bokemeyer
- Interdisciplinary Crohn Colitis Centre Minden, Minden, Germany
| | - Maria Witte
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jan-Hendrick Egberts
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- CEITEC, Masaryk University, Brno, Czech Republic
- Dmitry Rogachev National Research Center of Pediatric Hematology, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russian Federation
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
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Both indirect maternal and direct fetal genetic effects reflect the observational relationship between higher birth weight and lower adult bone mass. BMC Med 2022; 20:361. [PMID: 36192722 PMCID: PMC9531399 DOI: 10.1186/s12916-022-02531-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Birth weight is considered not only to undermine future growth, but also to induce lifelong diseases; the aim of this study is to explore the relationship between birth weight and adult bone mass. METHODS We performed multivariable regression analyses to assess the association of birth weight with bone parameters measured by dual-energy X-ray absorptiometry (DXA) and by quantitative ultrasound (QUS), independently. We also implemented a systemic Mendelian randomization (MR) analysis to explore the causal association between them with both fetal-specific and maternal-specific instrumental variables. RESULTS In the observational analyses, we found that higher birth weight could increase the adult bone area (lumbar spine, β-coefficient= 0.17, P < 2.00 × 10-16; lateral spine, β-coefficient = 0.02, P = 0.04), decrease bone mineral content-adjusted bone area (BMCadjArea) (lumbar spine, β-coefficient= - 0.01, P = 2.27 × 10-14; lateral spine, β-coefficient = - 0.05, P = 0.001), and decrease adult bone mineral density (BMD) (lumbar spine, β-coefficient = - 0.04, P = 0.007; lateral spine; β-coefficient = - 0.03, P = 0.02; heel, β-coefficient = - 0.06, P < 2.00 × 10-16), and we observed that the effect of birth weight on bone size was larger than that on BMC. In MR analyses, the higher fetal-specific genetically determined birth weight was identified to be associated with higher bone area (lumbar spine; β-coefficient = 0.15, P = 1.26 × 10-6, total hip, β-coefficient = 0.15, P = 0.005; intertrochanteric area, β-coefficient = 0.13, P = 0.0009; trochanter area, β-coefficient = 0.11, P = 0.03) but lower BMD (lumbar spine, β-coefficient = - 0.10, P = 0.01; lateral spine, β-coefficient = - 0.12, P = 0.0003, and heel β-coefficient = - 0.11, P = 3.33 × 10-13). In addition, we found that the higher maternal-specific genetically determined offspring birth weight was associated with lower offspring adult heel BMD (β-coefficient = - 0.001, P = 0.04). CONCLUSIONS The observational analyses suggested that higher birth weight was associated with the increased adult bone area but decreased BMD. By leveraging the genetic instrumental variables with maternal- and fetal-specific effects on birth weight, the observed relationship could be reflected by both the direct fetal and indirect maternal genetic effects.
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Coates E, Wickramasekera N, Barr A, Shackley P, Lee M, Hind D, Probert C, Sebastian S, Totton N, Blackwell S, Bedford H, Dames N, Lobo A. Patient preferences and current practice for adults with steroid-resistant ulcerative colitis: POPSTER mixed-methods study. Health Technol Assess 2022; 26:1-118. [DOI: 10.3310/rhxr5192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background
Corticosteroids are a mainstay of the treatment of moderately severe relapses of ulcerative colitis, yet almost 50% of patients do not respond fully to these and risk prolonged steroid use and side effects. There is a lack of clarity about the definitions of steroid resistance, the optimum choice of treatment, and patient and health-care professional treatment preferences.
Objectives
The overall aim of this research was to understand how steroid-resistant ulcerative colitis is managed in adult secondary care and how current practice compares with patient and health-care professional preferences.
Design
A mixed-methods study, including an online survey, qualitative interviews and discrete choice experiments.
Setting
NHS inflammatory bowel disease services in the UK.
Participants
Adults with ulcerative colitis and health-care professionals treating inflammatory bowel disease.
Results
We carried out a survey of health-care professionals (n = 168), qualitative interviews with health-care professionals (n = 20) and patients (n = 33), discrete choice experiments with health-care professionals (n = 116) and patients (n = 115), and a multistakeholder workshop (n = 9). The interviews with and survey of health-care professionals showed that most health-care professionals define steroid resistance as an incomplete response to 40 mg per day of prednisolone after 2 weeks. The survey also found that anti-tumour necrosis factor drugs (particularly infliximab) are the most frequently offered drugs across most steroid-resistant (and steroid-dependent) patient scenarios, but they are less frequently offered to thiopurine-naive patients. Patient interviews identified several factors influencing their treatment choices, including effectiveness of treatment, recommendations from health-care professionals, route of administration and side effects. Over time, depending on the severity and duration of symptoms and, crucially, as medical treatment options become exhausted, patients are willing to try alternative treatments and, eventually, to undergo surgery. The discrete choice experiments found that the probability of remission and of side effects strongly influences the treatment choices of both patients and health-care professionals. Patients are less likely to choose a treatment that takes longer to improve symptoms. Health-care professionals are willing to make difficult compromises by tolerating greater safety risks in exchange for therapeutic benefits. The treatments ranked most positively by patients were infliximab and tofacitinib (each preferred by 38% of patients), and the predicted probability of uptake by health-care professionals was greatest for infliximab (62%).
Limitations
The survey and the discrete choice experiments with patients and health-care professionals are limited by their relatively small sample sizes. The qualitative studies are subject to selection bias. The timing of the different substudies, both before and during the COVID-19 pandemic, is a potential limitation.
Conclusions
We have identified factors influencing treatment decisions for steroid-resistant ulcerative colitis and the characteristics to consider when choosing treatments to evaluate in future randomised controlled trials. The findings may be used to improve discussions between patients and health-care professionals when they review treatment options for steroid-resistant ulcerative colitis.
Future work
This research highlights the need for consensus work to establish an agreed definition of steroid resistance in ulcerative colitis and a greater understanding of the optimal use of tofacitinib and surgery for this patient group. A randomised controlled trial comparing infliximab with tofacitinib is also recommended.
Funding
This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 41. See the NIHR Journals Library website for further project information.
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Affiliation(s)
- Elizabeth Coates
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | | | - Amy Barr
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Phil Shackley
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Matthew Lee
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Daniel Hind
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Christopher Probert
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Shaji Sebastian
- Hull University Teaching Hospitals NHS Foundation Trust, Hull, UK
| | - Nikki Totton
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | | | | | | | - Alan Lobo
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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Identification of Novel Loci Involved in Adalimumab Response in Crohn’s Disease Patients Using Integration of Genome Profiling and Isoform-Level Immune-Cell Deconvoluted Transcriptome Profiling of Colon Tissue. Pharmaceutics 2022; 14:pharmaceutics14091893. [PMID: 36145641 PMCID: PMC9500628 DOI: 10.3390/pharmaceutics14091893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Crohn’s disease is a consequence of dysregulated inflammatory response to the host’s microbiota. Although anti-TNF treatment improves the quality of the patient’s life, a large proportion of patients lose response to the treatment. The past decade of research has led to a continuum of studies showcasing the heterogeneity of anti-TNF response; thus, the aim of the present study was to dissect transcriptome-wide findings to transcript isoform specific levels and combine the analyses with refined information of immune cell landscapes in colon tissue, and subsequently select promising candidates using gene ontology and genomic integration. We enrolled Slovenian Crohn’s disease patients who were naïve with respect to adalimumab treatment. We performed colon tissue RNA sequencing and peripheral blood mononuclear cell DNA genotyping with a subsequent contemporary integrative approach to combine immune cell deconvoluted isoform transcript specific transcriptome analysis, gene ontology layering and genomic data. We identified nine genes (MACF1, CTSE, HDLBP, HSPA9, HLA-DMB, TAP2, LGMN, ANAPC11, ACP5) with 15 transcripts and 16 variants involved in the adalimumab response. Our study identified loci, some of which were previously shown to contribute to inflammatory bowel disease susceptibility, as novel loci involved in adalimumab response in Crohn’s disease patients.
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Khan T, Rahman M, Ahmed I, Al Ali F, Jithesh PV, Marr N. Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens. Front Immunol 2022; 13:856497. [PMID: 36003377 PMCID: PMC9393332 DOI: 10.3389/fimmu.2022.856497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
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Affiliation(s)
| | | | | | | | - Puthen Veettil Jithesh
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Nico Marr,
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