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Watson A, Harris RA, Engevik AC, Oezguen N, Nicholson MR, Dooley S, Stubler R, Satter LF, Karam LB, Kellermayer R. MYO5B and the Polygenic Landscape of Very Early-Onset Inflammatory Bowel Disease in an Ethnically Diverse Population. Inflamm Bowel Dis 2024:izae169. [PMID: 39096520 DOI: 10.1093/ibd/izae169] [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: 04/23/2024] [Indexed: 08/05/2024]
Abstract
BACKGROUND Genetic discovery in very early-onset inflammatory bowel disease (VEO-IBD) can elucidate not only the origins of VEO-IBD, but also later-onset inflammatory bowel disease. We aimed to investigate the polygenic origins of VEO-IBD in a cohort with a high proportion of Hispanic patients. METHODS Patients with VEO-IBD who underwent whole exome sequencing at our center were included. Genes were categorized as genes of interest (GOIs) (129 genes previously described to be associated with VEO-IBD) or non-GOIs. VEO-IBD "susceptibility" single nucleotide variants (SNVs) were identified through enrichment compared with gnomAD (Genome Aggregation Database) and ALFA (Allele Frequency Aggregator) and were scored by Combined Annotation Dependent Depletion for deleteriousness. Gene networks carrying susceptibility SNVs were created. Myosin 5b immunofluorescence was also studied. RESULTS Fifty-six patients met inclusion criteria, and 32.1% identified as Hispanic. Monogenic disease was infrequent (8.9%). Significant enrichment of GOI susceptibility SNVs was observed, notably in MYO5B, especially in Hispanics. MEFV, TNFAIP3, SH3TC2, and NCF2 were also central participants in the GOI networks. Myosin 5b immunofluorescence in colonic mucosa was significantly reduced in those with MYO5B susceptibility SNVs compared with control subjects. Seven genes (ESRRA, HLA-DQ1, RETSAT, PABPC1, PARP4, CCDC102A, and SUSD2) were central participants in the non-GOI networks. CONCLUSIONS Our results support the polygenic nature of VEO-IBD, in which key participants, like MYO5B, were identified through network analytics. Rare variant load within susceptibility genes may be relevant not only for the genetic origins of inflammatory bowel disease, but also for the age of disease onset. Our findings could guide future work in precision medicine.
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Affiliation(s)
- Ashleigh Watson
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy C Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Maribeth R Nicholson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sarah Dooley
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Rachel Stubler
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Lisa Forbes Satter
- Department of Pediatric Allergy and Immunology, William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Lina B Karam
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Richard Kellermayer
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
- Children's Nutrition and Research Center, U.S. Department of Agriculture Agricultural Research Service, Houston, TX, USA
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2
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Li Y, Lei H, Wen X, Cao H. A powerful approach to identify replicable variants in genome-wide association studies. Am J Hum Genet 2024; 111:966-978. [PMID: 38701746 PMCID: PMC11080610 DOI: 10.1016/j.ajhg.2024.04.004] [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: 08/19/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Replicability is the cornerstone of modern scientific research. Reliable identifications of genotype-phenotype associations that are significant in multiple genome-wide association studies (GWASs) provide stronger evidence for the findings. Current replicability analysis relies on the independence assumption among single-nucleotide polymorphisms (SNPs) and ignores the linkage disequilibrium (LD) structure. We show that such a strategy may produce either overly liberal or overly conservative results in practice. We develop an efficient method, ReAD, to detect replicable SNPs associated with the phenotype from two GWASs accounting for the LD structure. The local dependence structure of SNPs across two heterogeneous studies is captured by a four-state hidden Markov model (HMM) built on two sequences of p values. By incorporating information from adjacent locations via the HMM, our approach provides more accurate SNP significance rankings. ReAD is scalable, platform independent, and more powerful than existing replicability analysis methods with effective false discovery rate control. Through analysis of datasets from two asthma GWASs and two ulcerative colitis GWASs, we show that ReAD can identify replicable genetic loci that existing methods might otherwise miss.
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Affiliation(s)
- Yan Li
- School of Computer Science and Technology, Changchun University of Science and Technology, Changchun, Jilin 130022, China; School of Mathematics, Jilin University, Changchun, Jilin 130012, China
| | - Haochen Lei
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA.
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Saenz Hinojosa S, Adrian Jinam T, Hosomichi K, Romero VI. HLA allelic diversity in the Waorani population of Ecuador: Its significance to their ancestry and migration. Hum Immunol 2024; 85:110771. [PMID: 38443236 DOI: 10.1016/j.humimm.2024.110771] [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: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
The Waorani, an isolated indigenous tribe in Ecuador, have long been characterized by limited genetic diversity, with few studies delving into their genetic background. Human Leukocyte Antigen (HLA) genes which are located in the human major histocompatibility complex (MHC) provides valuable insights into population evolution due to its highly polymorphic nature. However, little is known about the HLA diversity and ancestry of the Waorani population. In this study, we sequenced eight HLA genes using Next Generation Sequencing (NGS) from 134 Waorani individuals and obtained up to four-field HLA allele resolution. Cluster and phylogenetic analysis show that the Waorani are genetically distant from other Ecuador populations, but instead show genetic affinities with the Puyanawa and Terena tribes from Brazil, as well as the Mixe tribe from Mexico. The identification of alleles common within the Waorani population, previously linked to specific health conditions, notably paves the way for future association analyses. This extensive study, employing Next-Generation Sequencing (NGS) technology, significantly enriches the sparse and segmented understanding of HLA diversity in the South American region. Our findings enhance the global comprehension of human genetic diversity and underscore the value of studying indigenous populations. Such research is vital for deepening our insights into human migration patterns and evolutionary processes.
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Affiliation(s)
| | - Timothy Adrian Jinam
- Department of Para-Clinical Sciences, Faculty of Medicine & Health Sciences, University Malaysia Sarawak, Malaysia
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.
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4
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Tizu M, Calenic B, Hârza M, Cristea BM, Maruntelu I, Caragea AM, Talangescu A, Dima A, Constantinescu AE, Constantinescu I. HLA Gene Polymorphisms in Romanian Patients with Chronic Lymphocytic Leukemia. Genet Res (Camb) 2024; 2024:8852876. [PMID: 38449839 PMCID: PMC10917483 DOI: 10.1155/2024/8852876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/24/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
Materials and Methods This study included 66 patients with CLL, diagnosed between 2020 and 2022, and 100 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQA1/DQB1/DPA1/DPB1, and HLA-DRB1/3/4/5) were investigated using next-generation sequencing technology. Results Several HLA alleles were strongly associated with CLL. The most important finding was that HLA-DRB1∗04:02:01 (p=0.001, OR = 1.05) and HLA-DRB3∗02:01:01 (p=0.009, OR = 1.03) have a predisposing role in CLL development. Moreover, we identified that HLA-A∗24:02:01 0.01 (p=0.01, OR = 0.38), HLA-DQA1∗05:05:01 (p=0.01, OR = 0.56), HLA-DQB1∗03:02:01 (p=0.03, OR = 0.40), and HLA-DRB4∗01:03:01 (p=0.03, OR = 0.54 alleles have protective roles. Correlations between HLA expression and gender showed that women had a higher expression of protective HLA alleles when compared to men. Conclusions Our data are the first to indicate that in Romanian patients with CLL, the HLA-A∗24:02:01 and HLA-DQA1∗05:05:01 alleles have a protective role against CLL development, whereas HLA-DRB1∗04:02:01 and HLA-DRB3∗02:01:01alleles are positively associated with CLL.
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Affiliation(s)
- Maria Tizu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan Calenic
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Mihai Hârza
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan M. Cristea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ion Maruntelu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Andreea M. Caragea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Adriana Talangescu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Alina Dima
- Colentina Clinical Hospital, Rheumatology Department Bucharest, 19-21 Stefan Cel Mare Street, Bucharest 020125, Romania
| | - Alexandra E. Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ileana Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
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Davis González MR, Ballester MP, Romero-González E, Sánchez-Pardo AM, Marti-Aguado D, Tosca J, Suria C, Antón Ausejo R, Pascual Moreno I, Planelles Silvestre MD, Mínguez Pérez M, Bosca-Watts MM. Biological treatment interruption in inflammatory bowel disease: Motivation and predictive factors. GASTROENTEROLOGIA Y HEPATOLOGIA 2023; 46:671-681. [PMID: 36375696 DOI: 10.1016/j.gastrohep.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Loss-of-response and adverse events (AE) to biologics have been linked to HLA-DQA1*05 allele. However, the clinical factors or biologic used may influence treatment duration. Our objective was to evaluate the influence of clinical and therapeutic factors, along with HLA, in biological treatment discontinuation. METHODS A retrospective study of consecutive IBD patients treated with biologics between 2007 and 2011 was performed. Main outcome was treatment discontinuation due to primary non-response (PNR), secondary loss of response (SLR) or AE. HLA-DQA1 genotyping was done in all patients. Regression analyses were used to assess risk factors of treatment discontinuation. RESULTS One hundred fifty patients (61% male) with 312 biologic treatments were included. 147 (47%) were discontinued with a cumulative probability of 30%, 41% and 56% at 1, 2 and 5 years. The use of infliximab (p=0.006) and articular manifestations (p<0.05) were associated with treatment discontinuation. Considering cause of withdrawal, Ulcerative Colitis (UC) had a higher proportion of PNR (HR=4.99; 95% CI=1.71-14.63; p=0.003), SLR was higher if biologics had been indicated due to disease flare (HR=2.32; 95% CI=1.05-5.09; p=0.037) while AE were greater with infliximab (HR=2.46; 95% CI=1.48-4.08; p<0.001) or spondylitis (HR=2.46; 95% CI=1.78-6.89; p<0.001). According to the biological drug, HLA-DQA1*05 with adalimumab showed more SLR in cases with Crohn's disease (HR=3.49; 95% CI=1.39-8,78; p=0.008) or without concomitant immunomodulator (HR=2.8; 95% CI=1.1-6.93; p=0.026). CONCLUSIONS HLA-DQ A1*05 was relevant in SLR of IBD patients treated with adalimumab without immunosupression. In patients treated with other biologics, clinical factors were more important for treatment interruption, mainly extensive UC or extraintestinal manifestations and having indicated the biologic for flare.
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Affiliation(s)
- María Rocío Davis González
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - María Pilar Ballester
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain; Instituto de Investigación Sanitaria INCLIVA, Spain.
| | - Eva Romero-González
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Ana María Sánchez-Pardo
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - David Marti-Aguado
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Joan Tosca
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Carles Suria
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Rosario Antón Ausejo
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Isabel Pascual Moreno
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | | | - Miguel Mínguez Pérez
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
| | - Marta Maia Bosca-Watts
- IBD Unit, Digestive Disease Medicine, University of Valencia, University Clinic Hospital of Valencia, Spain
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Lombardi L, Le Clerc S, Wu CL, Bouassida J, Boukouaci W, Sugusabesan S, Richard JR, Lajnef M, Tison M, Le Corvoisier P, Barau C, Banaschewski T, Holt R, Durston S, Persico AM, Oakley B, Loth E, Buitelaar J, Murphy D, Leboyer M, Zagury JF, Tamouza R. A human leukocyte antigen imputation study uncovers possible genetic interplay between gut inflammatory processes and autism spectrum disorders. Transl Psychiatry 2023; 13:244. [PMID: 37407551 DOI: 10.1038/s41398-023-02550-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental conditions that are for subsets of individuals, underpinned by dysregulated immune processes, including inflammation, autoimmunity, and dysbiosis. Consequently, the major histocompatibility complex (MHC)-hosted human leukocyte antigen (HLA) has been implicated in ASD risk, although seldom investigated. By utilizing a GWAS performed by the EU-AIMS consortium (LEAP cohort), we compared HLA and MHC genetic variants, single nucleotide polymorphisms (SNP), and haplotypes in ASD individuals, versus typically developing controls. We uncovered six SNPs, namely rs9268528, rs9268542, rs9268556, rs14004, rs9268557, and rs8084 that crossed the Bonferroni threshold, which form the underpinnings of 3 independent genetic pathways/blocks that differentially associate with ASD. Block 1 (rs9268528-G, rs9268542-G, rs9268556-C, and rs14004-A) afforded protection against ASD development, whilst the two remaining blocks, namely rs9268557-T, and rs8084-A, associated with heightened risk. rs8084 and rs14004 mapped to the HLA-DRA gene, whilst the four other SNPs located in the BTNL2 locus. Different combinations amongst BTNL2 SNPs and HLA amino acid variants or classical alleles were found either to afford protection from or contribute to ASD risk, indicating a genetic interplay between BTNL2 and HLA. Interestingly, the detected variants had transcriptional and/or quantitative traits loci implications. As BTNL2 modulates gastrointestinal homeostasis and the identified HLA alleles regulate the gastrointestinal tract in celiac disease, it is proposed that the data on ASD risk may be linked to genetically regulated gut inflammatory processes. These findings might have implications for the prevention and treatment of ASD, via the targeting of gut-related processes.
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Affiliation(s)
- Laura Lombardi
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Sigrid Le Clerc
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Ching-Lien Wu
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Jihène Bouassida
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Wahid Boukouaci
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Sobika Sugusabesan
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Jean-Romain Richard
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Mohamed Lajnef
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Maxime Tison
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Philippe Le Corvoisier
- Université Paris Est Créteil, Inserm, Centre Investigation Clinique, CIC 1430, Henri Mondor, Créteil, F94010, France
| | - Caroline Barau
- Plateforme de Ressources Biologiques, HU Henri Mondor, Créteil, F94010, France
| | - Tobias Banaschewski
- Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rosemary Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Sarah Durston
- Education Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Antonio M Persico
- Child and Adolescent Neuropsychiatry Program at Modena University Hospital, & Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Bethany Oakley
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Eva Loth
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Declan Murphy
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Marion Leboyer
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, AP-HP, Hôpital Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision (FHU ADAPT) and Fondation FondaMental, Créteil, F-94010, France
| | - Jean-François Zagury
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Ryad Tamouza
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France.
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, AP-HP, Hôpital Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision (FHU ADAPT) and Fondation FondaMental, Créteil, F-94010, France.
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DelBaugh RM, Cook LJ, Siegel CA, Tsongalis GJ, Khan WA. Validation of a rapid HLA-DQA1*05 pharmacogenomics assay to identify at-risk resistance to anti-tumor necrosis factor therapy among patients with inflammatory bowel disease. Am J Clin Pathol 2023:7136686. [PMID: 37086490 DOI: 10.1093/ajcp/aqad036] [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: 12/07/2022] [Accepted: 03/12/2023] [Indexed: 04/24/2023] Open
Abstract
OBJECTIVES The HLA-DQA1*05 variant (rs2097432) is associated with increased risk of immunogenicity to tumor necrosis factor antagonists, with subsequent resistance to therapy in patients with inflammatory bowel disease. Identification of these patients would optimize personalized therapeutic selection. METHODS Genomic DNA was extracted from 80 deidentified samples in an unselected patient population with an unknown rs2097432 genotype. Split sample analysis was performed using a reference laboratory. Primer probes for a TaqMan quantitative polymerase chain reaction (qPCR) assay (Thermo Fisher Scientific) were custom designed. Synthesized genomic-block fragments were used as controls. All qPCR reactions were performed using a TaqMan GTXpress Master Mix (Thermo Fisher Scientific) on the Applied Biosystems 7500 system under fast cycling conditions. RESULTS Of 80 samples, 50% were wild-type reference genotypes, 22.5% were heterozygous, and 27.5% were homozygous variant calls, comparable to population data. Split analysis samples between 2 independent laboratories were 100% concordant. The detection limit tested across genomic-block controls processed in duplicate was reproducible on sample input from 10 ng titrated down to 1.25 ng across 2 independent runs. Further, analytical specificity assessed with previous wild-type reference and homozygous variant DNA spiked into genomic-block controls produced appropriate heterozygous genotypes. CONCLUSIONS Here we present validation of a lab-developed test for a rapid HLA-DQA1*05 (rs2097432) pharmacogenomics assay targeting a hotspot identified by genome-wide association studies. Targeted genotyping employed here will allow for expeditious personalized therapeutic selection.
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Affiliation(s)
- Regina M DelBaugh
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
| | - Leanne J Cook
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
| | - Corey A Siegel
- Inflammatory Bowel Disease Center, Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
- Departments of Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, US
| | - Gregory J Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
- Departments of Pathology and Laboratory Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, US
| | - Wahab A Khan
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
- Departments of Pathology and Laboratory Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, US
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8
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Human Leukocyte Antigen Alleles Compatibility and Immunophenotypic Profile Associations in Infertile Couples. Cureus 2023; 15:e36584. [PMID: 36968684 PMCID: PMC10035384 DOI: 10.7759/cureus.36584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 03/25/2023] Open
Abstract
Introduction: The maternal immune system has a major role in the successful embryo implantation and maintenance of the pregnancy. This study aimed to investigate the maternal immunophenotyping profile (percentage of Natural Killer [NK] cells and the CD4/CD8 [cluster designation] ratio in peripheral blood lymphocytes) and the HLA (Human Leukocyte Antigen)-DQA1 alleles sharing in infertile couples. Methods: This cross-sectional study included 78 women who had experienced at least two spontaneous miscarriages and 110 women with a history of recurrent implantation failures after in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) and embryo transfer (ET) (IVF-ET failures). The NK cell percentage and the CD4/CD8 ratio were determined by flow cytometry. Genotyping of the HLA-DQA1 alleles was carried out for all women and their partners, and couple HLA-DQA1 compatibility was expressed as the percentage of common HLA-DQA1 alleles (totaling 35 alleles) shared between spouses to the sum of the unique alleles observed. Results: In women with recurrent miscarriages, high values (%) of the NK population with a median (interquartile range [IQR]) of 10.3% (7.7% to 12.5%) and CD4/CD8 ratio (1.7) (1.5 to 2.1) were found. In women with IVF-ET failures, the (%) NK population (10.5%) (8.6% to 12.5%) and CD4/CD8 ratio (1.8) (1.5 to 2.1) were similarly increased (p=0.390, and p=0.490, respectively). The proportion of women with >10% NK cells was 53.8% and 58.2% in women with miscarriages and IVF-ET failures, respectively (p=0.554). The prevalence of HLA-DQA1*5 allele carriage was elevated in women with miscarriages as well as those with IVF-ET failures (52.6% and 61.8%, respectively; p=0.206). The proportion of couples with high (>50%) HLA-DQA1 sharing was 65.4% in the group with miscarriages and 73.6% in the group with IVF-ET failures, respectively (p=0.222). The CD4/CD8 ratio was statistically significantly positively correlated with the (%) NK population in women with IVF-ET failures (rho = 0.297, p=0.002) and with the (%) HLA-DQA1 sharing in the group with miscarriages (rho = 0.266, p=0.019). The couples in which both spouses were carriers of the HLA-DQA1*5 allele had an increased probability of high (>50%) HLA-DQA1 compatibility compared with the couples in which neither of the spouses carried the allele in the miscarriage group (OR = 24.3, 95% CI: 3.0 to 198.9, p<0.001), and the IVF-ET failure group (OR = 10.5, 95% CI: 2.2 to 49.8, p<0.001). Conclusion: The peripheral NK (%) population and CD4/CD8 ratio, as well as the prevalence of the HLA-DQA1*5 allele, were elevated in women with recurrent miscarriages and IVF-ET failures. Furthermore, these couples with negative reproductive outcomes had a high percentage of HLA-DQA1 allele similarity. The presence of the HLA-DQA1*5 allele in spouses was strongly associated with overall couple HLA-DQA1 compatibility, implying that it could be used as a surrogate marker for assessing overall immunological compatibility in infertile couples.
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Spencer EA, Dubinsky MC. Reply. Gastroenterology 2022; 163:1124-1125. [PMID: 35809614 DOI: 10.1053/j.gastro.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Elizabeth A Spencer
- Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine, Mount Sinai, New York, New York
| | - Marla C Dubinsky
- Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine, Mount Sinai, New York, New York
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