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Sartoris S, Del Pozzo G. Exploring the HLA complex in autoimmunity: From the risk haplotypes to the modulation of expression. Clin Immunol 2024; 265:110266. [PMID: 38851519 DOI: 10.1016/j.clim.2024.110266] [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: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The genes mapping at the HLA region show high density, strong linkage disequilibrium and high polymorphism, which affect the association of HLA class I and class II genes with autoimmunity. We focused on the HLA haplotypes, genomic structures consisting of an array of specific alleles showing some degrees of genetic association with different autoimmune disorders. GWASs in many pathologies have identified variants in either the coding loci or the flanking regulatory regions, both in linkage disequilibrium in haplotypes, that are frequently associated with increased risk and may influence gene expression. We discuss the relevance of the HLA gene expression because the level of surface heterodimers determines the number of complexes presenting self-antigen and, thus, the strength of pathogenic autoreactive T cells immune response.
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Affiliation(s)
- Silvia Sartoris
- Dept. of Medicine, Section of Immunology University of Verona School of Medicine, Verona, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" National Research Council (CNR), Naples, Italy.
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2
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Efstratiou A, Gaigher A, Künzel S, Teles A, Lenz TL. Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression. Mol Ecol Resour 2024; 24:e13935. [PMID: 38332480 DOI: 10.1111/1755-0998.13935] [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: 06/02/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the major histocompatibility complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ data sets of three-spined stickleback gDNA, cDNA and "artificial" plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, the gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks, and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes, and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.
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Affiliation(s)
- Artemis Efstratiou
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arnaud Gaigher
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ana Teles
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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3
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Petersdorf EW, McKallor C, Malkki M, He M, Spellman SR, Gooley T, Stevenson P. HLA Haplotypes and Relapse After Hematopoietic Cell Transplantation. J Clin Oncol 2024; 42:886-897. [PMID: 38051980 PMCID: PMC10927336 DOI: 10.1200/jco.23.01264] [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: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 12/07/2023] Open
Abstract
PURPOSE Recurrence of blood malignancy is the major cause of hematopoietic cell transplant failure. HLA class II molecules play a fundamental role in antitumor responses but the role of class II haplotypes is not known. METHODS HLA-DR, -DQ, -DM, and -DO allele variation was determined in 1,629 related haploidentical transplants to study the clinical significance of individual molecules and haplotypes. RESULTS Outcome correlated with patient and donor variation for HLA-DRβ residue 86 (Gly/Val), HLA-DQ (G1/G2) heterodimers, and donor HLA-DM (DM11,11/nonDM11,11) molecules, and depended on patient-donor mismatching. Risks of relapse were lower for DRβ-86 GlyGly patients when the donor was GlyVal (hazard ratio [HR], 0.46 [95% CI, 0.30 to 0.68]; P < .001); GlyVal patients benefited from HLA-DRB1-matched donors, whereas no donor was superior to another for ValVal patients. G1G2 patients with G1G2-mismatched donors had lower relapse. Transplantation from donors with DMα residue 184 ArgHis was associated with higher risk of relapse (HR, 1.60 [95% CI, 1.09 to 2.36]; P = .02) relative to ArgArg. Relapse and mortality risks differed across HLA-DR-DQ-DM haplotypes. CONCLUSION HLA class II haplotypes may be functional constituents of the transplantation barrier, and their consideration in patients and donors may improve the success of transplantation.
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Affiliation(s)
- Effie W. Petersdorf
- Division of Translational Science and Therapeutics, Fred Hutchinson Cancer Center, Seattle, WA
- University of Washington School of Medicine, Seattle, WA
| | - Caroline McKallor
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Mari Malkki
- Division of Translational Science and Therapeutics, Fred Hutchinson Cancer Center, Seattle, WA
| | - Meilun He
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Theodore Gooley
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
| | - Philip Stevenson
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
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4
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Shook MS, Lu X, Chen X, Parameswaran S, Edsall L, Trimarchi MP, Ernst K, Granitto M, Forney C, Donmez OA, Diouf AA, VonHandorf A, Rothenberg ME, Weirauch MT, Kottyan LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. Am J Hum Genet 2024; 111:280-294. [PMID: 38183988 PMCID: PMC10870143 DOI: 10.1016/j.ajhg.2023.12.008] [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: 05/24/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/08/2024] Open
Abstract
Eosinophilic esophagitis (EoE) is a rare atopic disorder associated with esophageal dysfunction, including difficulty swallowing, food impaction, and inflammation, that develops in a small subset of people with food allergies. Genome-wide association studies (GWASs) have identified 9 independent EoE risk loci reaching genome-wide significance (p < 5 × 10-8) and 27 additional loci of suggestive significance (5 × 10-8 < p < 1 × 10-5). In the current study, we perform linkage disequilibrium (LD) expansion of these loci to nominate a set of 531 variants that are potentially causal. To systematically interrogate the gene regulatory activity of these variants, we designed a massively parallel reporter assay (MPRA) containing the alleles of each variant within their genomic sequence context cloned into a GFP reporter library. Analysis of reporter gene expression in TE-7, HaCaT, and Jurkat cells revealed cell-type-specific gene regulation. We identify 32 allelic enhancer variants, representing 6 genome-wide significant EoE loci and 7 suggestive EoE loci, that regulate reporter gene expression in a genotype-dependent manner in at least one cellular context. By annotating these variants with expression quantitative trait loci (eQTL) and chromatin looping data in related tissues and cell types, we identify putative target genes affected by genetic variation in individuals with EoE. Transcription factor enrichment analyses reveal possible roles for cell-type-specific regulators, including GATA3. Our approach reduces the large set of EoE-associated variants to a set of 32 with allelic regulatory activity, providing functional insights into the effects of genetic variation in this disease.
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Affiliation(s)
- Molly S Shook
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lee Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael P Trimarchi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kevin Ernst
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Arame A Diouf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marc E Rothenberg
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 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; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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5
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Kulski JK, Suzuki S, Shiina T. Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes. Hum Genome Var 2022; 9:49. [PMID: 36543786 PMCID: PMC9772353 DOI: 10.1038/s41439-022-00226-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on 'The Current Landscape of HLA Genomics and Genetics', we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases.
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Affiliation(s)
- Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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Regulation of HLA class I expression by non-coding gene variations. PLoS Genet 2022; 18:e1010212. [PMID: 35666741 PMCID: PMC9170083 DOI: 10.1371/journal.pgen.1010212] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
The Human Leukocyte Antigen (HLA) is a critical genetic system for different outcomes after solid organ and hematopoietic cell transplantation. Its polymorphism is usually determined by molecular technologies at the DNA level. A potential role of HLA allelic expression remains under investigation in the context of the allogenic immune response between donors and recipients. In this study, we quantified the allelic expression of all three HLA class I loci (HLA-A, B and C) by RNA sequencing and conducted an analysis of expression quantitative traits loci (eQTL) to investigate whether HLA expression regulation could be associated with non-coding gene variations. HLA-B alleles exhibited the highest expression levels followed by HLA-C and HLA-A alleles. The max fold expression variation was observed for HLA-C alleles. The expression of HLA class I loci of distinct individuals demonstrated a coordinated and paired expression of both alleles of the same locus. Expression of conserved HLA-A~B~C haplotypes differed in distinct PBMC's suggesting an individual regulated expression of both HLA class I alleles and haplotypes. Cytokines TNFα /IFNβ, which induced a very similar upregulation of HLA class I RNA and cell surface expression across alleles did not modify the individually coordinated expression at the three HLA class I loci. By identifying cis eQTLs for the HLA class I genes, we show that the non-coding eQTLs explain 29%, 13%, and 31% of the respective HLA-A, B, C expression variance in unstimulated cells, and 9%, 23%, and 50% of the variance in cytokine-stimulated cells. The eQTLs have significantly higher effect sizes in stimulated cells compared to unstimulated cells for HLA-B and HLA-C genes expression. Our data also suggest that the identified eQTLs are independent from the coding variation which defines HLA alleles and thus may be influential on intra-allele expression variability although they might not represent the causal eQTLs.
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Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 2021; 12:1611. [PMID: 33712590 PMCID: PMC7955039 DOI: 10.1038/s41467-021-21854-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE. Thousands of genetic variants have been associated with lupus, but causal variants and mechanisms are unknown. Here, the authors combine a massively parallel reporter assay with genome-wide ChIP experiments to identify risk variants with allelic enhancer activity mediated through transcription factor binding.
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8
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Johansson T, Yohannes DA, Koskela S, Partanen J, Saavalainen P. HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression. Front Immunol 2021; 12:629059. [PMID: 33717155 PMCID: PMC7949471 DOI: 10.3389/fimmu.2021.629059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
The HLA gene complex is the most important single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. Most studies have focused on the vast allelic variation in these genes; only a few studies have explored differences in the expression levels of HLA alleles. In this study, we quantified mRNA expression levels of HLA class I and II genes from peripheral blood samples of 50 healthy individuals. The gene- and allele-specific mRNA expression was assessed using unique molecular identifiers, which enabled PCR bias removal and calculation of the number of original mRNA transcripts. We identified differences in mRNA expression between different HLA genes and alleles. Our results suggest that HLA alleles are differentially expressed and these differences in expression levels are quantifiable using RNA sequencing technology. Our method provides novel insights into HLA research, and it can be applied to quantify expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.
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Affiliation(s)
- Tiira Johansson
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Dawit A. Yohannes
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
| | - Satu Koskela
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Päivi Saavalainen
- Research Programs Unit, Translational Immunology Program, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
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9
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Kulski JK, Suzuki S, Shiina T. SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction. Front Genet 2021; 11:594318. [PMID: 33537058 PMCID: PMC7848197 DOI: 10.3389/fgene.2020.594318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.
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Affiliation(s)
- Jerzy K. Kulski
- Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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10
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HLA class II genes in precision-based care of childhood diseases: what we can learn from celiac disease. Pediatr Res 2021; 89:307-312. [PMID: 33122841 DOI: 10.1038/s41390-020-01217-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022]
Abstract
Celiac disease (CeD) is a chronic immuno-mediated enteropathy caused by dietary gluten with marked autoimmunity traits. The human leukocyte antigen (HLA) class II heterodimers represent the main predisposing factor, although environmental agents, as viral infection, gut microbiota, and dietary regimen, also contribute to CeD risk. These molecules are involved in autoimmunity as they present self-antigens to autoreactive T cells that have escaped the thymic negative selection. In CeD, the HLA class II risk alleles, DQA1*05-DQB1*02 and DQA1*03-DQB1*03, encode for DQ2.5 and DQ8 heterodimers, and, furthermore, disease susceptibility was found strictly dependent on the dose of these genes. This finding questioned how the expression of HLA-DQ risk genes, and of relative surface protein on antigen-presenting cells, might be relevant for the magnitude of anti-gluten inflammatory response in CeD patients, and impact the natural history of disease, its pathomechanisms, and compliance to dietary treatment. In this scenario, new personalized medical approaches will be desirable to support an early, accurate, and non-invasive diagnosis, and to define genotype-guided preventive and therapeutic strategies for CeD. To reach this goal, a stratification of genetic risk, disease outcome, and therapy compliance based on HLA genotypes, DQ2.5/DQ8 expression measurement and magnitude of T cell response to gluten is mandatory. IMPACT: This article revises the current knowledge on how different HLA haplotypes, carrying the DQ2.5/DQ8 risk alleles, impact the onset of CeD. This review discusses how the expression of susceptibility HLA-DQ genes can determine the risk assessment, outcome, and prevention of CeD. The recent insights on the environmental factors contributing to CeD in childhood are reviewed. This review discusses the use of HLA risk gene expression as a tool to support medical precision approaches for an early and non-invasive diagnosis of CeD, and to define genotype-guided preventive and therapeutic strategies.
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11
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Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. eLife 2020; 9:59929. [PMID: 33084571 PMCID: PMC7644215 DOI: 10.7554/elife.59929] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.
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Affiliation(s)
| | - Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, United States
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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12
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Differential expression of predisposing HLA-DQ2.5 alleles in DR5/DR7 celiac disease patients affects the pathological immune response to gluten. Sci Rep 2020; 10:17227. [PMID: 33057065 PMCID: PMC7560598 DOI: 10.1038/s41598-020-73907-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/16/2020] [Indexed: 11/08/2022] Open
Abstract
The DR5-DQ7/DR7-DQ2 genotype is very frequent among patients affected by celiac disease (CD), in Europe. This genotype, associated to high risk of CD, carries the HLA-DQA1*05 and HLA-DQB1*02 predisposing alleles, in trans configuration. The alleles encode the DQ2.5 heterodimer responsible of gluten peptide presentation on the surface of antigen-presenting cells (APCs), and consequent pathogenic CD4+ T cell activation. We demonstrated that DR5/DR7 APCs induce an anti-gluten CD4+ T cell response, of comparable intensity to that observed with APCs carrying DR1/DR3 genotype, which risk alleles are in cis configuration. In addition, we showed that DR5/DR7 APCs from celiac patients stimulated an effector CD4+ T cell response higher with respect to that induced by DR5/DR7 APCs from healthy subjects. To explain these findings, we assessed the DQ2.5 RNA and protein quantity. We showed that the expression of DQA1*05 and DQB1*02 risk alleles is much higher than the expression of non-CD-associated alleles, in agreement with the previous results obtained with DR1/DR3 genotype. The differential expression of transcripts influences the quantity of DQα1*05 and DQβ1*02 chains and, as consequence, the cell surface density of DQ2.5 heterodimers. Moreover, both RNA and proteins, are more abundant in APCs from celiac patients than controls. Finally, to unravel the mechanism regulating the expression of predisposing DQA1*05 and DQB1*02 alleles, we quantified the new synthetized RNA and found that the differential expression is explained by their transcription rate. Our results confirmed that the strength of antigen-specific CD4+ T cell response is mainly determined by the amount of gluten in the diet and provided a new possible approach for a personalized diagnosis and for risk stratification.
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Hässler S, Bachelet D, Duhaze J, Szely N, Gleizes A, Hacein-Bey Abina S, Aktas O, Auer M, Avouac J, Birchler M, Bouhnik Y, Brocq O, Buck-Martin D, Cadiot G, Carbonnel F, Chowers Y, Comabella M, Derfuss T, De Vries N, Donnellan N, Doukani A, Guger M, Hartung HP, Kubala Havrdova E, Hemmer B, Huizinga T, Ingenhoven K, Hyldgaard-Jensen PE, Jury EC, Khalil M, Kieseier B, Laurén A, Lindberg R, Loercher A, Maggi E, Manson J, Mauri C, Mohand Oumoussa B, Montalban X, Nachury M, Nytrova P, Richez C, Ryner M, Sellebjerg F, Sievers C, Sikkema D, Soubrier M, Tourdot S, Trang C, Vultaggio A, Warnke C, Spindeldreher S, Dönnes P, Hickling TP, Hincelin Mery A, Allez M, Deisenhammer F, Fogdell-Hahn A, Mariette X, Pallardy M, Broët P. Clinicogenomic factors of biotherapy immunogenicity in autoimmune disease: A prospective multicohort study of the ABIRISK consortium. PLoS Med 2020; 17:e1003348. [PMID: 33125391 PMCID: PMC7598520 DOI: 10.1371/journal.pmed.1003348] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/18/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Biopharmaceutical products (BPs) are widely used to treat autoimmune diseases, but immunogenicity limits their efficacy for an important proportion of patients. Our knowledge of patient-related factors influencing the occurrence of antidrug antibodies (ADAs) is still limited. METHODS AND FINDINGS The European consortium ABIRISK (Anti-Biopharmaceutical Immunization: prediction and analysis of clinical relevance to minimize the RISK) conducted a clinical and genomic multicohort prospective study of 560 patients with multiple sclerosis (MS, n = 147), rheumatoid arthritis (RA, n = 229), Crohn's disease (n = 148), or ulcerative colitis (n = 36) treated with 8 different biopharmaceuticals (etanercept, n = 84; infliximab, n = 101; adalimumab, n = 153; interferon [IFN]-beta-1a intramuscularly [IM], n = 38; IFN-beta-1a subcutaneously [SC], n = 68; IFN-beta-1b SC, n = 41; rituximab, n = 31; tocilizumab, n = 44) and followed during the first 12 months of therapy for time to ADA development. From the bioclinical data collected, we explored the relationships between patient-related factors and the occurrence of ADAs. Both baseline and time-dependent factors such as concomitant medications were analyzed using Cox proportional hazard regression models. Mean age and disease duration were 35.1 and 0.85 years, respectively, for MS; 54.2 and 3.17 years for RA; and 36.9 and 3.69 years for inflammatory bowel diseases (IBDs). In a multivariate Cox regression model including each of the clinical and genetic factors mentioned hereafter, among the clinical factors, immunosuppressants (adjusted hazard ratio [aHR] = 0.408 [95% confidence interval (CI) 0.253-0.657], p < 0.001) and antibiotics (aHR = 0.121 [0.0437-0.333], p < 0.0001) were independently negatively associated with time to ADA development, whereas infections during the study (aHR = 2.757 [1.616-4.704], p < 0.001) and tobacco smoking (aHR = 2.150 [1.319-3.503], p < 0.01) were positively associated. 351,824 Single-Nucleotide Polymorphisms (SNPs) and 38 imputed Human Leukocyte Antigen (HLA) alleles were analyzed through a genome-wide association study. We found that the HLA-DQA1*05 allele significantly increased the rate of immunogenicity (aHR = 3.9 [1.923-5.976], p < 0.0001 for the homozygotes). Among the 6 genetic variants selected at a 20% false discovery rate (FDR) threshold, the minor allele of rs10508884, which is situated in an intron of the CXCL12 gene, increased the rate of immunogenicity (aHR = 3.804 [2.139-6.764], p < 1 × 10-5 for patients homozygous for the minor allele) and was chosen for validation through a CXCL12 protein enzyme-linked immunosorbent assay (ELISA) on patient serum at baseline before therapy start. CXCL12 protein levels were higher for patients homozygous for the minor allele carrying higher ADA risk (mean: 2,693 pg/ml) than for the other genotypes (mean: 2,317 pg/ml; p = 0.014), and patients with CXCL12 levels above the median in serum were more prone to develop ADAs (aHR = 2.329 [1.106-4.90], p = 0.026). A limitation of the study is the lack of replication; therefore, other studies are required to confirm our findings. CONCLUSION In our study, we found that immunosuppressants and antibiotics were associated with decreased risk of ADA development, whereas tobacco smoking and infections during the study were associated with increased risk. We found that the HLA-DQA1*05 allele was associated with an increased rate of immunogenicity. Moreover, our results suggest a relationship between CXCL12 production and ADA development independent of the disease, which is consistent with its known function in affinity maturation of antibodies and plasma cell survival. Our findings may help physicians in the management of patients receiving biotherapies.
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Affiliation(s)
- Signe Hässler
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, UVSQ, Paris-Saclay University, Villejuif, France
- Sorbonne Université, INSERM UMR 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
- * E-mail: (SH); (PB)
| | - Delphine Bachelet
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, UVSQ, Paris-Saclay University, Villejuif, France
- Department of Biostatistical Epidemiology and Clinical Research, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris AP-HP.Nord, INSERM CIC-EC 1425, Paris, France
| | - Julianne Duhaze
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, UVSQ, Paris-Saclay University, Villejuif, France
- CHU Ste-Justine Research Center, Montreal, Canada
| | - Natacha Szely
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
| | - Aude Gleizes
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
- Clinical Immunology Laboratory, AP-HP, Le Kremlin-Bicêtre Hospital, Paris-Sud University Hospitals, Le Kremlin-Bicêtre, France
| | - Salima Hacein-Bey Abina
- Clinical Immunology Laboratory, AP-HP, Le Kremlin-Bicêtre Hospital, Paris-Sud University Hospitals, Le Kremlin-Bicêtre, France
- UTCBS, CNRS UMR 8258, INSERM U1022, Faculty of Pharmacy, Paris-Descartes-Sorbonne-Cite University, Paris, France
| | - Orhan Aktas
- University of Düsseldorf, Medical Faculty, Department of Neurology, Düsseldorf, Germany
| | - Michael Auer
- Innsbruck Medical University, Department of Neurology, Innsbruck, Austria
| | - Jerôme Avouac
- Paris University, Paris Descartes University, INSERM U1016, Paris, France
- Rheumatology department, Cochin Hospital, AP-HP.CUP, Paris, France
| | - Mary Birchler
- GlaxoSmithKline, Clinical Immunology–Biopharm, Collegeville, Pennsylvania, United States of America
| | - Yoram Bouhnik
- AP-HP, Hôpital Beaujon, Paris, France
- GETAID, Paris, France
| | | | | | - Guillaume Cadiot
- GETAID, Paris, France
- Service d'hépato-gastroentérologie, University Hospital of Reims, Reims, France
| | - Franck Carbonnel
- GETAID, Paris, France
- Department of Gastroenterology, AP-HP, Hôpital Kremlin-Bicêtre, France
| | - Yehuda Chowers
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel; Bruce Rappaport School of Medicine, Technion Israel Institute of Technology, Haifa, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa, Israel
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat). Institut de Recerca Vall d’Hebron (VHIR). Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tobias Derfuss
- Departments of Biomedicine and Neurology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Niek De Vries
- Rheumatology & Clinical Immunology, Amsterdam UMC | AMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Abiba Doukani
- Sorbonne Université, Inserm, UMS Production et Analyse des données en Sciences de la vie et en Santé, UMS 37 PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, Paris, France
| | - Michael Guger
- Clinic for Neurology 2, Med Campus III, Kepler University Hospital GmbH, Linz, Austria
| | - Hans-Peter Hartung
- University of Düsseldorf, Medical Faculty, Department of Neurology, Düsseldorf, Germany
| | - Eva Kubala Havrdova
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Bernhard Hemmer
- Department of Neurology, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tom Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kathleen Ingenhoven
- University of Düsseldorf, Medical Faculty, Department of Neurology, Düsseldorf, Germany
| | - Poul Erik Hyldgaard-Jensen
- Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Elizabeth C. Jury
- Centre for Rheumatology Research, University College London, London, United Kingdom
| | - Michael Khalil
- Department of Neurology, Medical University of Graz, Austria
| | - Bernd Kieseier
- University of Düsseldorf, Medical Faculty, Department of Neurology, Düsseldorf, Germany
| | | | - Raija Lindberg
- Departments of Biomedicine and Neurology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Amy Loercher
- GlaxoSmithKline, Clinical Immunology–Biopharm, Collegeville, Pennsylvania, United States of America
| | - Enrico Maggi
- Dipartimento di Medicina Sperimentale e Clínica, Università di Firenze, Firenze, Italy
- Immunology Area of Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Jessica Manson
- Department of Rheumatology, University College London Hospital, London, United Kingdom
| | - Claudia Mauri
- Centre for Rheumatology Research, University College London, London, United Kingdom
| | - Badreddine Mohand Oumoussa
- Sorbonne Université, Inserm, UMS Production et Analyse des données en Sciences de la vie et en Santé, UMS 37 PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, Paris, France
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat). Institut de Recerca Vall d’Hebron (VHIR). Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Multiple Sclerosis, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Maria Nachury
- GETAID, Paris, France
- University hospital of Lille, Maladies de l'appareil digestif, Lille, France
| | - Petra Nytrova
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Christophe Richez
- Rheumatology Department, CHU de Bordeaux-GH Pellegrin, Bordeaux, France
- UMR CNRS 5164, Bordeaux University, Bordeaux, France
| | - Malin Ryner
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Sievers
- Departments of Biomedicine and Neurology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Dan Sikkema
- GlaxoSmithKline, Clinical Immunology–Biopharm, Collegeville, Pennsylvania, United States of America
- Current address: Quanterix Corporation, Billerica, Massachusetts, United States of America
| | - Martin Soubrier
- Rheumatology, University Hospital of Clermont Ferrand, Clermont Ferrand, France
| | - Sophie Tourdot
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
| | - Caroline Trang
- GETAID, Paris, France
- Institut des maladies de l'Appareil Digestif, University Hospital of Nantes, Nantes, France
| | - Alessandra Vultaggio
- Dipartimento di Medicina Sperimentale e Clínica, Università di Firenze, Firenze, Italy
| | - Clemens Warnke
- University of Düsseldorf, Medical Faculty, Department of Neurology, Düsseldorf, Germany
- Department of Neurology, University Hospital Köln, Köln, Germany
| | - Sebastian Spindeldreher
- Drug Metabolism Pharmacokinetics-Biologics, Novartis Institutes for Biomedical Research, Basel, Switzerland
- Integrated Biologix GmbH, Basel, Switzerland
| | | | - Timothy P. Hickling
- BioMedicine Design, Pfizer, Inc., Andover, Massachusetts, United States of America
| | | | - Matthieu Allez
- GETAID, Paris, France
- Department of Gastroenterology, Hôpital Saint-Louis, AP-HP, Université Paris-Diderot, Paris, France
| | | | - Anna Fogdell-Hahn
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Xavier Mariette
- Centre for Immunology of Viral Infections and Autoimmune Diseases, INSERM UMR 1184, Université Paris-Saclay, AP-HP.Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Marc Pallardy
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
| | - Philippe Broët
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, UVSQ, Paris-Saclay University, Villejuif, France
- CHU Ste-Justine Research Center, Montreal, Canada
- AP-HP, Paris-Sud University Hospitals, Paul Brousse Hospital, Villejuif, France
- * E-mail: (SH); (PB)
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Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer 2020; 122:569-577. [PMID: 31806877 PMCID: PMC7028992 DOI: 10.1038/s41416-019-0614-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/23/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWASes) have identified many noncoding germline single-nucleotide polymorphisms (SNPs) that are associated with an increased risk of developing cancer. However, how these SNPs affect cancer risk is still largely unknown. METHODS We used a systems biology approach to analyse the regulatory role of cancer-risk SNPs in thirteen tissues. By using data from the Genotype-Tissue Expression (GTEx) project, we performed an expression quantitative trait locus (eQTL) analysis. We represented both significant cis- and trans-eQTLs as edges in tissue-specific eQTL bipartite networks. RESULTS Each tissue-specific eQTL network is organised into communities that group sets of SNPs and functionally related genes. When mapping cancer-risk SNPs to these networks, we find that in each tissue, these SNPs are significantly overrepresented in communities enriched for immune response processes, as well as tissue-specific functions. Moreover, cancer-risk SNPs are more likely to be 'cores' of their communities, influencing the expression of many genes within the same biological processes. Finally, cancer-risk SNPs preferentially target oncogenes and tumour-suppressor genes, suggesting that they may alter the expression of these key cancer genes. CONCLUSIONS This approach provides a new way of understanding genetic effects on cancer risk and provides a biological context for interpreting the results of GWAS cancer studies.
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Affiliation(s)
- Maud Fagny
- Genetique Quantitative et Evolution-Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, Paris, France
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marieke Lydia Kuijjer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - John Quackenbush
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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15
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TNF-Block Genotypes Influence Susceptibility to HIV-Associated Sensory Neuropathy in Indonesians and South Africans. Int J Mol Sci 2020; 21:ijms21020380. [PMID: 31936167 PMCID: PMC7014294 DOI: 10.3390/ijms21020380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 11/17/2022] Open
Abstract
HIV-associated sensory neuropathy (HIV-SN) is a disabling complication of HIV disease and antiretroviral therapies (ART). Since stavudine was removed from recommended treatment schedules, the prevalence of HIV-SN has declined and associated risk factors have changed. With stavudine, rs1799964*C (TNF-1031) associated with HIV-SN in Caucasians and Indonesians but not in South Africans. Here, we investigate associations between HIV-SN and rs1799964*C and 12 other polymorphisms spanning TNF and seven neighboring genes (the TNF-block) in Indonesians (n = 202; 34/168 cases) and South Africans (n = 75; 29/75 cases) treated without stavudine. Haplotypes were derived using fastPHASE and haplotype networks built with PopART. There were no associations with rs1799964*C in either population. However, rs9281523*C in intron 10 of BAT1 (alternatively DDX39B) independently associated with HIV-SN in Indonesians after correcting for lower CD4 T-cell counts and >500 copies of HIV RNA/mL (model p = 0.0011, Pseudo R2 = 0.09). rs4947324*T (between NFKBIL1 and LTA) independently associated with reduced risk of HIV-SN and shared haplotype 1 (containing no minor alleles) associated with increased risk of HIV-SN after correcting for greater body weight, a history of tuberculosis and nadir CD4 T-cell counts (model: p = 0.0003, Pseudo R2 = 0.22). These results confirm TNF-block genotypes influence susceptibility of HIV-SN. However, critical genotypes differ between ethnicities and with stavudine use.
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D'Antonio M, Reyna J, Jakubosky D, Donovan MKR, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. eLife 2019; 8:e48476. [PMID: 31746734 PMCID: PMC6904215 DOI: 10.7554/elife.48476] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account have substantially greater power compared with only using single variants. We examined the association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, postulating that downregulation of RNF5 expression is the likely causal mechanism. Our study provides insights into the genetic architecture of the MHC region and pinpoints disease associations that are due to differential expression of HLA genes and non-HLA genes.
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Affiliation(s)
- Matteo D'Antonio
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Joaquin Reyna
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - David Jakubosky
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
| | - Margaret KR Donovan
- Bioinformatics and Systems Biology Graduate ProgramUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical InformaticsUniversity of California, San DiegoSan DiegoUnited States
| | - Marc-Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Hiroko Matsui
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics InstituteCambridgeUnited Kingdom
| | - Naoki Nariai
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Agnieszka D'Antonio-Chronowska
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
| | - Kelly A Frazer
- Institute for Genomic MedicineUniversity of California, San DiegoSan DiegoUnited States
- Department of PediatricsRady Children’s Hospital, University of California, San DiegoSan DiegoUnited States
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Aguiar VRC, César J, Delaneau O, Dermitzakis ET, Meyer D. Expression estimation and eQTL mapping for HLA genes with a personalized pipeline. PLoS Genet 2019; 15:e1008091. [PMID: 31009447 PMCID: PMC6497317 DOI: 10.1371/journal.pgen.1008091] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 05/02/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
The HLA (Human Leukocyte Antigens) genes are well-documented targets of balancing selection, and variation at these loci is associated with many disease phenotypes. Variation in expression levels also influences disease susceptibility and resistance, but little information exists about the regulation and population-level patterns of expression. This results from the difficulty in mapping short reads originated from these highly polymorphic loci, and in accounting for the existence of several paralogues. We developed a computational pipeline to accurately estimate expression for HLA genes based on RNA-seq, improving both locus-level and allele-level estimates. First, reads are aligned to all known HLA sequences in order to infer HLA genotypes, then quantification of expression is carried out using a personalized index. We use simulations to show that expression estimates obtained in this way are not biased due to divergence from the reference genome. We applied our pipeline to the GEUVADIS dataset, and compared the quantifications to those obtained with reference transcriptome. Although the personalized pipeline recovers more reads, we found that using the reference transcriptome produces estimates similar to the personalized pipeline (r ≥ 0.87) with the exception of HLA-DQA1. We describe the impact of the HLA-personalized approach on downstream analyses for nine classical HLA loci (HLA-A, HLA-C, HLA-B, HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). Although the influence of the HLA-personalized approach is modest for eQTL mapping, the p-values and the causality of the eQTLs obtained are better than when the reference transcriptome is used. We investigate how the eQTLs we identified explain variation in expression among lineages of HLA alleles. Finally, we discuss possible causes underlying differences between expression estimates obtained using RNA-seq, antibody-based approaches and qPCR. The level at which a gene is expressed can have important influence on the phenotype of an organism, including its predisposition to develop diseases. One way to estimate gene expression is by quantifying the abundance of RNA. RNA-seq has become the method of choice to provide such estimates at the genomewide scale. However, the application of RNA-seq to HLA genes —key players in the immune adaptive response— has remained a rarely explored approach. This is due to the problem of mapping bias, which causes deficient read alignment at genes which are very polymorphic and different from the reference genome. This has motivated approaches that replace the single reference genome with personalized sequences, comprised of the individual’s specific HLA genotype. Here we explore the use of computational frameworks to obtain reliable expression levels for HLA genes from RNA-seq datasets. We present a pipeline in which the quantification of HLA expression is carried out using methods which account for HLA diversity, avoiding the biases of standard approaches. We then evaluate the impact of this form of quantifying HLA expression on downstream analyses. The pipeline also allows us to integrate information on eQTLs with expression levels at the HLA allele-level, which can help disentangle different contributions to disease phenotypes and help understand the regulatory architecture at the HLA region.
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Affiliation(s)
- Vitor R. C. Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
| | - Jônatas César
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Olivier Delaneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
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Petersdorf EW, O'hUigin C. The MHC in the era of next-generation sequencing: Implications for bridging structure with function. Hum Immunol 2019; 80:67-78. [PMID: 30321633 PMCID: PMC6542361 DOI: 10.1016/j.humimm.2018.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022]
Abstract
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms. These relationships are critical for understanding the qualitative and quantitative implications of HLA gene diversity. This article summarizes current understanding of non-coding region variation of HLA loci, the consequences of regulatory variation on HLA expression, the role for evolution in shaping lineage-specific expression, and the impact of HLA expression on disease susceptibility and transplantation outcomes. A role for phased sequencing methods for the MHC, and perspectives for future directions in basic and applied immunogenetic studies of the MHC are presented.
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Affiliation(s)
- Effie W Petersdorf
- University of Washington, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-115, Seattle, WA 98109, United States.
| | - Colm O'hUigin
- Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Microbiome and Genetics Core, Building 37, Room 4140B, Bethesda, MD 20852, United States.
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Gianfrani C, Pisapia L, Picascia S, Strazzullo M, Del Pozzo G. Expression level of risk genes of MHC class II is a susceptibility factor for autoimmunity: New insights. J Autoimmun 2018; 89:1-10. [PMID: 29331322 DOI: 10.1016/j.jaut.2017.12.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 02/08/2023]
Abstract
To date, the study of the impact of major hystocompatibility complex on autoimmunity has been prevalently focused on structural diversity of MHC molecules in binding and presentation of (auto)antigens to cognate T cells. Recently, a number of experimental evidences suggested new points of view to investigate the complex relationships between MHC gene expression and the individual predisposition to autoimmune diseases. Irrespective of the nature of the antigen, a threshold of MHC-peptide complexes needs to be reached, as well as a threshold of T cell receptors engaged is required, for the activation and proliferation of autoantigen-reactive T cells. Moreover, it is well known that increased expression of MHC class II molecules may alter the T cell receptor repertoire during thymic development, and affect the survival and expansion of mature T cells. Many evidences confirmed that the level of both transcriptional and post-transcriptional regulation are involved in the modulation of the expression of MHC class II genes and that both contribute to the predisposition to autoimmune diseases. Here, we aim to focus some of these regulative aspects to better clarify the role of MHC class II genes in predisposition and development of autoimmunity.
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Affiliation(s)
- Carmen Gianfrani
- Institute of Protein Biochemistry-CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Laura Pisapia
- Institute of Genetics and Biophysics-CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Stefania Picascia
- Institute of Protein Biochemistry-CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Maria Strazzullo
- Institute of Genetics and Biophysics-CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics-CNR, Via Pietro Castellino 111, 80131, Naples, Italy.
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