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Zhao LP, Skyler J, Papadopoulos GK, Pugliese A, Najera JA, Bondinas GP, Moustakas AK, Wang R, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å. Association of HLA-DQ Heterodimer Residues -18β and β57 With Progression From Islet Autoimmunity to Diabetes in the Diabetes Prevention Trial-Type 1. Diabetes Care 2022; 45:1610-1620. [PMID: 35621697 PMCID: PMC9274226 DOI: 10.2337/dc21-1628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/07/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The purpose was to test the hypothesis that the HLA-DQαβ heterodimer structure is related to the progression of islet autoimmunity from asymptomatic to symptomatic type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS Next-generation targeted sequencing was used to genotype HLA-DQA1-B1 class II genes in 670 subjects in the Diabetes Prevention Trial-Type 1 (DPT-1). Coding sequences were translated into DQ α- and β-chain amino acid residues and used in hierarchically organized haplotype (HOH) association analysis to identify motifs associated with diabetes onset. RESULTS The opposite diabetes risks were confirmed for HLA DQA1*03:01-B1*03:02 (hazard ratio [HR] 1.36; P = 2.01 ∗ 10-3) and DQA1*03:03-B1*03:01 (HR 0.62; P = 0.037). The HOH analysis uncovered residue -18β in the signal peptide and β57 in the β-chain to form six motifs. DQ*VA was associated with faster (HR 1.49; P = 6.36 ∗ 10-4) and DQ*AD with slower (HR 0.64; P = 0.020) progression to diabetes onset. VA/VA, representing DQA1*03:01-B1*03:02 (DQ8/8), had a greater HR of 1.98 (P = 2.80 ∗ 10-3). The DQ*VA motif was associated with both islet cell antibodies (P = 0.023) and insulin autoantibodies (IAAs) (P = 3.34 ∗ 10-3), while the DQ*AD motif was associated with a decreased IAA frequency (P = 0.015). Subjects with DQ*VA and DQ*AD experienced, respectively, increasing and decreasing trends of HbA1c levels throughout the follow-up. CONCLUSIONS HLA-DQ structural motifs appear to modulate progression from islet autoimmunity to diabetes among at-risk relatives with islet autoantibodies. Residue -18β within the signal peptide may be related to levels of protein synthesis and β57 to stability of the peptide-DQab trimolecular complex.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,School of Public Health, University of Washington, Seattle, WA
| | - Jay Skyler
- Diabetes Research Institute and Division of Endocrinology, Diabetes and Metabolism, University of Miami Miller School of Medicine, Miami, FL
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece
| | - Alberto Pugliese
- Diabetes Research Institute and Division of Endocrinology, Diabetes and Metabolism, University of Miami Miller School of Medicine, Miami, FL
| | | | - George P Bondinas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, Argostoli, Kefalonia, Greece
| | - Antonis K Moustakas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, Argostoli, Kefalonia, Greece
| | - Ruihan Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Wyatt C Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University Clinical Research Centre, Skåne University Hospital, Malmö, Sweden
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Nine residues in HLA-DQ molecules determine with susceptibility and resistance to type 1 diabetes among young children in Sweden. Sci Rep 2021; 11:8821. [PMID: 33893332 PMCID: PMC8065060 DOI: 10.1038/s41598-021-86229-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 11/09/2022] Open
Abstract
HLA-DQ molecules account over 50% genetic risk of type 1 diabetes (T1D), but little is known about associated residues. Through next generation targeted sequencing technology and deep learning of DQ residue sequences, the aim was to uncover critical residues and their motifs associated with T1D. Our analysis uncovered (αa1, α44, α157, α196) and (β9, β30, β57, β70, β135) on the HLA-DQ molecule. Their motifs captured all known susceptibility and resistant T1D associations. Three motifs, “DCAA-YSARD” (OR = 2.10, p = 1.96*10−20), “DQAA-YYARD” (OR = 3.34, 2.69*10−72) and “DQDA-YYARD” (OR = 3.71, 1.53*10−6) corresponding to DQ2.5 and DQ8.1 (the latter two motifs) associated with susceptibility. Ten motifs were significantly associated with resistance to T1D. Collectively, homozygous DQ risk motifs accounted for 43% of DQ-T1D risk, while homozygous DQ resistant motifs accounted for 25% protection to DQ-T1D risk. Of the identified nine residues five were within or near anchoring pockets of the antigenic peptide (α44, β9, β30, β57 and β70), one was the N-terminal of the alpha chain (αa1), one in the CD4-binding region (β135), one in the putative cognate TCR-induced αβ homodimerization process (α157), and one in the intra-membrane domain of the alpha chain (α196). Finding these critical residues should allow investigations of fundamental properties of host immunity that underlie tolerance to self and organ-specific autoimmunity.
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3
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Zhao LP, Papadopoulos GK, Kwok WW, Moustakas AK, Bondinas GP, Carlsson A, Elding Larsson H, Ludvigsson J, Marcus C, Samuelsson U, Wang R, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å. Next-Generation HLA Sequence Analysis Uncovers Seven HLA-DQ Amino Acid Residues and Six Motifs Resistant to Childhood Type 1 Diabetes. Diabetes 2020; 69:2523-2535. [PMID: 32868339 PMCID: PMC7576571 DOI: 10.2337/db20-0374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
HLA-DQA1 and -DQB1 genes have significant and potentially causal associations with autoimmune type 1 diabetes (T1D). To follow up on the earlier analysis on high-risk HLA-DQ2.5 and DQ8.1, the current analysis uncovers seven residues (αa1, α157, α196, β9, β30, β57, and β70) that are resistant to T1D among subjects with DQ4-, 5-, 6-, and 7-resistant DQ haplotypes. These 7 residues form 13 common motifs: 6 motifs are significantly resistant, 6 motifs have modest or no associations (P values >0.05), and 1 motif has 7 copies observed among control subjects only. The motifs "DAAFYDG," "DAAYHDG," and "DAAYYDR" have significant resistance to T1D (odds ratios [ORs] 0.03, 0.25, and 0.18; P = 6.11 × 10-24, 3.54 × 10-15, and 1.03 × 10-21, respectively). Remarkably, a change of a single residue from the motif "DAAYHDG" to "DAAYHSG" (D to S at β57) alters the resistance potential, from resistant motif (OR 0.15; P = 3.54 × 10-15) to a neutral motif (P = 0.183), the change of which was significant (Fisher P value = 0.0065). The extended set of linked residues associated with T1D resistance and unique to each cluster of HLA-DQ haplotypes represents facets of all known features and functions of these molecules: antigenic peptide binding, peptide-MHC class II complex stability, β167-169 RGD loop, T-cell receptor binding, formation of homodimer of α-β heterodimers, and cholesterol binding in the cell membrane rafts. Identification of these residues is a novel understanding of resistant DQ associations with T1D. Our analyses endow potential molecular approaches to identify immunological mechanisms that control disease susceptibility or resistance to provide novel targets for immunotherapeutic strategies.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Antonis K Moustakas
- Department of Food Science and Technology, Faculty of Environment, Ionian University, Argostoli, Cephalonia, Greece
| | - George P Bondinas
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece
| | | | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University Clinical Research Centre, Skåne University Hospital, Malmö, Sweden
| | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claude Marcus
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Samuelsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Ruihan Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Wyatt C Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University Clinical Research Centre, Skåne University Hospital, Malmö, Sweden
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4
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Simons ND, Eick GN, Ruiz-Lopez MJ, Omeja PA, Chapman CA, Goldberg TL, Ting N, Sterner KN. Cis-regulatory evolution in a wild primate: Infection-associated genetic variation drives differential expression of MHC-DQA1 in vitro. Mol Ecol 2017; 26:4523-4535. [PMID: 28665019 PMCID: PMC5570663 DOI: 10.1111/mec.14221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/10/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022]
Abstract
Few studies have combined genetic association analyses with functional characterization of infection-associated SNPs in natural populations of nonhuman primates. Here, we investigate the relationship between host genetic variation, parasitism and natural selection in a population of red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. We collected parasitological, cellular and genomic data to test the following hypotheses: (i) MHC-DQA1 regulatory genetic variation is associated with control of whipworm (Trichuris) infection in a natural population of red colobus; (ii) infection-associated SNPs are functional in driving differential gene expression in vitro; and (iii) balancing selection has shaped patterns of variation in the MHC-DQA1 promoter. We identified two SNPs in the MHC-DQA1 promoter, both in transcription factor binding sites, and both of which are associated with decreased control of Trichuris infection. We characterized the function of both SNPs by testing differences in gene expression between the two alleles of each SNP in two mammalian cell lines. Alleles of one of the SNPs drove differential gene expression in both cell lines, while the other SNP drove differences in expression in one of the cell lines. Additionally, we found evidence of balancing selection acting on the MHC-DQA1 promoter, including extensive trans-species polymorphisms between red colobus and other primates, and an excess of intermediate-frequency alleles relative to genome-wide, coding and noncoding RADseq data. Our data suggest that balancing selection provides adaptive regulatory flexibility that outweighs the consequences of increased parasite infection intensity in heterozygotes.
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Affiliation(s)
- Noah D. Simons
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | - Geeta N. Eick
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
| | | | - Patrick A. Omeja
- Makerere University Biological Field Station, P.O Box 967, Fort Portal, Uganda
| | - Colin A. Chapman
- Makerere University Biological Field Station, P.O Box 967, Fort Portal, Uganda
- Department of Anthropology and McGill School of Environment, Montreal, Quebec, H3A 2T7, Canada
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53725, USA
- Global Health Institute, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Nelson Ting
- Department of Anthropology, University of Oregon, Eugene, OR 97403, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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Cross AR, Lion J, Loiseau P, Charron D, Taupin JL, Glotz D, Mooney N. Donor Specific Antibodies are not only directed against HLA-DR: Minding your Ps and Qs. Hum Immunol 2016; 77:1092-1100. [PMID: 27060781 DOI: 10.1016/j.humimm.2016.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/08/2016] [Accepted: 04/04/2016] [Indexed: 12/30/2022]
Abstract
During solid organ transplantation, interactions between recipient and donor immune cells occur chiefly in the allograft microvasculature. All three HLA class II antigens, DR, DP and DQ, have been detected on renal EC with a markedly increased expression of HLA class II observed in renal allografts undergoing rejection. Recent studies of donor-specific antibodies (DSA) have exposed the prevalence of de novo DSA directed against HLA-DQ, as well as a strong association between these antibodies and allograft damage. The HLA-DQ molecule can be distinguished from the other class II antigens by its transcription, expression and peptide repertoire. The distinct intragraft expression and immunogenicity of HLA-DQ may contribute to the incidence of HLA-DQ DSA, as well as directing the DSA-mediated damage. The possibility of HLA class II antigen-specific signaling in EC may reveal different mechanisms of allograft damage that act in tandem with complement-dependent injury. This review addresses the features of the HLA-DQ heterodimer that may underlie the high incidence of HLA-DQ directed DSA and their association with allograft damage. We also consider existing data in hematopoietic stem cell transplantation concerning HLA directed DSA.
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Affiliation(s)
- Amy R Cross
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France
| | - Julien Lion
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France
| | - Pascale Loiseau
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France; Laboratoire de Histocompatibilité, Hôpital Saint Louis, Paris 75010, France
| | - Dominique Charron
- Laboratoire de Histocompatibilité, Hôpital Saint Louis, Paris 75010, France; Université Paris Diderot, Sorbonne Paris Cité, F-75013, France
| | - Jean-Luc Taupin
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France; Laboratoire de Histocompatibilité, Hôpital Saint Louis, Paris 75010, France; Université Paris Diderot, Sorbonne Paris Cité, F-75013, France
| | - Denis Glotz
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France; Service de Néphrologie et Transplantation, Hôpital Saint Louis, Paris 75010, France; Université Paris Diderot, Sorbonne Paris Cité, F-75013, France
| | - Nuala Mooney
- INSERM UMRs 1160, Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint Louis, Paris 75010, France; LabEx Transplantex, AP-HP, Hôpital Saint-Louis, Paris 75010, France.
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6
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Laplana M, Caruz A, Pineda JA, Puig T, Fibla J. Association of BST-2 Gene Variants With HIV Disease Progression Underscores the Role of BST-2 in HIV Type 1 Infection. J Infect Dis 2012; 207:411-9. [DOI: 10.1093/infdis/jis685] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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7
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Sironi M, Guerini FR, Agliardi C, Biasin M, Cagliani R, Fumagalli M, Caputo D, Cassinotti A, Ardizzone S, Zanzottera M, Bolognesi E, Riva S, Kanari Y, Miyazawa M, Clerici M. An evolutionary analysis of RAC2 identifies haplotypes associated with human autoimmune diseases. Mol Biol Evol 2011; 28:3319-29. [PMID: 21680873 DOI: 10.1093/molbev/msr164] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The human RAC2 gene encodes a small GTP-binding protein with a pivotal role in immune activation and in the induction of peripheral immune tolerance through restimulation-induced cell death (RICD). Different human pathogens target the protein product of RAC2, suggesting that the gene may be subject to natural selection, and that variants in RAC2 may affect immunological phenotypes in humans. We scanned the genomic region encompassing the entire transcription unit for the presence of putative noncoding regulatory elements conserved across mammals. This information was used to select two RAC2 gene regions and analyze their intraspecific genetic diversity. Results suggest that a region covering the 3' untranslated region has been a target of multiallelic balancing selection (or diversifying selection), and three major RAC2 haplogroups occur in human populations. Haplotypes belonging to one of these clades are associated with increased susceptibility to multiple sclerosis (P = 0.022) and earlier onset of disease symptoms (P = 0.025). This same haplogroup is significantly more common in patients with Crohn's disease compared with healthy controls (P = 0.048). These data reinforce recent evidences that susceptibility alleles/haplotypes are shared among multiple autoimmune disorders and support a causal "role for RAC2" variants in the pathogenesis of autoimmune diseases. Other genes with a role in RICD have previously been associated with autoimmunity in humans, suggesting that this pathway and RAC2 may represent novel therapeutic targets in autoimmune disorders.
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Affiliation(s)
- Manuela Sironi
- Bioinformatics Laboratory, Scientific Institute IRCCS E. Medea, Bosisio Parini (LC), Italy
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8
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Handunnetthi L, Ramagopalan SV, Ebers GC, Knight JC. Regulation of major histocompatibility complex class II gene expression, genetic variation and disease. Genes Immun 2010; 11:99-112. [PMID: 19890353 PMCID: PMC2987717 DOI: 10.1038/gene.2009.83] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/15/2009] [Indexed: 12/29/2022]
Abstract
Major histocompatibility complex (MHC) class II molecules are central to adaptive immune responses and maintenance of self-tolerance. Since the early 1970s, the MHC class II region at chromosome 6p21 has been shown to be associated with a remarkable number of autoimmune, inflammatory and infectious diseases. Given that a full explanation for most MHC class II disease associations has not been reached through analysis of structural variation alone, in this review we examine the role of genetic variation in modulating gene expression. We describe the intricate architecture of the MHC class II regulatory system, indicating how its unique characteristics may relate to observed associations with disease. There is evidence that haplotype-specific variation involving proximal promoter sequences can alter the level of gene expression, potentially modifying the emergence and expression of key phenotypic traits. Although much emphasis has been placed on cis-regulatory elements, we also examine the role of more distant enhancer elements together with the evidence of dynamic inter- and intra-chromosomal interactions and epigenetic processes. The role of genetic variation in such mechanisms may hold profound implications for susceptibility to common disease.
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Affiliation(s)
- Lahiru Handunnetthi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Clinical Neurology, University of Oxford, Oxford OX3 7BN, UK
| | - Sreeram V. Ramagopalan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Clinical Neurology, University of Oxford, Oxford OX3 7BN, UK
| | - George C. Ebers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Clinical Neurology, University of Oxford, Oxford OX3 7BN, UK
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M. A population genetics study of the Familial Mediterranean Fever gene: evidence of balancing selection under an overdominance regime. Genes Immun 2009; 10:678-86. [DOI: 10.1038/gene.2009.59] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Menozzi G, Bresolin N, Sironi M. The signature of long-standing balancing selection at the human defensin beta-1 promoter. Genome Biol 2008; 9:R143. [PMID: 18817538 PMCID: PMC2592704 DOI: 10.1186/gb-2008-9-9-r143] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/21/2008] [Accepted: 09/25/2008] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Defensins, small endogenous peptides with antimicrobial activity, are pivotal components of the innate immune response. A large cluster of defensin genes is located on human chromosome 8p; among them the beta defensin 1 (DEFB1) promoterhas been extensively studied since discovery that specific polymorphisms and haplotypes associate with asthma and atopy, susceptibility to severe sepsis, as well as HIV and Candida infection predisposition. RESULTS Here, we characterize the sequence variation and haplotype structure of the DEFB1 promoter region in six human populations. In all of them, we observed high levels of nucleotide variation, an excess of intermediate-frequency alleles, reduced population differentiation and a genealogy with common haplotypes separated by deep branches. Indeed, a significant departure from the expectation of evolutionary neutrality was observed in all populations and the possibility that this is due to demographic history alone was ruled out. Also, we verified that the selection signature is restricted to the promoter region and not due to a linked balanced polymorphism. A phylogeny-based estimation indicated that the two major haplotype clades separated around 4.5 million years ago, approximately the time when the human and chimpanzee lineages split. CONCLUSION Altogether, these features represent strong molecular signatures of long-term balancing selection, a process that is thought to be extremely rare outside major histocompatibility complex genes. Our data indicate that the DEFB1 promoter region carries functional variants and support previous hypotheses whereby alleles predisposing to atopic disorders are widespread in modern societies because they conferred resistance to pathogens in ancient settings.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Matteo Fumagalli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
- Bioengineering Department, Politecnico di Milano, Pzza L. da Vinci, 32, 20133 Milan, Italy
| | - Stefania Riva
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Giacomo P Comi
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, Via F. Sforza 35, 20100 Milan, Italy
| | - Giorgia Menozzi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Nereo Bresolin
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, Via F. Sforza 35, 20100 Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
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11
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Bondinas GP, Moustakas AK, Papadopoulos GK. The spectrum of HLA-DQ and HLA-DR alleles, 2006: a listing correlating sequence and structure with function. Immunogenetics 2007; 59:539-53. [PMID: 17497145 DOI: 10.1007/s00251-007-0224-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 04/03/2007] [Indexed: 10/23/2022]
Abstract
The list of alleles in the HLA-DRB, HLA-DQA, and HLA-DQB gene loci has grown enormously since the last listing in this journal 8 years ago. Crystal structure determination of several human and mouse HLA class II alleles, representative of two gene loci in each species, enables a direct comparison of ortholog and paralog loci. A new numbering system is suggested, extending earlier suggestions by [Fremont et al. in Immunity 8:305-317, (1998)], which will bring in line all the structural features of various gene loci, regardless of animal species. This system allows for structural equivalence of residues from different gene loci. The listing also highlights all amino acid residues participating in the various functions of these molecules, from antigenic peptide binding to homodimer formation, CD4 binding, membrane anchoring, and cytoplasmic signal transduction, indicative of the variety of functions of these molecules. It is remarkable that despite the enormous number of unique alleles listed thus far (DQA = 22, DQB = 54, DRA = 2, and DRB = 409), there is invariance at many specific positions in man, but slightly less so in mouse or rat, despite their much lower number of alleles at each gene locus in the latter two species. Certain key polymorphisms (from substitutions to an eight-residue insertion in the cytoplasmic tail of certain DQB alleles) that have thus far gone unnoticed are highly suggestive of differences or diversities in function and thus call for further investigation into the properties of these specific alleles. This listing is amenable to supplementation by future additions of new alleles and the highlighting of new functions to be discovered, providing thus a unifying platform of reference in all animal species for the MHC class II allelic counterparts, aiding research in the field and furthering our understanding of the functions of these molecules.
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Affiliation(s)
- George P Bondinas
- Laboratory of Biochemistry and Biophysics, Faculty of Agricultural Technology, Epirus Institute of Technology, GR47100 Arta, Greece
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12
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Loisel DA, Rockman MV, Wray GA, Altmann J, Alberts SC. Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region. Proc Natl Acad Sci U S A 2006; 103:16331-6. [PMID: 17053068 PMCID: PMC1637582 DOI: 10.1073/pnas.0607662103] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Precise regulation of MHC gene expression is critical to vertebrate immune surveillance and response. Polymorphisms in the 5' proximal promoter region of the human class II gene HLA-DQA1 have been shown to influence its transcriptional regulation and may contribute to the pathogenesis of autoimmune diseases. We investigated the evolutionary history of this cis-regulatory region by sequencing the DQA1 5' proximal promoter region in eight nonhuman primate species. We observed unexpectedly high levels of sequence variation and multiple strong signatures of balancing selection in this region. Specifically, the considerable DQA1 promoter region diversity was characterized by abundant shared (or trans-species) polymorphism and a pronounced lack of fixed differences between species. The majority of transcription factor binding sites in the DQA1 promoter region were polymorphic within species, and these binding site polymorphisms were commonly shared among multiple species despite evidence for negative selection eliminating a significant fraction of binding site mutations. We assessed the functional consequences of intraspecific promoter region diversity using a cell line-based reporter assay and detected significant differences among baboon DQA1 promoter haplotypes in their ability to drive transcription in vitro. The functional differentiation of baboon promoter haplotypes, together with the significant deviations from neutral sequence evolution, suggests a role for balancing selection in the evolution of DQA1 transcriptional regulation in primates.
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Affiliation(s)
- Dagan A. Loisel
- *Department of Biology, Duke University, Durham, NC 27705
- To whom correspondence may be addressed. E-mail:
or
| | - Matthew V. Rockman
- Lewis–Sigler Institute for Integrative Genomics and
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Gregory A. Wray
- *Department of Biology, Duke University, Durham, NC 27705
- Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705
| | - Jeanne Altmann
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
- Department of Conservation Biology, Chicago Zoological Society, Brookfield, IL 60513; and
- **Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
- To whom correspondence may be addressed. E-mail:
or
| | - Susan C. Alberts
- *Department of Biology, Duke University, Durham, NC 27705
- **Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
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13
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Lin W, Yang HH, Lee MP. Allelic variation in gene expression identified through computational analysis of the dbEST database. Genomics 2005; 86:518-27. [PMID: 15993562 DOI: 10.1016/j.ygeno.2005.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 05/07/2005] [Accepted: 05/22/2005] [Indexed: 11/21/2022]
Abstract
Differential expression between the two alleles of an individual and between people with different genotypes has been commonly observed. Quantitative differences in gene expression between people may provide the genetic basis for the phenotypic difference between individuals and may be the primary cause of complex diseases. In this paper, we developed a computational method to identify genes that displayed allelic variation in gene expression in human EST libraries. To model allele-specific gene expression, we first identified EST libraries in which both A and B alleles were expressed and then identified allelic variation in gene expression based on the EST counts for each allele using a binomial test. Among 1107 SNPs that had a sufficient number of ESTs for the analysis, 524 (47%) displayed allelic variation in at least one cDNA library. We verified experimentally the allelic variation in gene expression for 6 of these SNPs. The frequency of allelic variation observed in EST libraries was similar to the previous studies using the SNP chip and primer extension method. We found that genes that displayed allelic variation were distributed throughout the human genome and were enriched in certain chromosome regions. The SNPs and genes identified in this study will provide a rich source for evaluating the effects of those SNPs and associated haplotypes in human health and diseases.
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Affiliation(s)
- Wei Lin
- Laboratory of Population Genetics, National Cancer Institute, Bethesda, MD 20892, USA
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14
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Muhlethaler-Mottet A, Krawczyk M, Masternak K, Spilianakis C, Kretsovali A, Papamatheakis J, Reith W. The S Box of Major Histocompatibility Complex Class II Promoters Is a Key Determinant for Recruitment of the Transcriptional Co-activator CIITA. J Biol Chem 2004; 279:40529-35. [PMID: 15271997 DOI: 10.1074/jbc.m406585200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Tightly regulated expression of major histocompatibility complex (MHC) class II genes is critical for the immune system. A conserved regulatory module consisting of four cis-acting elements, the W, X, X2 and Y boxes, controls transcription of MHC class II genes. The X, X2, and Y boxes are bound, respectively, by RFX, CREB, and NF-Y to form a MHC class II-specific enhanceosome complex. The latter constitutes a landing pad for recruitment of the transcriptional co-activator CIITA. In contrast to the well defined roles of the X, X2, and Y boxes, the role of the W region has remained controversial. In vitro binding studies have suggested that it might contain a second RFX-binding site. We demonstrate here by means of promoter pull-down assays that the most conserved subsequence within the W region, called the S box, is a critical determinant for tethering of CIITA to the enhanceosome complex. Binding of CIITA to the enhanceosome requires both integrity of the S box and a remarkably stringent spacing between the S and X boxes. Even a 1-2-base pair change in the native S-X distance is detrimental for CIITA recruitment and promoter function. In contrast to current models, binding of RFX to a putative duplicated binding site in the W box is thus not required for either CIITA recruitment or promoter activity. This paves the way for the identification of novel factors mediating the contribution of the S box to the activation of MHC class II promoters.
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Affiliation(s)
- Annick Muhlethaler-Mottet
- University of Geneva Medical School, Department of Pathology and Immunology, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211, Geneva, Switzerland
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15
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Rees LE, Ayoub O, Haverson K, Birchall MA, Bailey M. Differential major histocompatibility complex class II locus expression on human laryngeal epithelium. Clin Exp Immunol 2004; 134:497-502. [PMID: 14632757 PMCID: PMC1808879 DOI: 10.1111/j.1365-2249.2003.02301.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The survival of a laryngeal allograft will be dependent on the immunological composition of the donor larynx and, in particular, on the expression of major histocompatibility complex (MHC) class II antigens on professional and non-professional antigen-presenting cells. Laryngeal and tonsillar biopsies from normal individuals aged 18-78 years were processed and prepared for quantitative, multiple-colour immunofluorescence using mouse antihuman monoclonal antibodies to human leucocyte antigen (HLA)-DR, HLA-DQ and CD45. The laryngeal epithelium expressed HLA-DR locus products at variable levels, but expression of HLA-DQ was virtually absent. Tonsillar epithelial cells expressed HLA-DR at the basal layer only, while HLA-DQ was similarly not expressed. In contrast, both HLA-DR and -DQ locus products were present on lamina propria and intraepithelial leucocytes in both laryngeal and tonsillar mucosae, although at varying levels. The finding that laryngeal epithelial cells express MHC class II antigens has implications for the survival of laryngeal allografts and suggests that they may require significant immunomodulation. In addition, antigen presentation by epithelial cells has been hypothesized to contribute to the immunoregulatory function of mucosal tissues, and the finding that HLA-DQ locus products are only expressed at low levels by laryngeal epithelium raises questions about the repertoire of peptides to which the mucosal immune system can respond.
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Affiliation(s)
- L E Rees
- Laryngeal Research Group, Department of Otolaryngology, Division of Surgery, University of Bristol, Bristol, UK.
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Abstract
Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.
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17
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Moustakas AK, Papadopoulos GK. Molecular properties of HLA-DQ alleles conferring susceptibility to or protection from insulin-dependent diabetes mellitus: keys to the fate of islet beta-cells. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 115:37-47. [PMID: 12116175 DOI: 10.1002/ajmg.10342] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The major histocompatibility complex Class II alleles, HLA-DQ, and the related HLA-DR, are the chief genetic elements of human type 1 diabetes. These genes code for polymorphic heterodimeric proteins, whose chief function is to trap peptide antigens in the endosome and present them on the surface of antigen-presenting cells (dendritic cells, B lymphocytes, monocytes/macrophages) to CD4(+) T helper cells. A systematic investigation of the molecular properties of HLA-DQ alleles linked to susceptibility or resistance to type 1 diabetes has shown that these properties segregate along lines of susceptibility or resistance. A correlation of these features with the function of each particular segment of the HLA-DQ molecule yields interesting insights into the possible pathways leading to type 1 diabetes. There remain, however, areas to be clarified, including mechanisms by which dominant protection is conferred by certain alleles, the interplay between HLA-DQ and the related locus HLA-DR, that also shows autoantigen-specific reactivity, and the cross-Class help delivered to CD8(+) T cells, the final effectors in pancreatic beta-cell destruction. Clarification of these issues may lead to ways to prevent diabetes in predisposed individuals already exhibiting the genetic and immunological characteristics, and perhaps a cure in those with the disease, by means of transplantation, and measures for prevention of disease recurrence.
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