1
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Pagliuca S, Ferraro F. Immune-driven clonal cell selection at the intersection among cancer, infections, autoimmunity and senescence. Semin Hematol 2024; 61:22-34. [PMID: 38341340 DOI: 10.1053/j.seminhematol.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Immune surveillance mechanisms play a crucial role in maintaining lifelong immune homeostasis in response to pathologic stimuli and aberrant cell states. However, their persistence, especially in the context of chronic antigenic exposure, can create a fertile ground for immune evasion. These escaping cell phenotypes, harboring a variety of genomic and transcriptomic aberrances, chiefly in human leukocyte antigen (HLA) and antigen presentation machinery genes, may survive and proliferate, featuring a scenario of clonal cell expansion with immune failure characteristics. While well characterized in solid and, to some extent, hematological malignancies, little is known about their occurrence and significance in other disease contexts. Historical literature highlights the role for escaping HLA-mediated recognition as a strategy adopted by virus to evade from the immune system, hinting at the potential for immune aberrant cell expansion in the context of chronic infections. Additionally, unmasked in idiopathic aplastic anemia as a mechanism able to rescue failing hematopoiesis, HLA clonal escape may operate in autoimmune disorders, particularly in tissues targeted by aberrant immune responses. Furthermore, senescent cell status emerging as immunogenic phenotypes stimulating T cell responses, may act as a bottleneck for the selection of such immune escaping clones, blurring the boundaries between neoplastic transformation, aging and inflammation. Here we provide a fresh overview and perspective on this immune-driven clonal cell expansion, linking pathophysiological features of neoplastic, autoimmune, infectious and senescence processes exposed to immune surveillance.
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Affiliation(s)
- Simona Pagliuca
- Hematology Department, Nancy University Hospital and UMR7365, IMoPA, University of Lorraine, Vandoeuvre-lès-Nancy, France.
| | - Francesca Ferraro
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
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2
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Lenz TL. HLA Genes: A Hallmark of Functional Genetic Variation and Complex Evolution. Methods Mol Biol 2024; 2809:1-18. [PMID: 38907887 DOI: 10.1007/978-1-0716-3874-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
The major histocompatibility complex (MHC) with its highly polymorphic HLA genes represents one of the most intensely studied genomic regions in the genome. MHC proteins play a key role in antigen-specific immunity and are associated with a wide range of complex diseases. Despite decades of research and many advances in the field, the characterization and interpretation of its genetic and genomic variability remain challenging. Here an overview is provided of the MHC, the nature of its exceptional variability, and the complex evolutionary processes assumed to drive this variability. Highlighted are also recent advances in the field that promise to improve our understanding of the variability in the MHC and in antigen-specific immunity more generally.
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Affiliation(s)
- Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany.
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3
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Davy T, Ju D, Mathieson I, Skoglund P. Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Curr Biol 2023; 33:1365-1371.e3. [PMID: 36963383 PMCID: PMC10153476 DOI: 10.1016/j.cub.2023.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10-56). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.
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Affiliation(s)
- Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
| | - Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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4
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Fu M, Eimes JA, Waldman B. Divergent allele advantage in the MHC and amphibian emerging infectious disease. INFECTION, GENETICS AND EVOLUTION 2023; 111:105429. [PMID: 36990307 DOI: 10.1016/j.meegid.2023.105429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Genetic variation in the major histocompatibility complex (MHC) may be associated with resistance to the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). The pathogen originated in Asia, then spread worldwide, causing amphibian population declines and species extinctions. We compared the expressed MHC IIβ1 alleles of a Bd-resistant toad species, Bufo gargarizans, from South Korea with those of a Bd-susceptible Australasian frog species, Litoria caerulea. We found at least six expressed MHC IIβ1 loci in each of the two species. Amino acid diversity encoded by these MHC alleles was similar between species, but the genetic divergence of those alleles known for broader pathogen-derived peptide binding was greater in the Bd-resistant species. In addition, we found a potentially rare allele in one resistant individual from the Bd-susceptible species. Deep next-generation sequencing recovered approximately triple the genetic resolution accessible from traditional cloning-based genotyping. Targeting more than one MHC IIβ1 expressed locus enables us to better understand how host MHC may adapt to emerging infectious diseases.
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5
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Huang W, Dicks KL, Hadfield JD, Johnston SE, Ballingall KT, Pemberton JM. Contemporary selection on MHC genes in a free-living ruminant population. Ecol Lett 2022; 25:828-838. [PMID: 35050541 PMCID: PMC9306867 DOI: 10.1111/ele.13957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Royal Zoological Society of Scotland, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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6
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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7
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Özer O, Lenz TL. Unique pathogen peptidomes facilitate pathogen-specific selection and specialization of MHC alleles. Mol Biol Evol 2021; 38:4376-4387. [PMID: 34110412 PMCID: PMC8476153 DOI: 10.1093/molbev/msab176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.
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Affiliation(s)
- Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
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8
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Immel A, Pierini F, Rinne C, Meadows J, Barquera R, Szolek A, Susat J, Böhme L, Dose J, Bonczarowska J, Drummer C, Fuchs K, Ellinghaus D, Kässens JC, Furholt M, Kohlbacher O, Schade-Lindig S, Franke A, Schreiber S, Krause J, Müller J, Lenz TL, Nebel A, Krause-Kyora B. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Commun Biol 2021; 4:113. [PMID: 33495542 PMCID: PMC7835224 DOI: 10.1038/s42003-020-01627-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/20/2020] [Indexed: 02/08/2023] Open
Abstract
The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections. Alexander Immel et al. performed genome-wide analyses of 42 individuals from a collective burial in Niedertiefenbach, Germany from the Wartberg Culture. The authors find that this population had a large hunter-gatherer ancestry component and a distinct HLA pool, which indicates immune defenses against viral pathogens.
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Affiliation(s)
- Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - John Meadows
- Leibniz Laboratory for AMS Dating and Isotope Research, Kiel University, Max-Eyth-Strasse 11-13, 24118, Kiel, Germany.,Centre for Baltic and Scandinavian Archaeology (ZBSA), Schloss Gottorf, 24837, Schleswig, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Lisa Böhme
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Joanna Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Clara Drummer
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Katharina Fuchs
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Jan Christian Kässens
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Martin Furholt
- Department of Archaeology, Conservation and History, University of Oslo, Blindernveien 11, 0371, Oslo, Norway
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Strasse 9, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Sabine Schade-Lindig
- Landesamt für Denkmalpflege Hessen, hessenARCHÄOLOGIE, Schloss Biebrich, 65203, Wiesbaden, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.,Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - Johannes Müller
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.
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9
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Radwan J, Babik W, Kaufman J, Lenz TL, Winternitz J. Advances in the Evolutionary Understanding of MHC Polymorphism. Trends Genet 2020; 36:298-311. [DOI: 10.1016/j.tig.2020.01.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/26/2022]
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10
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Zhang X, Yang H, Zhang J, Gao F, Dai L. HSD17B4, ACAA1, and PXMP4 in Peroxisome Pathway Are Down-Regulated and Have Clinical Significance in Non-small Cell Lung Cancer. Front Genet 2020; 11:273. [PMID: 32265992 PMCID: PMC7103649 DOI: 10.3389/fgene.2020.00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
To explore the potential functions and clinical significances of peroxisomes during lung cancer development and progression, we investigated the expressional profiles of peroxisome pathway genes and their correlations with clinical features in non-small cell lung cancer (NSCLC). The RNA-seq data of NSCLC including lung squamous carcinoma (LUSC) and lung adenocarcinoma (LUAD) patients with their clinical information were downloaded from The Cancer Genome Atlas (TCGA). Gene expression comparisons between tumor and normal samples were performed with edgeR package in R software and the results of the 83 peroxisome pathway genes were extracted. Through Venn diagram analysis, 38 common differentially expressed peroxisome pathway genes (C-DEPGs) in NSCLC were identified. Principal components analysis (PCA) was performed and the 38 C-DEPGs could discriminate NSCLC tumors from the non-tumor controls well. Through Kaplan-Meier survival and Cox regression analyses, 11 of the C-DEPGs were shown to have prognostic effects on NSCLC overall survival (OS) and were considered as key C-DEPGs (K-DEPGs). Through Oncomine, Human Protein Atlas (HPA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), three K-DEPGs (HSD17B4, ACAA1, and PXMP4) were confirmed to be down-regulated in NSCLC at both mRNA and protein level. Their dy-regulation mechanisms were revealed through their correlations with their copy number variations and methylation status. Their potential functions in NSCLC were explored through their NSCLC-specific co-expression network analysis, their correlations with immune infiltrations, immunomodulator gene expressions, MKI67 expression and their associations with anti-cancer drug sensitivity. Our findings suggested that HSD17B4, ACAA1, and PXMP4 might be new markers for NSCLC diagnosis and prognosis and might provide new clues for NSCLC treatment.
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Affiliation(s)
- Xiuzhi Zhang
- Department of Pathology, Henan Medical College, Zhengzhou, China.,Institute of Cancer Research, Henan Medical College, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongmei Yang
- Department of Pathology, Henan Medical College, Zhengzhou, China.,Institute of Cancer Research, Henan Medical College, Zhengzhou, China
| | - Jinzhong Zhang
- Institute of Cancer Research, Henan Medical College, Zhengzhou, China
| | - Fenglan Gao
- Department of Pathology, Henan Medical College, Zhengzhou, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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11
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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12
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Pierini F, Lenz TL. Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection. Mol Biol Evol 2020; 35:2145-2158. [PMID: 29893875 PMCID: PMC6106954 DOI: 10.1093/molbev/msy116] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The highly polymorphic genes of the major histocompatibility complex (MHC) play a key role in adaptive immunity. Divergent allele advantage, a mechanism of balancing selection, is proposed to contribute to their exceptional polymorphism. It assumes that MHC genotypes with more divergent alleles allow for broader antigen-presentation to immune effector cells, by that increasing immunocompetence. However, the direct correlation between pairwise sequence divergence and the corresponding repertoire of bound peptides has not been studied systematically across different MHC genes. Here, we investigated this relationship for five key classical human MHC genes (human leukocyte antigen; HLA-A, -B, -C, -DRB1, and -DQB1), using allele-specific computational binding prediction to 118,097 peptides derived from a broad range of human pathogens. For all five human MHC genes, the genetic distance between two alleles of a heterozygous genotype was positively correlated with the total number of peptides bound by these two alleles. In accordance with the major antigen-presentation pathway of MHC class I molecules, HLA-B and HLA-C alleles showed particularly strong correlations for peptides derived from intracellular pathogens. Intriguingly, this bias coincides with distinct protein compositions between intra- and extracellular pathogens, possibly suggesting adaptation of MHC I molecules to present specifically intracellular peptides. Eventually, we observed significant positive correlations between an allele’s average divergence and its population frequency. Overall, our results support the divergent allele advantage as a meaningful quantitative mechanism through which pathogen-mediated selection leads to the evolution of MHC diversity.
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Affiliation(s)
- Federica Pierini
- Research Group for Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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13
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Campbell MC, Ashong B, Teng S, Harvey J, Cross CN. Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6. BMC Evol Biol 2019; 19:218. [PMID: 31791241 PMCID: PMC6889576 DOI: 10.1186/s12862-019-1516-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lymphotoxin-α (LTα), located in the Major Histocompatibility Complex (MHC) class III region on chromosome 6, encodes a cytotoxic protein that mediates a variety of antiviral responses among other biological functions. Furthermore, several genotypes at this gene have been implicated in the onset of a number of complex diseases, including myocardial infarction, autoimmunity, and various types of cancer. However, little is known about levels of nucleotide variation and linkage disequilibrium (LD) in and near LTα, which could also influence phenotypic variance. To address this gap in knowledge, we examined sequence variation across ~ 10 kilobases (kbs), encompassing LTα and the upstream region, in 2039 individuals from the 1000 Genomes Project originating from 21 global populations. RESULTS Here, we observed striking patterns of diversity, including an excess of intermediate-frequency alleles, the maintenance of multiple common haplotypes and a deep coalescence time for variation (dating > 1.0 million years ago), in global populations. While these results are generally consistent with a model of balancing selection, we also uncovered a signature of positive selection in the form of long-range LD on chromosomes with derived alleles primarily in Eurasian populations. To reconcile these findings, which appear to support different models of selection, we argue that selective sweeps (particularly, soft sweeps) of multiple derived alleles in and/or near LTα occurred in non-Africans after their ancestors left Africa. Furthermore, these targets of selection were predicted to alter transcription factor binding site affinity and protein stability, suggesting they play a role in gene function. Additionally, our data also showed that a subset of these functional adaptive variants are present in archaic hominin genomes. CONCLUSIONS Overall, this study identified candidate functional alleles in a biologically-relevant genomic region, and offers new insights into the evolutionary origins of these loci in modern human populations.
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Affiliation(s)
- Michael C. Campbell
- Department of Biology, College of Arts and Sciences, Howard University, Washington, DC 20059 USA
| | - Bryan Ashong
- Department of Biology, College of Arts and Sciences, Howard University, Washington, DC 20059 USA
| | - Shaolei Teng
- Department of Biology, College of Arts and Sciences, Howard University, Washington, DC 20059 USA
| | - Jayla Harvey
- Department of Biology, College of Arts and Sciences, Howard University, Washington, DC 20059 USA
| | - Christopher N. Cross
- Department of Anatomy, College of Medicine, Howard University, Washington, DC 20059 USA
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Manczinger M, Boross G, Kemény L, Müller V, Lenz TL, Papp B, Pál C. Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations. PLoS Biol 2019; 17:e3000131. [PMID: 30703088 PMCID: PMC6372212 DOI: 10.1371/journal.pbio.3000131] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/12/2019] [Accepted: 01/15/2019] [Indexed: 02/03/2023] Open
Abstract
Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology. Whereas specialist major histocompatibility complex (MHC) molecules initiate immune response against only relatively few pathogens, generalists provide protection against a broad range. Accordingly, this study shows that the geographical distribution of generalist MHC alleles in human populations reflects exposure to diverse infectious diseases. Variation in the human genome influences our susceptibility to infectious diseases, but the causal link between disease and underlying mutation often remains enigmatic. Major histocompatibility complex II (MHC class II) molecules shape both our immune response against pathogens and our tolerance of self-peptides. The genomic region that encodes MHC molecules is of particular interest, as it is home to more genetic disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Here, we propose that MHC class II molecules can be categorized into two major types; specialists initiate effective immune response against only relatively few pathogens, while generalists provide protection against a broad range of pathogens. As support, we demonstrate that generalist MHC class II variants are more prevalent in human populations residing in pathogen-rich areas.
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Affiliation(s)
- Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Gábor Boross
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Tobias L. Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (CP); (BP)
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (CP); (BP)
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