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Tanegashima T, Shiota M, Fujiyama N, Narita S, Habuchi T, Fukuchi G, Takamatsu D, Oda Y, Miyake H, Takahashi M, Oya M, Tsuchiya N, Masumori N, Matsuyama H, Obara W, Shinohara N, Fujimoto K, Nozawa M, Ohba K, Ohyama C, Hashine K, Akamatsu S, Kamba T, Mita K, Gotoh M, Tatarano S, Fujisawa M, Tomita Y, Mukai S, Ito K, Tokunaga S, Eto M. Effect of HLA Genotype on Anti-PD-1 Antibody Treatment for Advanced Renal Cell Carcinoma in the SNiP-RCC Study. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:23-28. [PMID: 38758119 DOI: 10.4049/jimmunol.2300308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/16/2024] [Indexed: 05/18/2024]
Abstract
Immune checkpoint blockade therapies are widely used for cancer treatment, including advanced renal cell carcinoma (RCC). This study aimed to investigate the impact of zygosity in HLA genes and individual HLA genotypes on the efficacy of an anti-PD-1 Ab, nivolumab, in treating advanced RCC. Patient enrollment was conducted across 23 institutions in Japan from August 19, 2019, to September 30, 2020, with follow-up concluding on March 31, 2021. HLA genotype imputation of HLA-A, B, and C, DQB1, and DRB1 loci was performed. Among 222 patients, the presence of at least one homozygosity of the HLA-II allele significantly improved the best objective response (hazard ratio, 0.34; 95% confidence interval, 0.21-0.96; p = 0.042). The HLA evolutionary divergence (HED) of the HLA-A and HLA-B loci was higher than the HLA-C (p < 0.0001 and p < 0.0001, respectively), with high HED of the HLA-B locus correlating to clinical benefits in nivolumab treatment (hazard ratio, 0.44; 95% confidence interval, 0.21-0.90; p = 0.024) and improving cancer-specific survival compared with the low group (p = 0.0202). Additionally, high HED of the HLA-B locus was correlated with the number of infiltrated CD8+ cells in the tumor microenvironment (correlation coefficient, 0.4042). These findings indicate that the diversity of the HLA-B locus plays a significant role in the anti-tumor effect of nivolumab treatment in advanced RCC, potentially offering insights for improved risk stratification in nivolumab treatment and leading to better medical management of advanced RCC.
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Affiliation(s)
- Tokiyoshi Tanegashima
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Shiota
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuhiro Fujiyama
- Center for Kidney Disease and Transplantation, Akita University Hospital, Akita, Japan
| | - Shintaro Narita
- Department of Urology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Tomonori Habuchi
- Department of Urology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Genshiro Fukuchi
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dai Takamatsu
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideaki Miyake
- Department of Urology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masayuki Takahashi
- Department of Urology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Norihiko Tsuchiya
- Department of Urology, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Naoya Masumori
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hideyasu Matsuyama
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Wataru Obara
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Nobuo Shinohara
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | | | - Masahiro Nozawa
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kojiro Ohba
- Department of Urology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Katsuyoshi Hashine
- Department of Urology, National Hospital Organization Shikoku Cancer Center, Ehime, Japan
| | - Shusuke Akamatsu
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomomi Kamba
- Department of Urology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto Japan
| | - Koji Mita
- Department of Urology, Hiroshima City Asa Citizens Hospital, Hiroshima, Japan
| | - Momokazu Gotoh
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuichi Tatarano
- Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masato Fujisawa
- Department of Urology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshihiko Tomita
- Department of Urology and Molecular Oncology, Graduate School of Medicine and Dental Sciences, Niigata University, Niigata, Japan
| | - Shoichiro Mukai
- Department of Urology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Keiichi Ito
- Department of Urology, National Defense Medical College, Saitama, Japan
| | - Shoji Tokunaga
- Medical Information Center, Kyushu University Hospital, Fukuoka, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Wang Y, Wang X, Chen Y, Du J, Xiao Y, Guo D, Liu S. Adapting to stress: The effects of hibernation and hibernacula temperature on the hepatic transcriptome of Rhinolophus pusillus. FASEB J 2024; 38:e23462. [PMID: 38318662 DOI: 10.1096/fj.202301646r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/11/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Hibernation, a survival strategy in mammals for extreme climates, induces physiological phenomena such as ischemia-reperfusion and metabolic shifts that hold great potential for advancements in modern medicine. Despite this, the molecular mechanisms underpinning hibernation remain largely unclear. This study used RNA-seq and Iso-seq techniques to investigate the changes in liver transcriptome expression of Rhinolophus pusillus during hibernation and active periods, as well as under different microhabitat temperatures. We identified 11 457 differentially expressed genes during hibernation and active periods, of which 395 showed significant differential expression. Genes associated with fatty acid catabolism were significantly upregulated during hibernation, whereas genes related to carbohydrate metabolism and glycogen synthesis were downregulated. Conversely, immune-related genes displayed differential expression patterns: genes tied to innate immunity were significantly upregulated, while those linked to adaptive immunity and inflammatory response were downregulated. The analysis of transcriptomic data obtained from different microhabitat temperatures revealed that R. pusillus exhibited an upregulation of genes associated with lipid metabolism in lower microhabitat temperature. This upregulation facilitated an enhanced utilization rate of triglyceride, ultimately resulting in increased energy provision for the organism. Additionally, R. pusillus upregulated gluconeogenesis-related genes regardless of the microhabitat temperature, demonstrating the importance of maintaining blood glucose levels during hibernation. Our transcriptomic data reveal that these changes in liver gene expression optimize energy allocation during hibernation, suggesting that liver tissue adaptively responds to the inherent stress of its function during hibernation. This study sheds light on the role of differential gene expression in promoting more efficient energy allocation during hibernation. It contributes to our understanding of how liver tissue adapts to the stressors associated with this state.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xufan Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yu Chen
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Jianying Du
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Dongge Guo
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Sen Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
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Zucco AG, Bennedbæk M, Ekenberg C, Gabrielaite M, Leung P, Polizzotto MN, Kan V, Murray DD, Lundgren JD, MacPherson CR. Associations of functional human leucocyte antigen class I groups with HIV viral load in a heterogeneous cohort. AIDS 2023; 37:1643-1650. [PMID: 37534724 PMCID: PMC10399941 DOI: 10.1097/qad.0000000000003557] [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: 06/24/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
OBJECTIVE Human leucocyte antigen (HLA) class I alleles are the main host genetic factors involved in controlling HIV-1 viral load (VL). Nevertheless, HLA diversity has proven a significant challenge in association studies. We assessed how accounting for binding affinities of HLA class I alleles to HIV-1 peptides facilitate association testing of HLA with HIV-1 VL in a heterogeneous cohort. DESIGN Cohort from the Strategic Timing of AntiRetroviral Treatment (START) study. METHODS We imputed HLA class I alleles from host genetic data (2546 HIV+ participants) and sampled immunopeptidomes from 2079 host-paired viral genomes (targeted amplicon sequencing). We predicted HLA class I binding affinities to HIV-1 and unspecific peptides, grouping alleles into functional clusters through consensus clustering. These functional HLA class I clusters were used to test associations with HIV VL. RESULTS We identified four clades totaling 30 HLA alleles accounting for 11.4% variability in VL. We highlight HLA-B∗57:01 and B∗57:03 as functionally similar but yet overrepresented in distinct ethnic groups, showing when combined a protective association with HIV+ VL (log, β -0.25; adj. P-value < 0.05). We further demonstrate only a slight power reduction when using unspecific immunopeptidomes, facilitating the use of the inferred functional HLA groups in other studies. CONCLUSION The outlined computational approach provides a robust and efficient way to incorporate HLA function and peptide diversity, aiding clinical association studies in heterogeneous cohorts. To facilitate access to the proposed methods and results we provide an interactive application for exploring data.
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Affiliation(s)
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut
| | | | - Migle Gabrielaite
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Virginia Kan
- George Washington University, Veterans Affairs Medical Center, Washington, DC, USA
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Osei-Hwedieh DO, Sedlacek AL, Hernandez LM, Yamoah AA, Iyer SG, Weiss KR, Binder RJ. Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy. JCI Insight 2023; 8:e170324. [PMID: 37427594 PMCID: PMC10371341 DOI: 10.1172/jci.insight.170324] [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: 03/07/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
T cells recognize tumor-derived mutated peptides presented on MHC by tumors. The recognition of these neo-epitopes leads to rejection of tumors, an event that is critical for successful cancer immunosurveillance. Determination of tumor-rejecting neo-epitopes in human tumors has proved difficult, though recently developed systems approaches are becoming increasingly useful at evaluating their immunogenicity. We have used the differential aggretope index to determine the neo-epitope burden of sarcomas and observed a conspicuously titrated antigenic landscape, ranging from the highly antigenic osteosarcomas to the low antigenic leiomyosarcomas and liposarcomas. We showed that the antigenic landscape of the tumors inversely reflected the historical T cell responses in the tumor-bearing patients. We predicted that highly antigenic tumors with poor antitumor T cell responses, such as osteosarcomas, would be responsive to T cell-based immunotherapy regimens and demonstrated this in a murine osteosarcoma model. Our study presents a potentially novel pipeline for determining antigenicity of human tumors, provides an accurate predictor of potential neo-epitopes, and will be an important indicator of which cancers to target with T cell-enhancing immunotherapy.
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Affiliation(s)
| | | | | | | | | | - Kurt R. Weiss
- Department of Orthopaedic Surgery, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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6
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Srivastava A, Hollenbach JA. The immunogenetics of COVID-19. Immunogenetics 2022; 75:309-320. [PMID: 36534127 PMCID: PMC9762652 DOI: 10.1007/s00251-022-01284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
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Affiliation(s)
- Anshika Srivastava
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| | - Jill A. Hollenbach
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
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Basir HRG, Majzoobi MM, Ebrahimi S, Noroozbeygi M, Hashemi SH, Keramat F, Mamani M, Eini P, Alizadeh S, Solgi G, Di D. Susceptibility and Severity of COVID-19 Are Both Associated With Lower Overall Viral–Peptide Binding Repertoire of HLA Class I Molecules, Especially in Younger People. Front Immunol 2022; 13:891816. [PMID: 35911710 PMCID: PMC9331187 DOI: 10.3389/fimmu.2022.891816] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
An important number of studies have been conducted on the potential association between human leukocyte antigen (HLA) genes and COVID-19 susceptibility and severity since the beginning of the pandemic. However, case–control and peptide-binding prediction methods tended to provide inconsistent conclusions on risk and protective HLA alleles, whereas some researchers suggested the importance of considering the overall capacity of an individual’s HLA Class I molecules to present SARS-CoV-2-derived peptides. To close the gap between these approaches, we explored the distributions of HLA-A, -B, -C, and -DRB1 1st-field alleles in 142 Iranian patients with COVID-19 and 143 ethnically matched healthy controls, and applied in silico predictions of bound viral peptides for each individual’s HLA molecules. Frequency comparison revealed the possible predisposing roles of HLA-A*03, B*35, and DRB1*16 alleles and the protective effect of HLA-A*32, B*58, B*55, and DRB1*14 alleles in the viral infection. None of these results remained significant after multiple testing corrections, except HLA-A*03, and no allele was associated with severity, either. Compared to peptide repertoires of individual HLA molecules that are more likely population-specific, the overall coverage of virus-derived peptides by one’s HLA Class I molecules seemed to be a more prominent factor associated with both COVID-19 susceptibility and severity, which was independent of affinity index and threshold chosen, especially for people under 60 years old. Our results highlight the effect of the binding capacity of different HLA Class I molecules as a whole, and the more essential role of HLA-A compared to HLA-B and -C genes in immune responses against SARS-CoV-2 infection.
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Affiliation(s)
- Hamid Reza Ghasemi Basir
- Department of Pathology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Samaneh Ebrahimi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mina Noroozbeygi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Hamid Hashemi
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fariba Keramat
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mojgan Mamani
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Peyman Eini
- Brucellosis Research Centre, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeed Alizadeh
- Department of Radiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghasem Solgi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- *Correspondence: Ghasem Solgi, ; Da Di,
| | - Da Di
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- *Correspondence: Ghasem Solgi, ; Da Di,
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8
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Di D, Thomas JS, Currat M, Nunes JM, Sanchez-Mazas A. Challenging ancient DNA results about putative HLA protection or susceptibility to Yersina pestis. Mol Biol Evol 2022; 39:6564158. [PMID: 35383854 PMCID: PMC9021733 DOI: 10.1093/molbev/msac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059–4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland
| | - Jeanne Simon Thomas
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Jose Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Quai Ernest-Ansermet 30, CH-1205 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Daull AM, Dubois V, Labussière-Wallet H, Venet F, Barraco F, Ducastelle-Lepretre S, Larcher MV, Balsat M, Gilis L, Fossard G, Ghesquières H, Heiblig M, Ader F, Alcazer V. Class I/Class II HLA Evolutionary Divergence Ratio Is an Independent Marker Associated With Disease-Free and Overall Survival After Allogeneic Hematopoietic Stem Cell Transplantation for Acute Myeloid Leukemia. Front Immunol 2022; 13:841470. [PMID: 35309346 PMCID: PMC8931406 DOI: 10.3389/fimmu.2022.841470] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Class I Human Leukocyte Antigen (HLA) evolutionary divergence (HED) is a metric which reflects immunopeptidome diversity and has been associated with immune checkpoint inhibitor responses in solid tumors. Its impact and interest in allogeneic hematopoietic stem cell transplantation (HCT) have not yet been thoroughly studied. This study analyzed the clinical and immune impact of class I and II HED in 492 acute myeloid leukemia (AML) recipients undergoing HCT. The overall cohort was divided into a training (n=338) and a testing (n=132) set. Univariate cox screening found a positive impact of a high class I HED and a negative impact of a high class II HED on both disease-free (DFS) and overall survival (OS). These results were combined in a unique marker, class I/class II HED ratio, and assessed in the testing cohort. The final multivariate cox model confirmed the positive impact of a high versus low class I/class II HED ratio on both DFS (Hazard Ratio (HR) 0.41 [95% CI 0.2-0.83]; p=0.01) and OS (HR 0.34 [0.19-0.59]; p<0.001), independently of HLA matching and other HCT parameters. No significant association was found between the ratio and graft-versus-host disease (GvHD) nor with neutrophil and platelet recovery. A high class I HED was associated with a tendency for an increase in NK, CD8 T-cell, and B cell recovery at 12 months. These results introduce HED as an original and independent prognosis marker reflecting immunopeptidome diversity and alloreactivity after HCT.
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Affiliation(s)
- Anne-Marie Daull
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Valérie Dubois
- Laboratory of histocompatibility, Etablissement Français du Sang, Lyon, France
| | - Hélène Labussière-Wallet
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Fabienne Venet
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard-Lyon 1, Lyon, France
| | - Fiorenza Barraco
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | | | - Marie-Virginie Larcher
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Marie Balsat
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Lila Gilis
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Gaëlle Fossard
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Hervé Ghesquières
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Maël Heiblig
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
| | - Florence Ader
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Hospices Civils de Lyon, Department of infectious diseases, Croix-Rousse hospital, Lyon, France
- LegioPath team, CIRI INSERM U1111 CNRS UMR 5308, Lyon, France
| | - Vincent Alcazer
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
- *Correspondence: Vincent Alcazer,
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10
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Lu Z, Chen H, Jiao X, Wang Y, Wu L, Sun H, Li S, Gong J, Li J, Zou J, Yang K, Hu Y, Mao B, Zhang L, Zhang X, Peng Z, Lu M, Wang Z, Zhang H, Shen L. Germline HLA-B evolutionary divergence influences the efficacy of immune checkpoint blockade therapy in gastrointestinal cancer. Genome Med 2021; 13:175. [PMID: 34732240 PMCID: PMC8567649 DOI: 10.1186/s13073-021-00997-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The human leukocyte antigen class I (HLA-I) genotype has been linked with differential immune responses to infectious disease and cancer. However, the clinical relevance of germline HLA-mediated immunity in gastrointestinal (GI) cancer remains elusive. METHODS This study retrospectively analyzed the genomic profiling data from 84 metastatic GI cancer patients treated with immune checkpoint blockade (ICB) recruited from Peking University Cancer Hospital (PUCH). A publicly available dataset from the Memorial Sloan Kettering (MSK) Cancer Center (MSK GI cohort) was employed as the validation cohort. For the PUCH cohort, we performed HLA genotyping by whole exome sequencing (WES) analysis on the peripheral blood samples from all patients. Tumor tissues from 76 patients were subjected to WES analysis and immune oncology-related RNA profiling. We studied the associations of two parameters of germline HLA as heterozygosity and evolutionary divergence (HED, a quantifiable measure of HLA-I evolution) with the clinical outcomes of patients in both cohorts. RESULTS Our data showed that neither HLA heterozygosity nor HED at the HLA-A/HLA-C locus correlated with the overall survival (OS) in the PUCH cohort. Interestingly, in both the PUCH and MSK GI cohorts, patients with high HLA-B HED showed a better OS compared with low HLA-B HED subgroup. Of note, a combinatorial biomarker of HLA-B HED and tumor mutational burden (TMB) may better stratify potential responders. Furthermore, patients with high HLA-B HED were characterized with a decreased prevalence of multiple driver gene mutations and an immune-inflamed phenotype. CONCLUSIONS Our results unveil how HLA-B evolutionary divergence influences the ICB response in patients with GI cancers, supporting its potential utility as a combinatorial biomarker together with TMB for patient stratification in the future.
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Affiliation(s)
- Zhihao Lu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Huan Chen
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Xi Jiao
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Yujiao Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Lijia Wu
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Shuang Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Jifang Gong
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Jian Li
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Jianling Zou
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Keyan Yang
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Ying Hu
- Biomedical Innovation Center, Beijing Shijitan Hospital, School of Oncology, Capital Medical University, Beijing, People's Republic of China
| | - Beibei Mao
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Lei Zhang
- Genecast Biotechnology Co., Ltd., 88 Danshan Road, Xidong Chuangrong Building, Suite D-401, Xishan District, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Xiaotian Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Zhi Peng
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Ming Lu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Zhenghang Wang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China
| | - Henghui Zhang
- Biomedical Innovation Center, Beijing Shijitan Hospital, School of Oncology, Capital Medical University, Beijing, People's Republic of China.
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Fu-Cheng Road 52, Hai-Dian District, Beijing, 100142, People's Republic of China.
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11
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Di D, Nunes JM, Jiang W, Sanchez-Mazas A. Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules. Mol Biol Evol 2021; 38:1580-1594. [PMID: 33320202 PMCID: PMC8355449 DOI: 10.1093/molbev/msaa325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Jose Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
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12
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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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13
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Liu C, Lei H, Ran X, Wang J. Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 2020; 8:e9889. [PMID: 32999762 PMCID: PMC7505079 DOI: 10.7717/peerj.9889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
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Affiliation(s)
- Chang Liu
- College of Animal Sciences, Guizhou University, Guiyang, China.,College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hongmei Lei
- College of Animal Sciences, Guizhou University, Guiyang, China
| | - Xueqin Ran
- College of Animal Sciences, Guizhou University, Guiyang, China
| | - Jiafu Wang
- College of Animal Sciences, Guizhou University, Guiyang, China.,Tongren University, Tongren, China
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14
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Vangenot C, Nunes JM, Doxiadis GM, Poloni ES, Bontrop RE, de Groot NG, Sanchez-Mazas A. Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution. BMC Evol Biol 2020; 20:119. [PMID: 32933484 PMCID: PMC7491122 DOI: 10.1186/s12862-020-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. RESULTS Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. CONCLUSIONS We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.
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Affiliation(s)
- Christelle Vangenot
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Gaby M Doxiadis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Estella S Poloni
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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15
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Souza AS, Sonon P, Paz MA, Tokplonou L, Lima THA, Porto IOP, Andrade HS, Silva NDSB, Veiga-Castelli LC, Oliveira MLG, Sadissou IA, Massaro JD, Moutairou KA, Donadi EA, Massougbodji A, Garcia A, Ibikounlé M, Meyer D, Sabbagh A, Mendes-Junior CT, Courtin D, Castelli EC. Hla-C genetic diversity and evolutionary insights in two samples from Brazil and Benin. HLA 2020; 96:468-486. [PMID: 32662221 DOI: 10.1111/tan.13996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function because it also interacts with Killer-cell immunoglobulin-like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, are poorly addressed, and few population-based studies explored the HLA-C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA-C diversity, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA-C promoter and 3'UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3'UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in the HLA-C leader peptide, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA-C locus in both populations.
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Affiliation(s)
- Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paulin Sonon
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Léonidas Tokplonou
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France.,Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nayane Dos S B Silva
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ibrahim Abiodoun Sadissou
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin
| | - André Garcia
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo (USP), São Paulo, Brazil
| | - Audrey Sabbagh
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - David Courtin
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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16
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Barquera R, Collen E, Di D, Buhler S, Teixeira J, Llamas B, Nunes JM, Sanchez-Mazas A. Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide. HLA 2020; 96:277-298. [PMID: 32475052 PMCID: PMC7300650 DOI: 10.1111/tan.13956] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
We report detailed peptide‐binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV‐1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide‐binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV‐1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA‐A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV‐1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Evelyn Collen
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia
| | - Da Di
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - João Teixeira
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia.,School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia.,The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - José M Nunes
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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17
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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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18
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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: 100] [Impact Index Per Article: 25.0] [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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19
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Iskandar RPD, Alida, Triwardhani A, Narmada IB, Hanum F, Kusumo AH, Nidom CA, Sudjarwo SA. Soluble Human Leukocyte Antigen Molecules Detected in Orofacial Cleft Patients: A Case-Control Study. PESQUISA BRASILEIRA EM ODONTOPEDIATRIA E CLÍNICA INTEGRADA 2020. [DOI: 10.1590/pboci.2020.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - Alida
- Universitas Airlangga, Indonesia
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20
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Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nat Med 2019; 25:1715-1720. [PMID: 31700181 DOI: 10.1038/s41591-019-0639-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
Abstract
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes1-3. However, the effect of sequence divergence between HLA-I alleles-a quantifiable measure of HLA-I evolution-on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient's genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex-peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell School of Medicine, New York, NY, USA.
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21
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Narula AK, Azad CS, Nainwal LM. New dimensions in the field of antimalarial research against malaria resurgence. Eur J Med Chem 2019; 181:111353. [DOI: 10.1016/j.ejmech.2019.05.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/16/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
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22
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Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC. Proc Natl Acad Sci U S A 2019; 116:14098-14104. [PMID: 31227609 DOI: 10.1073/pnas.1714436116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The major histocompatibility complex (MHC) is a central component of the vertebrate immune system and hence evolves in the regime of a host-pathogen evolutionary race. The MHC is associated with quantitative traits which directly affect fitness and are subject to selection pressure. The evolution of haplotypes at the MHC HLA (HLA) locus is generally thought to be governed by selection for increased diversity that is manifested in overdominance and/or negative frequency-dependent selection (FDS). However, recently, a model combining purifying selection on haplotypes and balancing selection on alleles has been proposed. We compare the predictions of several population dynamics models of haplotype frequency evolution to the distributions derived from 6.59-million-donor HLA typings from the National Marrow Donor Program registry. We show that models that combine a multiplicative fitness function, extremely high haplotype discovery rates, and exponential fitness decay over time produce the best fit to the data for most of the analyzed populations. In contrast, overdominance is not supported, and population substructure does not explain the observed haplotype frequencies. Furthermore, there is no evidence of negative FDS. Thus, multiplicative fitness, rapid haplotype discovery, and rapid fitness decay appear to be the major factors shaping the HLA haplotype frequency distribution in the human population.
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23
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Nemat-Gorgani N, Guethlein LA, Henn BM, Norberg SJ, Chiaroni J, Sikora M, Quintana-Murci L, Mountain JL, Norman PJ, Parham P. Diversity of KIR, HLA Class I, and Their Interactions in Seven Populations of Sub-Saharan Africans. THE JOURNAL OF IMMUNOLOGY 2019; 202:2636-2647. [PMID: 30918042 DOI: 10.4049/jimmunol.1801586] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022]
Abstract
HLA class I and KIR sequences were determined for Dogon, Fulani, and Baka populations of western Africa, Mbuti of central Africa, and Datooga, Iraqw, and Hadza of eastern Africa. Study of 162 individuals identified 134 HLA class I alleles (41 HLA-A, 60 HLA-B, and 33 HLA-C). Common to all populations are three HLA-C alleles (C1+C*07:01, C1+C*07:02, and C2+C*06:02) but no HLA-A or -B Unexpectedly, no novel HLA class I was identified in these previously unstudied and anthropologically distinctive populations. In contrast, of 227 KIR detected, 22 are present in all seven populations and 28 are novel. A high diversity of HLA A-C-B haplotypes was observed. In six populations, most haplotypes are represented just once. But in the Hadza, a majority of haplotypes occur more than once, with 2 having high frequencies and 10 having intermediate frequencies. The centromeric (cen) part of the KIR locus exhibits an even balance between cenA and cenB in all seven populations. The telomeric (tel) part has an even balance of telA to telB in East Africa, but this changes across the continent to where telB is vestigial in West Africa. All four KIR ligands (A3/11, Bw4, C1, and C2) are present in six of the populations. HLA haplotypes of the Iraqw and Hadza encode two KIR ligands, whereas the other populations have an even balance between haplotypes encoding one and two KIR ligands. Individuals in these African populations have a mean of 6.8-8.4 different interactions between KIR and HLA class I, compared with 2.9-6.5 for non-Africans.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, NY 11794
| | | | - Jacques Chiaroni
- UMR 7268-Anthropologie Bio-Culturelle, Droit, Éthique et Santé, Aix-Marseille Université, l'Etablissement Français du Sang, Centre National de la Recherche Scientifique, 13344 Marseille, France
| | - Martin Sikora
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | | | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO 80045; and.,Department of Immunology, University of Colorado, Denver, CO 80045
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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24
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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25
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Sanchez-Mazas A, Nunes JM. Does NGS typing highlight our understanding of HLA population diversity? Hum Immunol 2019; 80:62-66. [DOI: 10.1016/j.humimm.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/08/2023]
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26
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Sanchez-Mazas A, Černý V, Di D, Buhler S, Podgorná E, Chevallier E, Brunet L, Weber S, Kervaire B, Testi M, Andreani M, Tiercy JM, Villard J, Nunes JM. The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection. Mol Ecol 2017; 26:6238-6252. [PMID: 28950417 DOI: 10.1111/mec.14366] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/11/2017] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) genes play a key role in the immune response to infectious diseases, some of which are highly prevalent in specific environments, like malaria in sub-Saharan Africa. Former case-control studies showed that one particular HLA-B allele, B*53, was associated with malaria protection in Gambia, but this hypothesis was not tested so far within a population genetics framework. In this study, our objective was to assess whether pathogen-driven selection associated with malaria contributed to shape the HLA-B genetic landscape of Africa. To that aim, we first typed the HLA-A and -B loci in 484 individuals from 11 populations living in different environments across the Sahel, and we analysed these data together with those available for 29 other populations using several approaches including linear modelling on various genetic, geographic and environmental parameters. In addition to relevant signatures of populations' demography and migrations history in the genetic differentiation patterns of both HLA-A and -B loci, we found that the frequencies of three HLA alleles, B*53, B*78 and A*74, were significantly associated with Plasmodium falciparum malaria prevalence, suggesting their increase through pathogen-driven selection in malaria-endemic environments. The two HLA-B alleles were further identified, by high-throughput sequencing, as B*53:01:01 (in putative linkage disequilibrium with one HLA-C allele, C*04:01:01:01) and B*78:01 in all but one individuals tested, making them appropriate candidates to malaria protection. These results highlight the role of environmental factors in the evolution of the HLA polymorphism and open key perspectives for functional studies focusing on HLA peptide-binding properties.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Elodie Chevallier
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Lydie Brunet
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Weber
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Barbara Kervaire
- Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Jean-Marie Tiercy
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Jean Villard
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - José Manuel Nunes
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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27
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Bettens F, Buhler S, Tiercy JM. Allorecognition of HLA-C Mismatches by CD8 + T Cells in Hematopoietic Stem Cell Transplantation Is a Complex Interplay between Mismatched Peptide-Binding Region Residues, HLA-C Expression, and HLA-DPB1 Disparities. Front Immunol 2016; 7:584. [PMID: 28018351 PMCID: PMC5151176 DOI: 10.3389/fimmu.2016.00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
HLA-C locus mismatches (MMs) are the most frequent class I disparities in unrelated hematopoietic stem cell transplantation (HSCT) and have a detrimental impact on clinical outcome. Recently, a few retrospective clinical studies have reported some variability in the immunogenicity of HLA-C incompatibilities. To get better insight into presumably permissive HLA-C MMs, we have developed a one-way in vitro mixed lymphocyte reaction (MLR) assay allowing to quantify activated CD56-CD137+CD8+ lymphocytes in HLA-C incompatible combinations. T cell-mediated alloresponses were correlated with genetic markers such as HLA-C mRNA expression and the number of amino acid (aa) MMs in the α1/α2 domains (peptide-binding region). Because of the high rate of HLA-DPB1 incompatibilities in HLA-A-, B-, C-, DRB1-, and DQB1-matched unrelated HSCT patient/donor pairs, the impact of HLA-DPB1 mismatching, a potential bystander of CD4+ T cell activation, was also considered. Heterogeneous alloresponses were measured in 63 HLA-C-mismatched pairs with a positive assay in 52% of the combinations (2.3-18.6% activated CTLs), representing 24 different HLA-A~B~DRB1~DQB1 haplotypes. There was no correlation between measured alloresponses and mRNA expression of the mismatched HLA-C alleles. The HLA-C*03:03/03:04 MM did not induce any positive alloresponse in five MLRs. We also identified HLA-C*02:02 and HLA-C*06:02 as mismatched alleles with lower immunogenicity, and HLA-C*14:02 as a more immunogenic MM. A difference of at least 10 aa residues known to impact peptide/T cell receptor (TCR) binding and a bystander HLA-DPB1 incompatibility had a significant impact on CTL alloreactivity (p = 0.021). The same HLA-C MM, when recognized by two different responders with the same HLA haplotypes, was recognized differently, emphasizing the role of the T-cell repertoire of responding cells. In conclusion, mismatched HLA-C alleles differing by 10 or more aas in the peptide/TCR-binding region, when occurring together with HLA-DPB1 incompatibilities, should be considered as high-risk MMs in unrelated HSCT.
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Affiliation(s)
- Florence Bettens
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
| | - Stéphane Buhler
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
| | - Jean-Marie Tiercy
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva , Geneva , Switzerland
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28
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Yasukochi Y, Ohashi J. Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression? Immunogenetics 2016; 69:63-67. [PMID: 27695917 PMCID: PMC5203853 DOI: 10.1007/s00251-016-0952-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/16/2016] [Indexed: 12/01/2022]
Abstract
A previous study reported that some of the human leukocyte antigen (HLA) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged HLA-B*73 allele was proposed to be transmitted from Denisovans, although the DNA sequence of HLA-B*73 has not been detected in the Denisovan genome. Here, we argue against the hypothesis that HLA-B*73 introgressed from Denisovans into early modern humans. A phylogenetic analysis revealed that HLA-B*73:01 formed a monophyletic group with a chimpanzee MHC-B allele, strongly suggesting that the HLA-B*73 allelic lineage has been maintained in humans as well as in chimpanzees since the divergence of humans and chimpanzees. The global distribution of HLA-B*73 allele showed that the population frequency of HLA-B*73 in west Asia (0.24 %)—a possible site of admixture with Denisovans—is lower than that in Europe (0.72 %) and in south Asia (0.69 %). Furthermore, HLA-B*73 is not observed in Melanesia even though the Melanesian genome contains the highest proportion of Denisovan ancestry in present-day human populations. Single nucleotide polymorphisms in HLA-A*11-HLA-C*12:02 or HLA-A*11-C*15 haplotypes, one of which was assumed to be transmitted together with HLA-B*73 from Denisovans by the study of Abi-Rached and colleagues, were not differentiated from those in other HLA-A-C haplotypes in modern humans. These results do not support the introgression hypothesis. Thus, we conclude that it is highly likely that HLA-B*73 allelic lineage has been maintained in the direct ancestors of modern humans.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Human Functional Genomics, Life Science Research Center, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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