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Valencia A, Vergara C, Thio CL, Vince N, Douillard V, Grifoni A, Cox AL, Johnson EO, Kral AH, Goedert JJ, Mangia A, Piazzolla V, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Price JC, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Carrington M, Gourraud PA, Sette A, Thomas DL, Duggal P. Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1. Am J Hum Genet 2022; 109:299-310. [PMID: 35090584 PMCID: PMC8874224 DOI: 10.1016/j.ajhg.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022] Open
Abstract
Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQβ1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQβ1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQβ1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQβ1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQβ1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.
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Affiliation(s)
- Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Universidad Pontificia Bolivariana, Medellín, Antioquia 050031, Colombia
| | - Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Venceslas Douillard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alba Grifoni
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Alex H Kral
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alessandra Mangia
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gregory D Kirk
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jennifer C Price
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Laurent Alric
- Internal Medicine-Department of Digestive Diseases, Rangueil Hospital, Toulouse University, 1, 31400 Toulouse, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, NY 11203, USA
| | - Michael P Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, The Royal Free Hospital, Pond St, Hampstead, London NW3 2QG, UK
| | | | - Edward L Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Pierre-Antoine Gourraud
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alessandro Sette
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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An P, Zeng Z, Winkler CA. The Loss-of-Function S267F Variant in HBV Receptor NTCP Reduces Human Risk for HBV Infection and Disease Progression. J Infect Dis 2019; 218:1404-1410. [PMID: 29905807 DOI: 10.1093/infdis/jiy355] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Background Sodium taurocholate cotransporting polypeptide (NTCP, SLC10A1) is a hepatocyte receptor for hepatitis B virus (HBV) infection. The natural NTCP S267F variant causes loss of NTCP HBV receptor function. We assessed the association of S267F with HBV resistance, HBV infection clearance, and HBV-related cirrhosis and hepatocellular carcinoma (HCC). Methods We tested the effects of S267F in 1117 Han Chinese patients with various HBV infection outcomes using multivariate logistic regression analysis. Results The frequency of S267F (T allele) was higher in HBV-resistant healthy controls (n = 179, 4.0%) compared to HBV-infected patients (n = 648, 1.5%); odds ratio (OR) 0.32 (95% confidence interval [CI] 0.15-0.68; P = .003; dominant model). 267F variant genotypes were also associated with reduced risk for cirrhosis (n = 192, 0.5%) and HCC (n = 258, 1.0%) compared to those with chronic HBV infection (n = 202, 3.0%); OR 0.15 (95% CI, 0.03-0.70) and OR 0.21 (95% CI, 0.062-0.72), respectively. There was no association of the S267F variant with spontaneous HBV clearance. Conclusion The S267F variant for the HBV cell-entry receptor NTCP was associated with increased resistance to HBV infection and decreased risk for cirrhosis and liver cancer among those with chronic HBV infection.
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Affiliation(s)
- Ping An
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute.,Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Zheng Zeng
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute.,Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
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De Re V, Tornesello ML, De Zorzi M, Caggiari L, Pezzuto F, Leone P, Racanelli V, Lauletta G, Gragnani L, Buonadonna A, Vaccher E, Zignego AL, Steffan A, Buonaguro FM. Clinical Significance of Polymorphisms in Immune Response Genes in Hepatitis C-Related Hepatocellular Carcinoma. Front Microbiol 2019; 10:475. [PMID: 30930876 PMCID: PMC6429030 DOI: 10.3389/fmicb.2019.00475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
Background and Aims: Polymorphisms in the immune response genes can contribute to clearance of hepatitis C virus (HCV) infection but also mediate liver inflammation and cancer pathogenesis. This study aimed to investigate the association of polymorphisms in PD-1 (PDCD1), IFNL3 (IL28B), and TLR2 immune related genes in chronic HCV patients with different hepatic and lymphoproliferative HCV-related diseases. Methods: Selected PDCD1, IFNL3, and TLR2 genes were tested by molecular approaches in 450 HCV-positive patients with increasing severity of underlying liver diseases [including chronic infection (CHC), cirrhosis and hepatocellular carcinoma (HCC)], in 238 HCV-positive patients with lymphoproliferative diseases [such as cryoglobulinemia and non-Hodgkin lymphoma (NHL)] and in 94 blood donors (BD). Results: While the rs12979860 IFNL3 T allele was found a good marker associated with HCV-outcome together with the rs111200466 TLR2 del variant, the rs10204525 PD-1.6 A allele was found to have an insignificant role in patients with HCV-related hepatic disorders. Though in Asian patients the combination of IFNL3 and PD-1.6 markers better define the HCV-related outcomes, in our series of Caucasian patients the PD-1.6 A-allele variant was observed very rarely. Conclusion: Differences in the incidence of HCV-related HCC and clinical response between Asians and Europeans may be partially due to the distribution of PD-1.6 genotype that we found divergent between these two populations. On the other hand, we confirmed in this study that the polymorphic variants within IFNL3 and TLR2 immune response genes are significantly associated with HCV-related disease progression in our cohort of Italian patients.
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Affiliation(s)
- Valli De Re
- Centro di Riferimento Oncologico, Cancer Institute, Aviano, Italy
| | | | | | - Laura Caggiari
- Centro di Riferimento Oncologico, Cancer Institute, Aviano, Italy
| | - Francesca Pezzuto
- Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Patrizia Leone
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Gianfranco Lauletta
- Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Laura Gragnani
- Department of Experimental and Clinical Medicine and Department of Oncology, Interdepartmental Hepatology Center MASVE, Azienda Ospedaliero-Universitaria Careggi (AOUC), Florence, Italy
| | | | - Emanuela Vaccher
- Centro di Riferimento Oncologico, Cancer Institute, Aviano, Italy
| | - Anna Linda Zignego
- Department of Experimental and Clinical Medicine and Department of Oncology, Interdepartmental Hepatology Center MASVE, Azienda Ospedaliero-Universitaria Careggi (AOUC), Florence, Italy
| | - Agostino Steffan
- Centro di Riferimento Oncologico, Cancer Institute, Aviano, Italy
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Abstract
In this brief review and perspective, we address the question of whether the immune responses that bring about immune control of acute HIV infection are the same as, or distinct from, those that maintain long-term viral suppression once control of viremia has been achieved. To this end, we describe the natural history of elite and post-treatment control, noting the lack of data regarding what happens acutely. We review the evidence suggesting that the two clinical phenotypes may differ in terms of the mechanisms required to achieve and maintain control, as well as the level of inflammation that persists once a steady state is achieved. We then describe the evidence from longitudinal studies of controllers who fail and studies of biologic sex (male versus female), age (children versus adults), and simian immunodeficiency virus (SIV) (pathogenic/experimental versus nonpathogenic/natural infection). Collectively, these studies demonstrate that the battle between the inflammatory and anti-inflammatory pathways during acute infection has long-term consequences, both for the degree to which control is maintained and the health of the individual. Potent and stringent control of HIV may be required acutely, but once control is established, the chronic inflammatory response can be detrimental. Interventional approaches designed to bring about HIV cure and/or remission should be nuanced accordingly.
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Affiliation(s)
- Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, California, United States of America
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