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Panduro A, Roman S, Mariscal-Martinez IM, Jose-Abrego A, Gonzalez-Aldaco K, Ojeda-Granados C, Ramos-Lopez O, Torres-Reyes LA. Personalized medicine and nutrition in hepatology for preventing chronic liver disease in Mexico. Front Nutr 2024; 11:1379364. [PMID: 38784134 PMCID: PMC11113077 DOI: 10.3389/fnut.2024.1379364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 05/25/2024] Open
Abstract
Chronic liver disease is a global health issue. Patients with chronic liver disease require a fresh approach that focuses on the genetic and environmental factors that contribute to disease initiation and progression. Emerging knowledge in the fields of Genomic Medicine and Genomic Nutrition demonstrates differences between countries in terms of genetics and lifestyle risk factors such as diet, physical activity, and mental health in chronic liver disease, which serves as the foundation for the implementation of Personalized Medicine and Nutrition (PerMed-Nut) strategies. Most of the world's populations have descended from various ethnic groupings. Mexico's population has a tripartite ancestral background, consisting of Amerindian, European, and African lineages, which is common across Latin America's regional countries. The purpose of this review is to discuss the genetic and environmental components that could be incorporated into a PerMed-Nut model for metabolic-associated liver disease, viral hepatitis B and C, and hepatocellular carcinoma in Mexico. Additionally, the implementation of the PerMed-Nut approach will require updated medicine and nutrition education curricula. Training and equipping future health professionals and researchers with new clinical and investigative abilities focused on preventing liver illnesses in the field of genomic hepatology globally is a vision that clinicians and nutritionists should be concerned about.
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Affiliation(s)
- Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Irene M. Mariscal-Martinez
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alexis Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Karina Gonzalez-Aldaco
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Ojeda-Granados
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Catania, Italy
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Baja California, Mexico
| | - Luis A. Torres-Reyes
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Zhang Q, Kisand K, Feng Y, Rinchai D, Jouanguy E, Cobat A, Casanova JL, Zhang SY. In search of a function for human type III interferons: insights from inherited and acquired deficits. Curr Opin Immunol 2024; 87:102427. [PMID: 38781720 PMCID: PMC11209856 DOI: 10.1016/j.coi.2024.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 03/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The essential and redundant functions of human type I and II interferons (IFNs) have been delineated over the last three decades by studies of patients with inborn errors of immunity or their autoimmune phenocopies, but much less is known about type III IFNs. Patients with cells that do not respond to type III IFNs due to inherited IL10RB deficiency display no overt viral disease, and their inflammatory disease phenotypes can be explained by defective signaling via other interleukine10RB-dependent pathways. Moreover, patients with inherited deficiencies of interferon-stimulated gene factor 3 (ISGF-3) (STAT1, STAT2, IRF9) present viral diseases also seen in patients with inherited deficiencies of the type I IFN receptor (IFNAR1/2). Finally, patients with autoantibodies neutralizing type III IFNs have no obvious predisposition to viral disease. Current findings thus suggest that type III IFNs are largely redundant in humans. The essential functions of human type III IFNs, particularly in antiviral defenses, remain to be discovered.
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Affiliation(s)
- Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France.
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Yi Feng
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France; Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France; Howard Hughes Medical Institute, New York, USA
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France
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Laplana M, Royo JL, Real LM. Genetic Association Studies in Host-Pathogen Interaction Analysis. Methods Mol Biol 2024; 2751:19-30. [PMID: 38265707 DOI: 10.1007/978-1-0716-3617-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Studying host-pathogen interactions at a molecular level has always been technically challenging. Identifying the different biochemical and genetic pathways involved in the different stages of infection traditionally require complex molecular biology tools and often the use of costly animal models. In this chapter, we illustrate a complementary approach to address host-pathogen interactions, taking advantage of the natural interindividual genetic diversity. The application of genetic association studies allows us to identify alleles involved in infection progression or resistance. Thus, this strategy may be useful to unravel new molecular pathways underlying host-pathogen interactions. Here we present the general steps that might be followed to plan, execute, and analyze a population-based study in order to identify genetic variants affecting human exposition to pathogens.
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Affiliation(s)
- Marina Laplana
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain.
| | - Luis Miguel Real
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Instituto de Biomedicina de Sevilla, Sevilla, Spain
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4
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Response to antiviral therapy for chronic hepatitis C and risk of hepatocellular carcinoma occurrence in Japan: a systematic review and meta-analysis of observational studies. Sci Rep 2023; 13:3445. [PMID: 36859564 PMCID: PMC9977913 DOI: 10.1038/s41598-023-30467-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
In Japan, hepatocellular carcinoma (HCC) is a leading cause of cancer mortality and hepatitis C virus infection is a major cause of HCC. We conducted a systematic review and meta-analysis of published studies evaluating patient response to antiviral therapy for chronic hepatitis C on the risk of HCC occurrence in Japan. Articles were searched using terms determined a priori through PubMed, screened by title and abstract, and selected by full-text assessment according to criteria determined a priori, including HCC occurrence in response to interferon (IFN)-based or IFN-free therapy, Japanese study, and 2 or more years of follow-up. We excluded studies on HCC recurrence. We calculated the pooled estimate of the crude incidence rate ratio with data from the selected studies using the person-years method with Poisson regression model and pooled estimate of the hazard ratio adjusted for potential confounders reported by the studies using a random effects model. A total of 26 studies were identified, all of which examined only IFN-based therapy as a result of the selection process. The pooled estimate (95% confidence interval [CI]) of 25 studies was 0.37 (0.33-0.43) for sustained virologic response (SVR) and 1.70 (1.61-1.80) for non-SVR for the HCC incidence rate per 100 person-years, and 0.22 (0.19-0.26) for the incidence rate ratio (SVR vs. non-SVR). The pooled estimate of the hazard ratio (95% CI) of HCC incidence adjusted for potential confounders of 8 studies was 0.25 (0.19-0.34). SVR to interferon therapy for chronic hepatitis C reduces the risk of HCC occurrence.
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Duchen D, Vergara C, Thio CL, Kundu P, Chatterjee N, Thomas DL, Wojcik GL, Duggal P. Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects. Am J Hum Genet 2023; 110:336-348. [PMID: 36649706 PMCID: PMC9943744 DOI: 10.1016/j.ajhg.2022.12.013] [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: 06/13/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
Genome-wide association studies (GWASs) have been performed to identify host genetic factors for a range of phenotypes, including for infectious diseases. The use of population-based common control subjects from biobanks and extensive consortia is a valuable resource to increase sample sizes in the identification of associated loci with minimal additional expense. Non-differential misclassification of the outcome has been reported when the control subjects are not well characterized, which often attenuates the true effect size. However, for infectious diseases the comparison of affected subjects to population-based common control subjects regardless of pathogen exposure can also result in selection bias. Through simulated comparisons of pathogen-exposed cases and population-based common control subjects, we demonstrate that not accounting for pathogen exposure can result in biased effect estimates and spurious genome-wide significant signals. Further, the observed association can be distorted depending upon strength of the association between a locus and pathogen exposure and the prevalence of pathogen exposure. We also used a real data example from the hepatitis C virus (HCV) genetic consortium comparing HCV spontaneous clearance to persistent infection with both well-characterized control subjects and population-based common control subjects from the UK Biobank. We find biased effect estimates for known HCV clearance-associated loci and potentially spurious HCV clearance associations. These findings suggest that the choice of control subjects is especially important for infectious diseases or outcomes that are conditional upon environmental exposures.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chloe L Thio
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Prosenjit Kundu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David L Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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Huang P, Wu JJ, Zhang JW, Hou YQ, Zhu P, Yin R, Yu RB, Zhang Y, Yue M, Hou W. Genetic variants of IFIH1 and DHX58 affect the chronicity of hepatitis C in the Chinese Han population. PeerJ 2023; 11:e14740. [PMID: 36743960 PMCID: PMC9893905 DOI: 10.7717/peerj.14740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 12/22/2022] [Indexed: 01/31/2023] Open
Abstract
Hepatitis C remains a major public health problem in the world. The host immune system plays a key role in viral clearance. This study aimed to investigate the connection between retinoic acid-inducible gene I-like (RIG-I-like) receptor gene polymorphism and hepatitis C chronicity in the Chinese Han population. The current study genotyped three SNPs (IFIH1 rs10930046 and DHX58 rs2074158, rs2074160) to assess their association with the chronicity of hepatitis C virus (HCV) infection among 1,590 participants (590 spontaneous HCV clearance cases and 1,000 persistent infection patients). Our research shows that DHX58 rs2074158-G allele (dominant model: adjusted OR = 1.53, 95% CI [1.20-1.95], P = 0.001; additive model: adjusted OR = 1.50, 95% CI [1.27-1.78], P < 0.001) and IFIH1 rs10930046-C allele (additive model: adjusted OR = 1.26, 95% CI [1.07-1.49], P = 0.005) were associated with chronic hepatitis C (CHC). And the risk of CHC increased in people carrying more unfavorable genotypes (rs2074158-AG/GG or rs10930046-CC), with the chronic rates for genotypes number from zero to two in 60.69%, 57.33%, and 85.93%, respectively (adjusted OR = 3.64, 95% CI [2.18-6.08]; P < 0.001). Genetic polymorphism of IFIH1 and DHX58 may be related to CHC in the Chinese Han population. Furthermore, the risk of CHC increases as the number of unfavorable genotypes carried by the HCV-infected person increases. IFIH1 rs10930046, DHX58 rs2074158, age, ALT, and AST levels were all independent predictors of CHC.
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Affiliation(s)
- Peng Huang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China,The State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jing-Jing Wu
- The Department of Environmental Health, Yangzhou Center for Disease Control and Prevention, Yang-zhou, China
| | - Jin-Wei Zhang
- Department of Anesthesiology, Nanjing Drum Tower Hospital, Nanjing, China
| | - Yu-Qing Hou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ping Zhu
- Department of Medical Affairs, Jiangsu Provincial People’s Hospital, Nanjing, China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Rong-Bin Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Hou
- The State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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7
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Suslov A, Heim MH, Wieland S. Studying Hepatitis Virus-Host Interactions in Patient Liver Biopsies. Viruses 2022; 14:v14112490. [PMID: 36366588 PMCID: PMC9699472 DOI: 10.3390/v14112490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Infectious diseases are a major contributor to human suffering and the associated socioeconomic burden worldwide. A better understanding of human pathogen-host interactions is a prerequisite for the development of treatment strategies aimed at combatting human pathogen-induced diseases. Model systems that faithfully recapitulate the pathogen-host interactions in humans are critical to gain meaningful insight. Unfortunately, such model systems are not yet available for a number of pathogens. The strict tropism of the hepatitis B (HBV) and C (HCV) viruses for the human liver has made it difficult to study their virus-host interactions during the natural history of these infections. In this case, surplus liver biopsy tissue donated by patients provides an opportunity to obtain a snapshot of the phenomenological and molecular aspects of the human liver of chronically HCV or HBV-infected patients. In this review, we will briefly summarize our own efforts over the years to advance our knowledge of the virus-host interactions during the natural history of chronic HCV and HBV infection.
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Affiliation(s)
- Aleksei Suslov
- Department of Biomedicine, University Hospital Basel, University of Basel, CH-4031 Basel, Switzerland
| | - Markus H. Heim
- Department of Biomedicine, University Hospital Basel, University of Basel, CH-4031 Basel, Switzerland
- Division of Gastroenterology and Hepatology, University Hospital Basel, CH-4031 Basel, Switzerland
| | - Stefan Wieland
- Department of Biomedicine, University Hospital Basel, University of Basel, CH-4031 Basel, Switzerland
- Correspondence:
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8
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The role of IFNL4 in liver inflammation and progression of fibrosis. Genes Immun 2022; 23:111-117. [PMID: 35585257 DOI: 10.1038/s41435-022-00173-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022]
Abstract
The discovery that genetic variation within the interferon lambda locus has a profound effect on the outcome of hepatitis C virus (HCV) treatment and spontaneous clearance of HCV is one of the great triumphs of genomic medicine. Subsequently, the IFNL4 gene was discovered and proposed as the causal gene underlying this association. However, there has been a lively debate within the field concerning the causality, which has been further complicated by a change in naming. This review summarizes the genetic data available for the IFNL3/IFNl4 loci and provides an in-depth discussion of causality. We also discuss a new series of interesting data suggesting that the genetic variation at the IFNL4 loci influences the evolution of the HCV virus and the implication this relationship between our genetic makeup and virus evolution has upon our understanding of the IFNL4 system. Finally, new data support an influence of the IFNL4 gene upon liver inflammation and fibrosis that is independent of etiology, thereby linking the IFNL4 gene to some of the major liver diseases of today.
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Youssef SS, Abbas EAER, Youness RA, Elemeery MN, Nasr AS, Seif S. PNPLA3 and IL 28B signature for predicting susceptibility to chronic hepatitis C infection and fibrosis progression. Arch Physiol Biochem 2022; 128:483-489. [PMID: 31793339 DOI: 10.1080/13813455.2019.1694039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Association studies identified genetic polymorphisms as predictive risk factors of rapid fibrosis progression in chronic hepatitis C (CHC). This study aims to assess the impact of IL28B rs8099917 polymorphism on CHC genotype 4 (G4) susceptibility and liver fibrosis progression individually; and in combination with PNPLA3 rs738409. PATIENTS AND METHODS IL28B rs8099917 and PNPLA3 rs738409 were genotyped in 150 Egyptian CHC patients and 175 healthy controls using real-time PCR. RESULTS IL28B rs8099917 genotype distribution significantly differs in healthy individuals versus CHC patients (p = .018); and in low versus advanced fibrosis IL28B (p = .013). The haplotype CC -GG (PNPLA3-IL28B) is considered a high-risk signature for susceptibility to CHC infection. Similarly, GG-GG (PNPLA3-IL28B) is considered a high-risk signature for higher degree of fibrosis. CONCLUSION IL28B rs8099917 and PNPLA3 rs738409 introduce genetic signature to identify patients at higher risk for CHC susceptibility and fibrosis progression in CHC G4.
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Affiliation(s)
- Samar Samir Youssef
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Egypt
| | - Eman Abd El Razek Abbas
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Egypt
| | - Rana Ahmed Youness
- Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Moustafa Nouh Elemeery
- Microbial Biotechnology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Egypt
- Département de Neurosciences, CRCHUM, Université de Montréal, Montréal, Quebec, Canada
| | - Amal Soliman Nasr
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Sameh Seif
- National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt
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10
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Auwerx C, Sadler MC, Reymond A, Kutalik Z. From Pharmacogenetics to Pharmaco-Omics:Milestones and Future Directions. HGG ADVANCES 2022; 3:100100. [PMID: 35373152 PMCID: PMC8971318 DOI: 10.1016/j.xhgg.2022.100100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The origins of pharmacogenetics date back to the 1950s, when it was established that inter-individual differences in drug response are partially determined by genetic factors. Since then, pharmacogenetics has grown into its own field, motivated by the translation of identified gene-drug interactions into therapeutic applications. Despite numerous challenges ahead, our understanding of the human pharmacogenetic landscape has greatly improved thanks to the integration of tools originating from disciplines as diverse as biochemistry, molecular biology, statistics, and computer sciences. In this review, we discuss past, present, and future developments of pharmacogenetics methodology, focusing on three milestones: how early research established the genetic basis of drug responses, how technological progress made it possible to assess the full extent of pharmacological variants, and how multi-dimensional omics datasets can improve the identification, functional validation, and mechanistic understanding of the interplay between genes and drugs. We outline novel strategies to repurpose and integrate molecular and clinical data originating from biobanks to gain insights analogous to those obtained from randomized controlled trials. Emphasizing the importance of increased diversity, we envision future directions for the field that should pave the way to the clinical implementation of pharmacogenetics.
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11
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Ateya RM, Afifi SA, Abd Al Monem N, Al-Karamany AS, Bessar AA, Rageh F, Ahmed SS, Ghareeb D. Impact of IL-28B gene polymorphism on chronic hepatitis-C patients progression with diabetes and non-diabetes. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Chronic hepatitis C (CHC) is a silent viral infection; however, elevated mortality and morbidity rates are noted in Egypt due to its adverse effects. The augmented incidence of diabetes in patients with viral C infection may be owing to glucose intolerance, high BMI, senility, and inherited factors.
Purpose of the study
Little information is available about the connection between interleukin-28B (IL-28B) genotype in disease progression among CHC patients with diabetes. Thus, we aimed to assess the association between IL-28B genotype (rs12979860) in CHC with type 2 diabetes mellitus (T2DM) versus those without diabetes in disease progression among Egyptian patients.
Results
CC genotype was significantly lower in diabetics than in non-diabetics (13.7% vs. 36.3%). While (CT/TT) were significantly higher in diabetics than in non-diabetics (CT 58.8% vs. 43.7%), (TT 27.5% vs. 20%) (p = 0.03) and likewise alleles (p = 0.04). Multivariate logistic regression analysis was significant with viral load p < 0.001, alanine aminotransferase (ALT) p < 0.001, genotype CC versus TT p = 0.04 & T2DM p = 0.03.
Conclusion
CC genotype might be used as a protective factor and TT genotype as a risk factor in disease progression among CHC patients with T2DM. Additionally, viral load, ALT & T2DM might interplay as predictors of disease severity. Detecting the genetic factors can be helpful in predicting and preventing the complications of diabetes associated with the hepatitis C virus (HCV).
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12
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Mansy SS, AbouSamra MM. Electron microscopy overview of SARS-COV2 and its clinical impact. Ultrastruct Pathol 2022; 46:1-17. [PMID: 35139747 DOI: 10.1080/01913123.2022.2035475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Research centers around the world are competing to develop therapeutic and prophylactic agents to provide new intervention strategies that could halt or even help slow the progression of the COVID19 pandemic. This requires a deep understanding of the biology and cytopathology of the interaction of SARS-CoV-2 with the cell. This review highlights the importance of electron microscopy (EM) in better understanding the morphology, the subcellular morphogenesis, and pathogenesis of SARS-CoV-2, given its nanometric dimensions. The study also underscores the value of cryo-electron microscopy for analyzing the structure of viral protein complex at atomic resolution in its native state and the development of novel antibodies, vaccines, and therapies targeting the trimeric S spike proteins and the viral replication organelles. This review highlighted the emergence in a short period of time of several viral variants of concern with enhanced transmissibility and increased infectivity. This is due to the elevated affinity of the host receptor with acquired adaptive mutations in the spike protein gene of the virus.Subsequently, to the technical improvement of EM resolutions and the recent promising results with SARS-CoV2 variant structure determination, antibodies production, and vaccine development, it is necessary to maximize our investigations regarding the potential occurrence of immune pressure and viral adaptation secondary to repeated infection and vaccination.
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Affiliation(s)
- Soheir Saiid Mansy
- Electron Microscopy Research Department, Theodor Bilharz Research Institute, Egypt
| | - Mona Mahmoud AbouSamra
- Pharmaceutical Technology Department, Pharmaceutical and Drug Industries Institute, National Research Centre, Cairo, Egypt
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13
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Hajizadeh L, Samaei NM, Bazgir A, Agha Gholizadeh M, Khosravi A. Association of Interleukin-28B Polymorphisms (rs12979860 C/T, rs12980275 A/G, rs8099917 T/G) and Risk of Hepatocellular Carcinoma in an Iranian Population. Middle East J Dig Dis 2022; 14:118-123. [PMID: 36619736 PMCID: PMC9489329 DOI: 10.34172/mejdd.2022.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/18/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND: Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. The association of interleukin 28B (IL-28B) polymorphisms and HCC has been investigated in several populations. However, the findings are controversial. This study aimed to address the association between IL-28B polymorphisms (rs 8099917 T/G, rs12979860 C/T, rs12980275 A/G) and the risk of HCC in an Iranian population. METHODS: We have evaluated the association between IL-28B polymorphisms (rs 8099917 T/G, rs12979860 C/T, rs12980275 A/G) and HCC in 180 Iranian individuals (60 patients with HCC and 120 healthy matched controls) using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method. Single nucleotide polymorphism (SNP) association analysis and also haplotypes were estimated using the SNPstats online software. RESULTS: There was no significant association between these three polymorphisms of IL-28B and HCC (P>0.05). Moreover, haplotype analysis showed no significant association between the haplotypes and HCC. CONCLUSION: There was no association between IL-28B polymorphisms and HCC in an Iranian population.
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Affiliation(s)
- Leila Hajizadeh
- Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nader Mansour Samaei
- Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran,Corresponding Author: Nader Mansour Samaei, MD, PhD Human Genetics Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran Telefax:+98 1732430563 ,
| | - Afsaneh Bazgir
- Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Agha Gholizadeh
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ayoob Khosravi
- Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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14
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Xu T, Peng B, Liu M, Liu Q, Yang J, Qu M, Liu N, Lin L, Wu J. Favorable Genotypes of Type III Interferon Confer Risk of Dyslipidemia in the Population With Obesity. Front Endocrinol (Lausanne) 2022; 13:871352. [PMID: 35784542 PMCID: PMC9243353 DOI: 10.3389/fendo.2022.871352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Studies have indicated that the chronic state of inflammation caused by obesity leads to dyslipidemia. However, how the polymorphisms involved in these inflammatory pathways affect the lipid metabolism in people with obesity is poorly understood. We investigated the associations of inflammation-related gene polymorphisms with dyslipidemia in individuals with obesity living in China. METHODS This case-control study in a population with obesity involved 194 individuals with dyslipidemia and 103 individuals without dyslipidemia. Anthropometric indices of obesity, fasting plasma glucose, blood pressure, blood lipids, and C-reactive protein were evaluated. The genes we tested were IL6 (interleukin 6), IL6R (interleukin 6 receptor), FOXP3 (forkhead box P3), TLR2 (toll-like receptor 2), TLR4 (toll-like receptor 4), IFNL3 (interferon lambda 3, formerly known as IL28B), and IFNL4 (interferon lambda 4, formerly known as IL29). Polymorphisms were genotyped using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. RESULTS There were significant differences in the allelic and genotype frequencies of IFNL3 (IL28B) rs12971396, rs8099917, rs11882871, rs12979860, rs4803217 between non-dyslipidemia and dyslipidemia groups in people with obesity. These single nucleotide polymorphisms (SNPs) of IFNL3 were highly linked (D' and r > 0.90), so the result of one SNP could represent the result of other SNPs. For IFNL3 rs12971396, people with the homozygous genotype (the major group) carried a higher risk of dyslipidemia than people with the heterozygous genotype (P < 0.001, OR = 4.46, 95%CI, 1.95-10.22). CONCLUSIONS The favorable genotypes of type III interferon, which have a beneficial role in anti-virus function, were associated with dyslipidemia in a Chinese population with obesity. Type III interferon could have a pathologic role and confer risk of dyslipidemia in people with obesity and chronic inflammation.
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Affiliation(s)
- Tiantian Xu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Bo Peng
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Mengmeng Liu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qingjing Liu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Junya Yang
- School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
| | - Minli Qu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Na Liu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lizhen Lin
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Wu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Jing Wu,
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15
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Öksüz Z, Üçbilek E, Serin MS, Yaraş S, Temel GÖ, Sezgin O. Possible relationship between IL28B rs12979860 and TLR2 -196 to -174 del/ins polymorphisms and the liver fibrosis stage in hepatitis C patients. Arch Virol 2022; 167:153-161. [PMID: 34817649 DOI: 10.1007/s00705-021-05302-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/01/2021] [Indexed: 10/19/2022]
Abstract
It has been shown that host factors play an important role in the progression of hepatitis C virus (HCV) infection. Toll-like receptor 2 (TLR2) del and interleukin 28B (IL28B) T alleles can mediate liver inflammation and pathogenesis of hepatocellular carcinoma. In the present study, the possible relationship between the IL28B rs12979860 C/T and TLR2 -196 to -174 del/ins gene variants and different fibrosis stages and host factors in hepatitis C patients was investigated. IL28B and TLR2 polymorphisms in the blood of 50 hepatitis C patients at different stages of fibrosis (24 mild/moderate, 26 advanced) and 24 healthy controls were examined by RT-qPCR. The highest frequency of the TLR2 del (26.9%) and IL28B T (46.2%) alleles was found in hepatitis C patients with the most advanced fibrosis, and the lowest frequency was found in healthy controls. There was a statistically significant difference between hepatitis C patients with advanced fibrosis and healthy controls in terms of the TLR2 del (p = 0.0062) and IL28B T (p = 0.0017) allele frequencies. However, no statistically significant difference was found between the mild/moderate fibrosis and severe fibrosis patient groups in terms of genotype or IL28B and TLR2 polymorphisms (p > 0.05). In addition, there was a significant difference between patients with mild/moderate or advanced fibrosis who carried the TLR2 del allele together with the IL28B CT genotype and healthy controls. The present study emphasizes that the TLR2 and IL28B gene variants cannot be single biomarkers for the determination of fibrosis stage in hepatitis C infection but together can play an important role in predicting severe disease.
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Affiliation(s)
- Zehra Öksüz
- Department of Pharmaceutical Microbiology, Mersin University Faculty of Pharmacy, Mersin, Turkey.
| | - Enver Üçbilek
- Department of Gastroenterology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Mehmet Sami Serin
- Department of Pharmaceutical Microbiology, Mersin University Faculty of Pharmacy, Mersin, Turkey
| | - Serkan Yaraş
- Department of Gastroenterology, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Gülhan Örekici Temel
- Department of Biostatistics, Mersin University Faculty of Medicine, Mersin, Turkey
| | - Orhan Sezgin
- Department of Gastroenterology, Mersin University Faculty of Medicine, Mersin, Turkey
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16
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Ibrahim MK, AbdElrahman M, Bader El Din NG, Tawfik S, Abd-Elsalam S, Omran D, Barakat AZ, Farouk S, Elbatae H, El Awady MK. The impact of genetic variations in sofosbuvir metabolizing enzymes and innate immunity mediators on treatment outcome in HCV-infected patients. Microb Pathog 2021; 162:105311. [PMID: 34843922 DOI: 10.1016/j.micpath.2021.105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) is the leading cause of liver diseases worldwide. At present, combinations of different classes of direct-acting antiviral agents (DAAs) are used as treatment options for HCV, in which sofosbuvir (SOF) is the common DAA among different therapeutic regimes. In Egypt, SOF plus daclatasvir (DCV) is the widely used anti-HCV treatment protocol. Herein, we aimed to assess the association between 3 single-nucleotide polymorphisms (SNPs) at the genes coding for 2 SOF metabolizing enzymes: histidine triad nucleotide-binding protein 1 (HINT1) rs4696/rs7728773 and nucleoside diphosphate kinase 1 (NME1) rs3760468, together with the most potent anti-HCV innate molecule, i.e., interferon lambda 3 (IFNL3) rs12979860 and the response to SOF/DCV in Egyptian patients chronically infected with genotype 4 (GT4). SNPs were genotyped using real-time PCR in DNA from patients who achieved sustained virological response (SVR) at 12 weeks post-SOF/DCV treatment (i.e., responders; n = 188), patients who failed to achieve SVR12 (i.e., non-responders; n = 109), and healthy controls (n = 62). Our results demonstrated that patients bearing HINT1 rs7728773 CT/TT (odds ratio 2.119, 95% CI 1.263-3.559, p = 0.005) and IFNL3 rs12979860 CC (odds ratio 3.995, 95% CI 2.126-7.740, p = 0.0001) were more likely to achieve SVR12. However, neither HINT1 rs4696 nor NME1 rs3760468 seems to contribute to the responsiveness to SOF/DCV. Binary regression analysis defined 5 predictor factors independently associated with SVR12: age, bilirubin, hemoglobin, early stages of fibrosis, and combined HINT1 rs7728773 and IFNL3 rs12979860 favorable and mixed genotypes (odds ratio 3.134, 95% CI 1.518-6.47, p = 0.002), and that was confirmed by the combined ROC curve for the 5 predictor factors (AUC = 0.91, 95% CI 0.869-0.95, P = 0.0001). In conclusion, these data suggest that the two SNPs have the potential in predicting the response rate to SOF/DCV treatment in patients infected with HCV GT4. This study is the first to investigate the pharmacogenetics of SOF metabolizing enzyme and introduce HINT1 rs7728773 as a novel SNP that predicts the treatment efficacy.
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Affiliation(s)
- Marwa K Ibrahim
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt.
| | - Mohamed AbdElrahman
- Department of Pharmacy, Al-Mustaqbal University College, Babylon, Iraq; Clinical Pharmacy Unit, Badr University Hospital, Faculty of Medicine, Helwan University, Egypt
| | - Noha G Bader El Din
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Salwa Tawfik
- Department of Internal Medicine, National Research Center, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Sherief Abd-Elsalam
- Department of Tropical Medicine and Infectious Diseases, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Dalia Omran
- Department of Endemic Medicine and Hepatology, Faculty of Medicine, Cairo University, Egypt
| | - Amal Z Barakat
- Department of Molecular Biology, Biotechnology Research Institute, National Research Center, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Sally Farouk
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
| | - Hassan Elbatae
- Department of Tropical Medicine, Faculty of Medicine, Kafer Elshiek University, Kafer Elshiek, Egypt
| | - Mostafa K El Awady
- Department of Microbial Biotechnology, Biotechnology Research Institute, National Research Centre, 33 EL Bohouth St. (formerly El Tahrir St.), Dokki, Giza, P.O. 12622, Egypt
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17
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Comment on "Safe use of livers from deceased donors older than 70 years in recipients with HCV cirrhosis treated with direct-action antivirals. Retrospective cohort study" (Int J Surg 2021:105981). Int J Surg 2021; 94:106096. [PMID: 34537398 DOI: 10.1016/j.ijsu.2021.106096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022]
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18
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Kumar N, Prabhu SS, Monga I, Banerjee I. Influence of IL28B gene polymorphisms on PegINF-RBV-mediated HCV clearance in HIV-HCV co-infected patients: A meta-analysis. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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19
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Maurya R, Kanakan A, Vasudevan JS, Chattopadhyay P, Pandey R. Infection outcome needs two to tango: human host and the pathogen. Brief Funct Genomics 2021; 21:90-102. [PMID: 34402498 PMCID: PMC8385967 DOI: 10.1093/bfgp/elab037] [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: 06/15/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen’s genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host–pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.
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Affiliation(s)
- Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi-110007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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20
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Chen Q, Coto-Llerena M, Suslov A, Teixeira RD, Fofana I, Nuciforo S, Hofmann M, Thimme R, Hensel N, Lohmann V, Ng CKY, Rosenberger G, Wieland S, Heim MH. Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses. Nat Commun 2021; 12:4882. [PMID: 34385466 PMCID: PMC8360984 DOI: 10.1038/s41467-021-25218-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic variants of the interferon lambda (IFNL) gene locus are strongly associated with spontaneous and IFN treatment-induced clearance of hepatitis C virus (HCV) infections. Individuals with the ancestral IFNL4-dG allele are not able to clear HCV in the acute phase and have more than a 90% probability to develop chronic hepatitis C (CHC). Paradoxically, the IFNL4-dG allele encodes a fully functional IFNλ4 protein with antiviral activity against HCV. Here we describe an effect of IFNλ4 on HCV antigen presentation. Only minor amounts of IFNλ4 are secreted, because the protein is largely retained in the endoplasmic reticulum (ER) where it induces ER stress. Stressed cells are significantly weaker activators of HCV specific CD8+ T cells than unstressed cells. This is not due to reduced MHC I surface presentation or extracellular IFNλ4 effects, since T cell responses are restored by exogenous loading of MHC with HCV antigens. Rather, IFNλ4 induced ER stress impairs HCV antigen processing and/or loading onto the MHC I complex. Our results provide a potential explanation for the IFNλ4-HCV paradox.
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Affiliation(s)
- Qian Chen
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Aleksei Suslov
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Isabel Fofana
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sandro Nuciforo
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Maike Hofmann
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Nina Hensel
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research (CIID), University of Heidelberg, Heidelberg, Germany
| | - Charlotte K Y Ng
- Department for BioMedical Research (DBMR), Oncogenomics Lab, University of Bern, Bern, Switzerland
| | | | - Stefan Wieland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus H Heim
- Department of Biomedicine, University of Basel, Basel, Switzerland. .,Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland.
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21
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McInnes G, Yee SW, Pershad Y, Altman RB. Genomewide Association Studies in Pharmacogenomics. Clin Pharmacol Ther 2021; 110:637-648. [PMID: 34185318 PMCID: PMC8376796 DOI: 10.1002/cpt.2349] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
The increasing availability of genotype data linked with information about drug-response phenotypes has enabled genomewide association studies (GWAS) that uncover genetic determinants of drug response. GWAS have discovered associations between genetic variants and both drug efficacy and adverse drug reactions. Despite these successes, the design of GWAS in pharmacogenomics (PGx) faces unique challenges. In this review, we analyze the last decade of GWAS in PGx. We review trends in publications over time, including the drugs and drug classes studied and the clinical phenotypes used. Several data sharing consortia have contributed substantially to the PGx GWAS literature. We anticipate increased focus on biobanks and highlight phenotypes that would best enable future PGx discoveries.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California, USA
| | - Yash Pershad
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Departments of Genetics, Medicine, Biomedical Data Science, Stanford, California, USA
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22
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Shen C, Ge Z, Dong C, Wang C, Shao J, Cai W, Huang P, Fan H, Li J, Zhang Y, Yue M. Genetic Variants in KIR/HLA-C Genes Are Associated With the Susceptibility to HCV Infection in a High-Risk Chinese Population. Front Immunol 2021; 12:632353. [PMID: 34220799 PMCID: PMC8253047 DOI: 10.3389/fimmu.2021.632353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Background KIR/HLA-C signaling pathway influences the innate immune response which is the first defense to hepatitis C virus (HCV) infection. The aim of this study was to determine the association between the genetic polymorphisms of KIR/HLA-C genes and the outcomes of HCV infection in a high-risk Chinese population. Methods In this case-control study, four single nucleotide polymorphisms (SNPs) of KIR/HLA-C genes (KIR2DS4/KIR2DS1/KIR2DL1 rs35440472, HLA-C rs2308557, HLA-C rs1130838, and HLA-C rs2524094) were genotyped by TaqMan assay among drug users and hemodialysis (HD) patients including 1,378 uninfected control cases, 307 subjects with spontaneous viral clearance, and 217 patients with persistent HCV infection. Bioinformatics analysis was used to functionally annotate the SNPs. Results After logistic regression analysis, the rs35440472-A and rs1130838-A alleles were found to be associated with a significantly elevated risk of HCV infection (OR = 1.562, 95% CI: 1.229–1.987, P < 0.001; OR = 2.134, 95% CI: 1.180–3.858, P = 0.012, respectively), which remained significant after Bonferroni correction (0.05/4). The combined effect of their risk alleles and risk genotypes (rs35440472-AA and rs1130838-AA) were linked to the increased risk of HCV infection in a locus-dosage manner (all Ptrend < 0.001). Based on the SNPinfo web server, rs35440472 was predicted to be a transcription factor binding site (TFBS) while rs1130838 was predicted to have a splicing (ESE or ESS) function. Conclusion KIR2DS4/KIR2DS1/KIR2DL1 rs35440472-A and HLA-C rs1130838-A variants are associated with increased susceptibility to HCV infection in a high-risk Chinese population.
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Affiliation(s)
- Chao Shen
- Department of Epidemiology and Biostatistics, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhijun Ge
- Department of Critical Care Medicine, The Affiliated Yixing Hospital of Jiangsu University, Yixing, China
| | - Chen Dong
- Department of Epidemiology and Statistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Chunhui Wang
- Institute of Epidemiology and Microbiology, Eastern Theater Command Centers for Disease Control and Prevention, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianguo Shao
- Department of Digestive Medicine, Third Affiliated Hospital of Nantong University, Nantong, China
| | - Weihua Cai
- Department of General Surgery, Third Affiliated Hospital of Nantong University, Nantong, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haozhi Fan
- Department of Information, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Infectious Diseases, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Zhang
- Institute of Epidemiology and Microbiology, Eastern Theater Command Centers for Disease Control and Prevention, Nanjing, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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23
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Roy S, Guha Roy D, Bhushan A, Bharatiya S, Chinnaswamy S. Functional genetic variants of the IFN-λ3 (IL28B) gene and transcription factor interactions on its promoter. Cytokine 2021; 142:155491. [PMID: 33725487 PMCID: PMC7611124 DOI: 10.1016/j.cyto.2021.155491] [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: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022]
Abstract
Interferon lambda 3 (IFN-λ3 or IFNL3, formerly IL28B), a type III interferon, modulates immune responses during infection/inflammation. Several human studies have reported an association of single nucleotide polymorphisms (SNP) in the IFNL3 locus with expression level of IFNL3. Previous genetic studies, in the context of hepatitis C virus infections, had predicted three regulatory SNPs: rs4803219, rs28416813 and rs4803217 that could have functional/causal roles. Subsequent studies confirmed this prediction for rs28416813 and rs4803217. A dinucleotide TA-repeat variant (rs72258881) has also been reported to be regulating the IFN-λ3 promoter. In this study, we tested all these genetic variants using a sensitive reporter assay. We show that the minor/ancestral alleles of both rs28416813 and rs4803217, together have a strong inhibitory effect on reporter gene expression. We also show an interaction between the two principal transcription factors regulating IFNL3 promoter: IRF7 and NF-kB RelA/p65. We show that IRF7 and p65 physically interact with each other. By using a transient ChIP assay, we show that presence of p65 increases the promoter occupancy of IRF7, thereby leading to synergistic activation of the IFNL3 promoter. We reason that, in contrast to p65, a unique nature of IRF7 binding to its specific DNA sequence makes it more sensitive to changes in DNA phasing. As a result, we see that IRF7, but not p65-mediated transcriptional activity is affected by the phase changes introduced by the TA-repeat polymorphism. Overall, we see that three genetic variants: rs28416813, rs4803217 and rs72258881 could have functional roles in controlling IFNL3 gene expression.
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Affiliation(s)
- Subhajit Roy
- National Institute of Biomedical Genomics, P.O.:N.S.S., Kalyani, West Bengal 741251, India
| | - Debarati Guha Roy
- National Institute of Biomedical Genomics, P.O.:N.S.S., Kalyani, West Bengal 741251, India
| | - Anand Bhushan
- National Institute of Biomedical Genomics, P.O.:N.S.S., Kalyani, West Bengal 741251, India
| | - Seema Bharatiya
- National Institute of Biomedical Genomics, P.O.:N.S.S., Kalyani, West Bengal 741251, India
| | - Sreedhar Chinnaswamy
- National Institute of Biomedical Genomics, P.O.:N.S.S., Kalyani, West Bengal 741251, India.
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Germline genetic factors influence the outcome of interferon-α therapy in polycythemia vera. Blood 2021; 137:387-391. [PMID: 32814349 DOI: 10.1182/blood.2020005792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022] Open
Abstract
Interferon-α (IFN-α)-based treatments can induce hematologic and molecular responses (HRs and MRs, respectively) in polycythemia vera (PV); however, patients do not respond equally. Germline genetic factors have been implicated in differential drug responses. We addressed the effect of common germline polymorphisms on HR and MR after treatment of PV in the PROUD-PV and CONTINUATION-PV studies in a total of 122 patients who received ropeginterferon alfa-2b. Genome-wide association studies using longitudinal data on HR and MR over a 36-month follow-up did not reveal any associations at the level of genome-wide statistical significance. Furthermore, we performed targeted association analyses at the interferon lambda 4 (IFNL4) locus, well known for its role in hepatitis C viral clearance and recently reported to influence HR during treatment of myeloproliferative neoplasms. We did not observe any association of IFNL4 polymorphisms with HR in our study cohort; however, we demonstrated a statistically significant effect of the functionally causative IFNL4 diplotype (haplotype pair, including the protein-coding variants rs368234815/rs117648444) on MR (P = 3.91 × 10-4; odds ratio, 10.80; 95% confidence interval, 2.39-69.97) as reflected in differential JAK2V617F mutational burden changes according to IFNL4 diplotype status. Stratification of patients with PV based on IFNL4 functionality may allow for optimizing patient management during IFN-α-based therapy.
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Genetic factors affect the susceptibility to bacterial infections in diabetes. Sci Rep 2021; 11:9464. [PMID: 33947878 PMCID: PMC8096814 DOI: 10.1038/s41598-021-88273-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Diabetes increases the risk of bacterial infections. We investigated whether common genetic variants associate with infection susceptibility in Finnish diabetic individuals. We performed genome-wide association studies and pathway analysis for bacterial infection frequency in Finnish adult diabetic individuals (FinnDiane Study; N = 5092, Diabetes Registry Vaasa; N = 4247) using national register data on antibiotic prescription purchases. Replication analyses were performed in a Swedish diabetic population (ANDIS; N = 9602) and in a Finnish non-diabetic population (FinnGen; N = 159,166). Genome-wide data indicated moderate but significant narrow-sense heritability for infection susceptibility (h2 = 16%, P = 0.02). Variants on chromosome 2 were associated with reduced infection susceptibility (rs62192851, P = 2.23 × 10–7). Homozygotic carriers of the rs62192851 effect allele (N = 44) had a 37% lower median annual antibiotic purchase rate, compared to homozygotic carriers of the reference allele (N = 4231): 0.38 [IQR 0.22–0.90] and 0.60 [0.30–1.20] respectively, P = 0.01). Variants rs6727834 and rs10188087, in linkage disequilibrium with rs62192851, replicated in the FinnGen-cohort (P < 0.05), but no variants replicated in the ANDIS-cohort. Pathway analysis suggested the IRAK1 mediated NF-κB activation through IKK complex recruitment-pathway to be a mediator of the phenotype. Common genetic variants on chromosome 2 may associate with reduced risk of bacterial infections in Finnish individuals with diabetes.
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Støy S, Terczynska-Dyla E, Veidal SS, Rigbolt K, Vilstrup H, Grønbaek H, Hartmann R, Sandahl TD. Interferon lambda 4 genotype and pathway in alcoholic hepatitis. Scand J Gastroenterol 2021; 56:304-311. [PMID: 33602032 DOI: 10.1080/00365521.2021.1874046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Single nucleotide polymorphisms within the interferon lambda 4 (IFNL4) gene influence liver inflammation and fibrosis in chronic liver disease. We investigated whether this is also the case during acute liver disease, alcoholic hepatitis. We, therefore, related variants within the IFNL4 gene to the clinical course of acute alcoholic hepatitis, and characterized the activation state of the IFN lambda system in these patients. METHODS In this pilot study, 58 patients with alcoholic hepatitis were genotyped for the rs368234815IFNL4 single nucleotide polymorphism (deltaG, deltaG/TT: IFN lambda 4 positive, TT/TT: IFN lambda 4 negative). The genotypes were related to mortality, infection and inflammation and expression of the IFNL receptor 1 and IFN inducible genes were measured in liver and peripheral leukocytes. RESULTS Amongst the alcoholic hepatitis patients who died, the IFN negative patients live longer after diagnosis, and also the IFN negative patients tended to have an overall short-term survival benefit compared to IFN lambda positive patients (p = .058). The IFN lambda 4 negative patients at diagnosis had fewer circulating monocytes and lower plasma soluble CD163. The patients with alcoholic hepatitis had reduced expression of the IFNL receptor 1in both liver and blood compared with healthy controls. In blood, the expression of IFN stimulated genes was lower than in healthy controls and most so in the patients, who died. CONCLUSIONS The IFN lambda 4 pathway seems involved in the acute disease processes of alcoholic hepatitis and patients without IFN lambda expression seem to have a short-term survival benefit.
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Affiliation(s)
- Sidsel Støy
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Hendrik Vilstrup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Henning Grønbaek
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Thomas D Sandahl
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
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Chihab H, Badre W, Tahiri M, Jadid FZ, Zaidane I, Elfihry R, Marchio A, Pineau P, Ezzikouri S, Benjelloun S. IFNL4 rs12979860 polymorphism influences HBV DNA viral loads but not the outcome of HBV infection in Moroccan patients. Microbes Infect 2021; 23:104802. [PMID: 33607264 DOI: 10.1016/j.micinf.2021.104802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/20/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The interferon (IFN) is known to bridge innate and adaptive immune responses, and to play a critical role particularly against hepatitis B virus (HBV) infection. Defects in IFN signals may result, therefore, in attenuated responses against HBV. Accordingly, polymorphisms in genes coding for immune response effectors may affect the clinical outcome of HBV infection. We analyzed the putative association between IFNL4 rs12979860 polymorphism and the outcome of HBV infection in Moroccan patients. METHODS In this study, 237 chronic HBV (CHB) patients and 129 spontaneously resolved HBV (SRB) individuals were enrolled and genotyped using a predesigned Taqman allelic discrimination assay. RESULTS Our data show a significant increase of HBV DNA loads in patients with IFNL4 rs12979860 CC genotype compared to patients with CT and TT genotypes (p = 0.0008). However, there was no consistent association between IFNL4 rs12979860 polymorphism and the outcome of HBV infection. CONCLUSIONS Although IFNL4 rs12979860 polymorphism seems to modulate circulating HBV DNA levels, it is disconnected from chronic disease progression. This observation suggests that the role of rs12979860 in liver disease is restricted to viral control and inactive in the deleterious immune pathology that affects liver tissue. Taken together, our data suggest that rs12979860 CC genotypes could be useful as a predictor of success or failure of IFN-based therapy in chronic HBV-infected patients.
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Affiliation(s)
- Hajar Chihab
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Wafaa Badre
- Faculté de Médecine de Casablanca, CHU Ibn Rochd, Casablanca, Morocco
| | - Mohamed Tahiri
- Faculté de Médecine de Casablanca, CHU Ibn Rochd, Casablanca, Morocco
| | - Fatima-Zahra Jadid
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Zaidane
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Raouia Elfihry
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Agnès Marchio
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Pascal Pineau
- Unité "Organisation Nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, Paris, France
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
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Schwerk J, Negash A, Savan R, Gale M. Innate Immunity in Hepatitis C Virus Infection. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a036988. [PMID: 32341066 PMCID: PMC7849348 DOI: 10.1101/cshperspect.a036988] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Activation and viral control of the innate immune response are hallmarks of hepatitis C virus (HCV) infection and are major determinants of spontaneous clearance or progression to chronic infection and liver disease. In this review, we provide a contemporary overview of how HCV is sensed by the host cell to trigger innate immune activation and the mechanisms deployed by the virus to evade this response. Type I and III interferons (IFNs) are crucial mediators of antiviral innate immunity against HCV, and we specifically highlight the importance of IFN-λ host genetics for the outcome of HCV infection. Last, we focus on the proinflammatory responses elicited by HCV infection and describe our current understanding of how interleukin (IL)-1β signaling and cross talk between the IL-1β and IFN signaling pathways lead to sustained inflammation and increased risk of liver pathology.
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de Bitencorte JT, Rech TF, Lunge VR, dos Santos DC, Álvares-da-Silva MR, Simon D. Association of interferon lambda-4 rs12979860 polymorphism with hepatocellular carcinoma in patients with chronic hepatitis C infection. World J Hepatol 2021; 13:109-119. [PMID: 33584990 PMCID: PMC7856861 DOI: 10.4254/wjh.v13.i1.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a public health concern worldwide. Several factors, including genetic polymorphisms, may be evolved in the progression of HCV infection to liver diseases. Interferon lambdas (IFNLs) modulate the immune response during viral infections. IFNLs induce antiviral activity, interfering in the viral replication by promoting the expression of several genes that regulate immunological functions. The interferon lambda-4 (IFNL4) rs12979860 polymorphism, which is characterized by a C to T transition in intron 1, is associated with spontaneous and treatment-induced clearance of HCV infection and may play a role in the development of HCV-associated liver diseases, including hepatocellular carcinoma (HCC).
AIM To investigate the association of IFNL4 rs12979860 polymorphism with fibrosis, cirrhosis, and HCC in patients with chronic HCV infection.
METHODS This study was comprised of 305 chronic HCV-infected patients (53 fibrosis, 154 cirrhosis, and 98 HCC cases). The control group was comprised of 260 HCV-negative healthy individuals. The IFNL4 rs12979860 polymorphism was genotyped using the TaqMan assay. Fibrosis was diagnosed based on liver biopsy findings, while cirrhosis was diagnosed through clinical, laboratory, anatomopathological, and/or imaging data. HCC was diagnosed through imaging tests, tumor, and/or anatomopathological markers.
RESULTS The T allele was observed in the three groups of patients (fibrosis, cirrhosis, and HCC) at a significantly higher frequency when compared with the control group (P = 0.047, P < 0.001, and P = 0.01, respectively). Also, genotype frequencies presented significant differences between the control group and cirrhosis patients (P < 0.001) as well as HCC patients (P = 0.002). The risk analysis was performed using the codominant and dominant T allele models. In the codominant model, it was observed that the CT genotype showed an increased risk of developing cirrhosis in comparison with the CC genotype [odds ratio (OR) = 2.53; 95% confidence interval (CI): 1.55-4.15; P < 0.001] as well as with HCC (OR = 2.54; 95%CI: 1.44-4.56; P = 0.001). A similar result was observed in the comparison of the TT vs CC genotype between the control group and cirrhosis group (OR = 2.88; 95%CI: 1.44-5.77; P = 0.001) but not for HCC patients. In the dominant T allele model, the CT + TT genotypes were associated with an increased risk for progression to cirrhosis (OR = 2.60; 95%CI: 1.63-4.19; P < 0.001) and HCC (OR = 2.45; 95%CI: 1.42-4.31; P = 0.001).
CONCLUSION These findings suggest that the T allele of IFNL4 rs12979860 polymorphism is associated with the development of cirrhosis and HCC in chronic HCV-infected patients.
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Affiliation(s)
- Jóice Teixeira de Bitencorte
- PPG Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas 92425-900, Rio Grande do Sul, Brazil
| | - Tássia Flores Rech
- PPG Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas 92425-900, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- PPG Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas 92425-900, Rio Grande do Sul, Brazil
| | - Deivid Cruz dos Santos
- Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Mário Reis Álvares-da-Silva
- Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Daniel Simon
- PPG Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas 92425-900, Rio Grande do Sul, Brazil
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30
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Grzegorzewska AE, Mostowska A, Świderska MK, Marcinkowski W, Stolarek I, Figlerowicz M, Jagodziński PP. Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. BMC Infect Dis 2021; 21:102. [PMID: 33482747 PMCID: PMC7821534 DOI: 10.1186/s12879-021-05777-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In non-uremic subjects, IFNL4 rs368234815 predicts HCV clearance. We investigated whether rs368234815 is associated with spontaneous HCV clearance in haemodialysis patients and whether it is a stronger predictor of HCV resolution than the IFNL polymorphisms already associated with HCV clearance in dialysis subjects. We also evaluated an association of rs368234815 with patients` survival and alterations in transcription factor binding sites (TFBS) caused by IFNL polymorphisms. METHODS Among 161 haemodialysis patients with positive anti-HCV antibodies, 68 (42.2%) spontaneously resolved HCV infection, whereas 93 remained HCV RNA positive. Patients were tested for near IFNL3 rs12980275, IFNL3 rs4803217, IFNL4 rs12979860, IFNL4 rs368234815, and near IFNL4 rs8099917. IFNL4 rs368234815 polymorphism (TT/TT, ΔG/TT, ΔG/ΔG) was genotyped by restriction fragment length polymorphism analysis; other IFNL polymorphisms - by high resolution melting curve analysis. We used the Kaplan-Meier method with the log-rank test for survival analysis. In silico analysis included the use of ENCODE TFBS ChIP-seq data, HOCOMOCO, JASPAR CORE, and CIS-BP databases, and FIMO software. RESULTS The probability (OR, 95%CI, P) of spontaneous HCV clearance for rs368234815 TT/TT patients was higher than for the ΔG allele carriers (2.63, 1.38-5.04, 0.003). This probability for other major homozygotes varied between 2.80, 1.45-5.43, 0.002 for rs12980275 and 2.44, 1.27-4.69, 0.007 for rs12979860. In the additive model, rs368234815 TT/TT was the strongest predictor of HCV clearance (6.38, 1.69-24.2, 0.003). Survival analysis suggested an association of the ΔG allele with mortality due to neoplasms (log-rank P = 0.005). The rs368234815 ∆G allele caused TFBS removal for PLAGL1. CONCLUSIONS In haemodialysis patients, the association of rs368234815 with the spontaneous HCV clearance is better than that documented for other IFNL3/IFNL4 polymorphisms only in the additive mode of inheritance. However, identifying the homozygosity in the variant ∆G allele of rs368234815 means a more potent prediction of persistent HCV infection in haemodialysis subjects that we observe in the case of the variant homozygosity of other tested IFNL3/IFNL4 polymorphisms. Removal of PLAGL1 TFBS in subjects harbouring the rs368234815 ∆G allele may contribute to cancer susceptibility. The association of rs368234815 with cancer-related mortality needs further studies in HCV-exposed subjects.
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Affiliation(s)
- Alicja E. Grzegorzewska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznań, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781 Poznań, Poland
| | - Monika K. Świderska
- Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznań, Poland
| | | | - Ireneusz Stolarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Paweł P. Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6, 60-781 Poznań, Poland
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El-Garawani I, Hassab El-Nabi S, Gadallah M, Abdelsameea E. Association between IFN-λ 3 Gene Polymorphisms and Outcome of Treatment with Direct Acting Antivirals in Chronic HCV-Infected Egyptian Patients. Immunol Invest 2021; 50:12-22. [PMID: 32024403 DOI: 10.1080/08820139.2020.1722158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background: Single nucleotide polymorphisms (SNPs) of the interferon lambda 3 (IFN-λ 3) gene are associated with viral clearance and treatment response in chronic hepatitis C virus (HCV) infection. Aim: to assess whether specific IFN-λ 3 gene SNP, known as rs12979860 (C > T), could predict the outcome of treatment with direct acting antivirals (DAAs) among Egyptian patients with chronic HCV genotype 4 infection. Methods: Tetra-primer (ARMS-PCR) and PCR-RFLP methods were used for SNP genotyping in 100 chronic HCV-infected patients and 50 healthy subjects as control group. Results: The CC (wild type) genotype of rs12979860 was identified in 20 patients, 50% of them achieved sustained virological response (SVR). SNP genotype TT was found in 17 patients and only 2 of them (11.76%) were responders. The frequency of CT genotypes was significantly higher in responders than in non-responders (p= .021). In contrast, the frequency of TT genotypes was significantly higher in non-responders (42.85%, p< .001). On univariate and multivariate logistic regression analyses of the significant predictors of SVR, there were six predictive factors (Age, diabetes mellitus, AST, albumin, type of therapy and IFN-λ 3 genotype). Conclusion: The TT genotype and T allele were significantly associated with failure to achieve SVR. However, CT genotype of IFN-λ 3 (rs12979860) may be considered as a predictor for SVR in patients who received DAAs.
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Affiliation(s)
- Islam El-Garawani
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Sobhy Hassab El-Nabi
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Marwa Gadallah
- Zoology Department, Faculty of Science, Menoufia University , Shibin Al Kawm, Egypt
| | - Eman Abdelsameea
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University , Shibin Al Kawm, Egypt
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Coto-Llerena M, Lepore M, Spagnuolo J, Di Blasi D, Calabrese D, Suslov A, Bantug G, Duong FH, Terracciano LM, De Libero G, Heim MH. Interferon lambda 4 can directly activate human CD19 + B cells and CD8 + T cells. Life Sci Alliance 2021; 4:e201900612. [PMID: 33158978 PMCID: PMC7668538 DOI: 10.26508/lsa.201900612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Compared with the ubiquitous expression of type I (IFNα and IFNβ) interferon receptors, type III (IFNλ) interferon receptors are mainly expressed in epithelial cells of mucosal barriers of the of the intestine and respiratory tract. Consequently, IFNλs are important for innate pathogen defense in the lung and intestine. IFNλs also determine the outcome of hepatitis C virus (HCV) infections, with IFNλ4 inhibiting spontaneous clearance of HCV. Because viral clearance is dependent on T cells, we explored if IFNλs can directly bind to and regulate human T cells. We found that human B cells and CD8+ T cells express the IFNλ receptor and respond to IFNλs, including IFNλ4. IFNλs were not inhibitors but weak stimulators of B- and T-cell responses. Furthermore, IFNλ4 showed neither synergistic nor antagonistic effects in co-stimulatory experiments with IFNλ1 or IFNα. Multidimensional flow cytometry of cells from liver biopsies of hepatitis patients from IFNλ4-producers showed accumulation of activated CD8+ T cells with a central memory-like phenotype. In contrast, CD8+ T cells with a senescent/exhausted phenotype were more abundant in IFNλ4-non-producers. It remains to be elucidated how IFNλ4 promotes CD8 T-cell responses and inhibits the host immunity to HCV infections.
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Affiliation(s)
- Mairene Coto-Llerena
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
| | - Marco Lepore
- Department of Biomedicine, Experimental Immunology, University Hospital and University of Basel, Basel, Switzerland
| | - Julian Spagnuolo
- Department of Biomedicine, Experimental Immunology, University Hospital and University of Basel, Basel, Switzerland
| | - Daniela Di Blasi
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
- Department of Biomedicine, Experimental Immunology, University Hospital and University of Basel, Basel, Switzerland
| | - Diego Calabrese
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
| | - Aleksei Suslov
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
| | - Glenn Bantug
- Department of Biomedicine, Immunobiology, University Hospital and University of Basel, Basel, Switzerland
| | - Francois Ht Duong
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
| | - Luigi M Terracciano
- Molecular Pathology Division, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Gennaro De Libero
- Department of Biomedicine, Experimental Immunology, University Hospital and University of Basel, Basel, Switzerland
| | - Markus H Heim
- Department of Biomedicine, Hepatology, University Hospital and University of Basel, Basel, Switzerland
- Division of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
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Vergara C, Duggal P, Thio CL, Valencia A, O'Brien TR, Latanich R, Timp W, Johnson EO, Kral AH, Mangia A, Goedert JJ, Piazzola V, Mehta SH, Kirk GD, Peters MG, Donfield SM, Edlin BR, Busch MP, Alexander G, Murphy EL, Kim AY, Lauer GM, Chung RT, Cramp ME, Cox AL, Khakoo SI, Rosen HR, Alric L, Wheelan SJ, Wojcik GL, Thomas DL, Taub MA. Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection. Genes Immun 2020; 21:348-359. [PMID: 33116245 PMCID: PMC7657970 DOI: 10.1038/s41435-020-00115-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Clearance of acute infection with hepatitis C virus (HCV) is associated with the chr19q13.13 region containing the rs368234815 (TT/ΔG) polymorphism. We fine-mapped this region to detect possible causal variants that may contribute to HCV clearance. First, we performed sequencing of IFNL1-IFNL4 region in 64 individuals sampled according to rs368234815 genotype: TT/clearance (N = 16) and ΔG/persistent (N = 15) (genotype-outcome concordant) or TT/persistent (N = 19) and ΔG/clearance (N = 14) (discordant). 25 SNPs had a difference in counts of alternative allele >5 between clearance and persistence individuals. Then, we evaluated those markers in an association analysis of HCV clearance conditioning on rs368234815 in two groups of European (692 clearance/1 025 persistence) and African ancestry (320 clearance/1 515 persistence) individuals. 10/25 variants were associated (P < 0.05) in the conditioned analysis leaded by rs4803221 (P value = 4.9 × 10-04) and rs8099917 (P value = 5.5 × 10-04). In the European ancestry group, individuals with the haplotype rs368234815ΔG/rs4803221C were 1.7× more likely to clear than those with the rs368234815ΔG/rs4803221G haplotype (P value = 3.6 × 10-05). For another nearby SNP, the haplotype of rs368234815ΔG/rs8099917T was associated with HCV clearance compared to rs368234815ΔG/rs8099917G (OR: 1.6, P value = 1.8 × 10-04). We identified four possible causal variants: rs368234815, rs12982533, rs10612351 and rs4803221. Our results suggest a main signal of association represented by rs368234815, with contributions from rs4803221, and/or nearby SNPs including rs8099917.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Latanich
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | | | - Alex H Kral
- RTI International, Research Triangle Park, NC, USA
| | - Alessandra Mangia
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valeria Piazzola
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | | | - Brian R Edlin
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael P Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA, USA
| | - Graeme Alexander
- University College London Institute for Liver and Digestive Health, The Royal Free Hospital, London, UK
| | - Edward L Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, UK
| | | | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Rangueil, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, Toulouse, France
| | - Sarah J Wheelan
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
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Ebid AHIM, Ahmed OA, Agwa SH, Abdel-Motaleb SM, Hagag RS. Impact of IL28B gene polymorphism on efficacy and safety of direct acting antivirals in hepatitis C Egyptian patients. Int J Clin Pharm 2020; 42:1207-1216. [PMID: 32712884 DOI: 10.1007/s11096-020-01085-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
Background Hepatitis C virus infection is one of the major causes of liver cirrhosis and hepatocellular carcinoma worldwide. IL28B gene polymorphism has a direct relation to the response of interferon-based regimens. However, the effect of IL28B gene polymorphism on efficacy of the new direct acting antivirals used in treatment of chronic hepatitis C Egyptian patients hasn't been studied yet. Objective This study aimed to investigate the frequency of IL28B genotypes and impact of its polymorphism on the efficacy and safety of two direct acting antiviral regimens. Setting Patients were recruited form faculty of Medicine Ain shams research institute, Cairo, Egypt. Methods Easy to treat chronic hepatitis C Egyptian patients were included in this prospective study. Patients were randomized into two groups, group 1 received sofosbuvir plus daclatasvir and group 2 received paritaprevir, ombitasvir and ritonavir plus ribavirin. Both treatment regimens were given for 3 months. Laboratory evaluation and IL28B rs 12979860 genotyping were performed at baseline. Follow ups were performed monthly. Fibrosis was assessed at baseline and after treatment. Main outcome measures The frequency of IL28B genotypes and their correlation with safety and efficacy of direct acting antiviral regimens. Results CT genotype was present in 52.42% of patients while CC and TT genotypes were present in 28.16% and 19.42% of patients, respectively. IL28B genotypes weren't correlated to sustained virologic response in both treatment groups. Baseline fibroscan scores didn't show any significant relations with IL28B genotypes. Aspartate aminotransferase/alanine aminotransferase ratio increased significantly at the end of treatment in group1. CC genotype had shown higher ratio values at the end of treatment in Group 2. Conclusion CT genotype is the predominant genotype in easy to treat HCV Egyptian patients. IL28B genotypes hasn't any predictive value on the efficacy or the safety of direct acting antiviral regimens.
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Affiliation(s)
| | - Ossama Ashraf Ahmed
- Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sara Hassan Agwa
- Department of Clinical and Chemical Pathology at MASRI, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Radwa Samir Hagag
- Department of Pharmacy Practice, Faculty of Pharmacy, Egyptian Russian University, Badr City, Egypt.
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da Silva Cezar RD, da Silva Castanha PM, Matos Freire N, Mola C, Feliciano do Carmo R, Tenório Cordeiro M, Baptista P, Silva Vasconcelos LR, Moura P, da Silva Teixeira VG. Association between interferon lambda 3 rs12979860 polymorphism and clinical outcome in dengue virus-infected children. Int J Immunogenet 2020; 47:351-358. [PMID: 32065450 DOI: 10.1111/iji.12477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 12/26/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023]
Abstract
Single nucleotide polymorphisms (SNPs) in immune-related genes have been shown to play a role in driving the development of the severe phenotypes of dengue virus (DENV) infection. We assessed the association between IFNL3 gene SNP (rs12979860) and dengue clinical outcomes in children. Patients with dengue-related symptoms (aged 1-15 years) admitted at a public hospital in Northeast Brazil were invited to participate. The association between rs12979860 polymorphism and dengue classification and clinical signs and symptoms were analysed. A total of 206 DENV-infected children were included: 53.4% of the infections were classified as severe dengue. The T allele carriers had higher risk of developing severe dengue when compared to CC genotype carriers (OR: 1.81; 95% CI: 0.98-3.32 p = .054). The T allele carriers also showed longer fever episodes when compared to patients with the CC genotype (OR: 1.90; 95%CI: 1.07-3.38; p = .027). On the other hand, the ones carrying the CT/TT genotype had 70% lower chance of developing thrombocytopenia when compared to those with the CC genotype (OR: 0.30; 95%CI: 0.08-0.88; p = .042). Our findings demonstrated that the T allele carriers of the IFNL3 gene had higher risk of developing severe dengue, suggesting a link between IFN-λ expression and DENV immunopathogenesis.
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Affiliation(s)
| | | | | | - Carla Mola
- Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Brasil
| | | | | | - Paulo Baptista
- Faculdade de Ciências Médicas, Universidade de Pernambuco, Recife, Brasil
| | - Luydson Richardson Silva Vasconcelos
- Faculdade de Ciências Médicas, Universidade de Pernambuco, Recife, Brasil
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brasil
- Instituto do Fígado, Recife, Brasil
| | - Patrícia Moura
- Instituto de Ciências Biológicas, Faculdade de Ciências Médicas, Recife, Brasil
- Campus Arcoverde, Universidade de Pernambuco, Recife, Brasil
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Deshpande P, Bundell C, McKinnon E, Hellard M, Ffrench R, Wilkinson AL, Drummer H, Gaudieri S, Lucas M. Frequent occurrence of low-level positive autoantibodies in chronic hepatitis C. Pathology 2020; 52:576-583. [PMID: 32580891 DOI: 10.1016/j.pathol.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 04/17/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Evidence of autoimmune disease associated with hepatitis C virus (HCV)-infection has important clinical implications. A systematic profile of these autoantibodies in relevant clinical cohorts relative to healthy controls is needed to better inform current standard of care for chronic hepatitis C. Samples from an Australian cohort of chronic HCV-infected subjects (n=127) were tested for the presence of 19 diagnostic autoantibodies and compared with data available from a control cohort representing a general Caucasian population (n=198). Chronic HCV-infected individuals had a greater number of autoantibodies than controls (p<0.0001). Anti-nuclear antibodies (ANA) followed by anti-smooth muscle antibodies (SMA) were the most frequently detected autoantibodies within the HCV cohort and significantly more than in the control cohort (p<0.0001 and p=0.006, respectively). However, for most autoantibody assays the 95th percentile approximated the reference value for positivity. None of the autoantibodies were significantly associated with age or sex for the HCV cohort, except SMA positivity that was significantly higher in chronic HCV-infected male subjects (p<0.0001). Autoantibodies found in chronic HCV-infected subjects were commonly low positive and not disease-specific. Accordingly, general screening for autoimmunity in HCV-infected subjects should not be performed unless there is high clinical suspicion of an underlying autoimmune disease.
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Affiliation(s)
- Pooja Deshpande
- School of Human Sciences, University of Western Australia, WA, Australia
| | - Christine Bundell
- School of Biomedical Sciences, University of Western Australia, WA, Australia
| | - Elizabeth McKinnon
- Institute for Immunology and Infectious Diseases, Murdoch University, WA, Australia
| | - Margaret Hellard
- Disease Elimination Program, Burnet Institute, Vic, Australia; Department of Infectious Diseases, The Alfred Hospital, Vic, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Vic, Australia; Centre for Research Excellence in Injecting Drug Use, Burnet Institute, Vic, Australia
| | - Rosemary Ffrench
- Centre for Biomedicine, Biomedical Research, Vic, Australia; Department of Immunology, Monash University, Vic, Australia
| | - Anna L Wilkinson
- Disease Elimination Program, Burnet Institute, Vic, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Vic, Australia
| | - Heidi Drummer
- Centre for Biomedicine, Biomedical Research, Vic, Australia; Department of Immunology, Monash University, Vic, Australia; Department of Microbiology, Monash University, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Vic, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, WA, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, WA, Australia; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Tennessee, USA.
| | - Michaela Lucas
- School of Biomedical Sciences, University of Western Australia, WA, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, WA, Australia; Department of Clinical Immunology, PathWest, Laboratory Medicine, Queen Elizabeth II Medical Centre, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, WA, Australia
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37
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HCV genotypes and their determinative role in hepatitis C treatment. Virusdisease 2020; 31:235-240. [PMID: 32904762 DOI: 10.1007/s13337-020-00592-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 04/24/2020] [Indexed: 02/05/2023] Open
Abstract
Nowadays, exposure to infectious diseases caused by pathogenic viruses has become one of the major human concerns in health fields. In the meantime, hepatitis viruses are associated with health problems, especially in liver tissue. So far, several types of these viruses have been known including: HAV, HBV, HCV, HDV, HEV, and HGV. Nevertheless, it seems that hepatitis C is the major viral infection among all of the hepatitis infections. The cirrhosis and hepatocellular carcinoma are known as the most important pathological complications of this virus, from which seven genotypes have been identified. However, among these genotypes, the incidence rate of genotypes 1 and 3 is more than others. In this review, we have investigated the relationship between all HCV genotypes and therapeutic responses against them. Regarding heterogeneity between hepatitis C genotypes, it is not possible to access an effective vaccine against this virus, and treatment is the only applicable strategy. Response to treatment is different among genotypes, and it has resulted that each genotype has a specific therapeutic regimen of itself. Therefore, it seems that determination of hepatitis C genotype, as a key tool, is essential in controlling therapeutic regimen, improving local control programs and eventually producing an effective vaccine.
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38
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Youssef AR, Hamam SS, Elkholy RM. Single nucleotide polymorphisms rs12979860 and rs8099917 in IL-28B and spontaneous clearance of hepatitis C genotype 4. Br J Biomed Sci 2020; 77:91-93. [PMID: 31642723 DOI: 10.1080/09674845.2019.1683310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Affiliation(s)
- A R Youssef
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - S S Hamam
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Menoufia University, Shibin el Kom, Egypt
| | - R M Elkholy
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Shibin el Kom, Egypt
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Abstract
Social network characteristics of people who inject drugs (PWID) have previously been flagged as potential risk factors for HCV transmission such as increased injection frequency. To understand the role of the injecting network on injection frequency, we investigated how changes in an injecting network over time can modulate injecting risk behaviour. PWID were sourced from the Networks 2 Study, a longitudinal cohort study of PWID recruited from illicit drug street markets across Melbourne, Australia. Network-related correlates of injection frequency and the change in frequency over time were analysed using adjusted Cox Proportional Hazards and Generalised Estimating Equations modelling. Two-hundred and eighteen PWID followed up for a mean (s.d.) of 2.8 (1.7) years were included in the analysis. A greater number of injecting partners, network closeness centrality and eigenvector centrality over time were associated with an increased rate of infection frequency. Every additional injection drug partner was associated with an increase in monthly injection frequency. Similarly, increased network connectivity and centrality over time was also associated with an increase in injection frequency. This study observed that baseline network measures of connectivity and centrality may be associated with changes in injection frequency and, by extension, may predict subsequent HCV transmission risk. Longitudinal changes in network position were observed to correlate with changes in injection frequency, with PWID who migrate from the densely-connected network centre out to the less-connected periphery were associated with a decreased rate of injection frequency.
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40
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Fenizia C, Saulle I, Clerici M, Biasin M. Genetic and epigenetic regulation of natural resistance to HIV-1 infection: new approaches to unveil the HESN secret. Expert Rev Clin Immunol 2020; 16:429-445. [PMID: 32085689 DOI: 10.1080/1744666x.2020.1732820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Since the identification of HIV, several studies reported the unusual case of small groups of subjects showing natural resistance to HIV infection. These subjects are referred to as HIV-1-exposed seronegative (HESN) individuals and include people located in different areas, with diverse ethnic backgrounds and routes of exposure. The mechanism/s responsible for protection from infection in HESN individuals are basically indefinite and most likely are multifactorial.Areas covered: Host factors, including genetic background as well as natural and acquired immunity, have all been associated with this phenomenon. Recently, epigenetic factors have been investigated as possible determinants of reduced susceptibility to HIV infection. With the advent of the OMICS era, the availability of techniques such as GWAS, RNAseq, and exome-sequencing in both bulk cell populations and single cells will likely lead to great strides in the understanding of the HESN mystery.Expert opinion: The employment of increasingly sophisticated techniques is allowing the gathering of enormous amounts of data. The integration of such information will provide important hints that could lead to the identification of viral and host correlates of protection against HIV infection, allowing the development of more effective preventative and therapeutic regimens.
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Affiliation(s)
- Claudio Fenizia
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
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41
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Human genetics of HCV infection phenotypes in the era of direct-acting antivirals. Hum Genet 2020; 139:855-863. [PMID: 32100095 DOI: 10.1007/s00439-020-02136-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
The recent introduction of direct-acting antivirals (DAAs) has revolutionized hepatitis C virus (HCV) therapy by improving virus eradication rates to over 90% in most patient groups. However, the impact of DAAs on global disease burden is currently limited, and a large number of chronically infected individuals remain at risk of developing liver complications, such as liver cirrhosis and hepatocellular carcinoma (HCC). The identification of patients at risk of liver complications and a greater understanding of the biological mechanisms involved in HCV disease progression might improve disease control. Recent genome-wide association and exome sequencing studies have identified several host genetic variants influencing the progression of liver fibrosis and the development of HCC associated with HCV infection and are reviewed here. Interestingly, some of the genetic variants associated with those HCV-associated liver complications were also associated with the clinical course of non-viral chronic hepatitis. Future challenges include the incorporation of this genetic information into clinical risk models for personalized disease management and the study of emerging phenotypes such as liver fibrosis regression and HCC development after HCV eradication.
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42
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Fang MZ, Jackson SS, O'Brien TR. IFNL4: Notable variants and associated phenotypes . Gene 2019; 730:144289. [PMID: 31846709 DOI: 10.1016/j.gene.2019.144289] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
Interferon lambda proteins activate the JAK-STAT signalling pathway, resulting in upregulation of genes with antiviral effects. The interferon lambda family was initially thought to be redundant to the interferon alpha family, which signals through the same pathway, except for the more limited expression of the IFNLR1 receptor. However, recent studies show that interferon lambdas uniquely protect tissue barriers against a wide range of important viral infections. The interferon lambda 4 gene (IFNL4) was discovered in 2013. The IFNL4 protein is determined by the IFNL4-ΔG/TT (rs368234815) variant. The ancestral IFNL4-ΔG allele generates IFNL4, whereas IFNL4-TT causes pre-mature termination of the protein. Surprisingly, although interferons are generally antiviral proteins, the genotypes that generate the IFNL4 protein are strongly linked to impaired clearance of hepatitis C virus (HCV). IFNL4 genotype has also been linked to variation within the HCV genome, as well as risk of hepatic fibrosis, certain cancers and some infectious diseases. There has been very strong evolutionary selection against the ancestral IFNL4-ΔG allele, which is the major form in African populations, but the minor allele in Europeans and Asians. The reason for this selection and the biological mechanisms underlying observed phenotypic associations remain to be explained.
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Affiliation(s)
- Michelle Z Fang
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA
| | - Sarah S Jackson
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA
| | - Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Dr, 6E108, MSC 9767, Bethesda, MD 20892, USA.
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43
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Hou W, Qiao K, Huo Z, Du Y, Wang C, Syn WK. Association of IFNL3 rs12979860 polymorphism with HCV-related hepatocellular carcinoma susceptibility in a Chinese population. Clin Exp Gastroenterol 2019; 12:433-439. [PMID: 31807049 PMCID: PMC6842746 DOI: 10.2147/ceg.s206194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background The association between interferon lambda-3 (IFNL3,also known as interleukin 28B, IL28B) rs12979860 polymorphism and the development of hepatocellular carcinoma (HCC) has been investigated in recent studies with inconclusive and inconsistent results. IFNL3 rs12979860 polymorphism has been shown a marked differential distribution with regional and ethnic variation. Whether this single nucleotide polymorphism influences susceptibility to hepatitis C virus (HCV)-related HCC remains elusive. Methods In this case–control study, a total of 157 Chinese Han patients with chronic HCV infection were enrolled, including 62 HCV-related HCC patients and 95 chronic hepatitis C (CHC) patients without HCC, and the genetic polymorphism of IFNL3 rs12979860 was genotyped via a DNA microarray-based assay. The logistic regression analysis was employed to determine the correlation between the genetic polymorphism and risk of HCV-related HCC. Results A higher proportion of CT/TT genotype and T allele was observed in HCC patients compared to the CHC group. Under the genetic model of allele frequency, the T allele was associated with elevated risk of HCV-related HCC in the Chinese population compared to C allele after an adjustment for age, gender, body mass index, HCV infection duration, and HCV genotypes (P=0.046). In the subgroup analysis stratified by HCV genotype, subjects with CHC genotype 1b infection carrying rs12979860 T allele and CT+TT genotype had higher susceptibility to HCC than those with C allele and CC genotype (P=0.020, P=0.037, respectively). Conclusion IFNL3 rs12979860 polymorphism with T allele could be a factor that increases the risk of HCV-related HCC in the Chinese population, especially those subjects with CHC genotype 1b infection.
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Affiliation(s)
- Wei Hou
- Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, People's Republic of China.,Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Kunyan Qiao
- Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, People's Republic of China
| | - Zhixiao Huo
- Tianjin Second People's Hospital and Tianjin Institute of Hepatology, Tianjin, People's Republic of China
| | - Yanan Du
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, People's Republic of China
| | - Cindy Wang
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Wing-Kin Syn
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.,Section of Gastroenterology, Ralph H Johnson Veterans Affairs Medical Center, Charleston, SC, USA
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44
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Grzegorzewska AE. Genetic Polymorphisms within Interferon-λ Region and Interferon-λ3 in the Human Pathophysiology: Their Contribution to Outcome, Treatment, and Prevention of Infections with Hepatotropic Viruses. Curr Med Chem 2019; 26:4832-4851. [DOI: 10.2174/0929867325666180719121142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 03/21/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022]
Abstract
:
Genetic polymorphisms within the interferon λ (IFN-λ) chromosomal region,
mainly rs12979860 of IFN-λ4 gene (IFNL4), are known as associated with spontaneous hepatitis
C virus (HCV) resolution and sustained viral response to therapy with pegylated interferon-
α and ribavirin. Strong linkage disequilibrium of IFNL4 rs12979860 with IFNL4
rs368234815, which is casually associated with HCV spontaneous and therapeutical eradication,
at least partially explains favorable HCV outcomes attributed to major homozygosity in
rs12979860. Effects of IFN-based antiviral treatment are associated with pretreatment expression
of the IFN-λ1 receptor, expression of hepatic IFN-stimulated genes, production of IFN-
λ4, and preactivation of the JAK-STAT signaling. Nowadays direct-acting antivirals (DAAs)
became a potent tool in the treatment of hepatitis C, but IFN-λs are still under investigation as
potential antivirals and might be an option in HCV infection (DAA resistance, recurrent viremia,
adverse effects).
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Patients with altered immunocompetence are especially prone to infections. In uremic subjects,
polymorphisms within the IFN-λ chromosomal region associate with spontaneous HCV
clearance, similarly like in the non-uremic population. Circulating IFN-λ3 shows a positive
correlation with plasma titers of antibodies to surface antigen of hepatitis B virus (anti-HBs),
which are crucial for protection against hepatitis B virus. More efficient anti-HBs production
in the presence of higher IFN-λ3 levels might occur due to IFN-λ3-induced regulation of indoleamine
2,3-dioxygenase (IDO) expression. IFN-stimulated response element is a part of
IDO gene promoter. It is worth further investigation whether IDO gene, circulating IDO, genetic
polymorphisms within the IFN-λ region, and circulating IFN-λ3 act in concordance in
immunological response to hepatotropic viruses.
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Affiliation(s)
- Alicja E. Grzegorzewska
- Chair and Department of Nephrology, Transplantology and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
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45
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Møhlenberg M, Gad HH, Hartmann R. The Influence of the rs30461 Single Nucleotide Polymorphism on IFN-λ1 Activity and Secretion. J Interferon Cytokine Res 2019; 39:661-667. [PMID: 31120365 DOI: 10.1089/jir.2019.0051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic variation within the IFNL loci is associated with several diseases and evidence indicates that the IFNL genes have been subjects of strong selection during recent human evolution. The nonsynonymous rs30461 single nucleotide polymorphism (SNP), generating interferon (IFN)-λ1 D188N, shows a strong signature of positive selection in European and Asian populations. Nevertheless, genetic association studies have failed to show any coupling of rs30461 to diseases such as psoriasis and periodontitis. Based on these observations, we purified IFN-λ1 N188 and IFN-λ1 D188 to compare the biological activity of these 2 IFN-λ1 versions. Furthermore, we evaluated the secretion of the 2 different IFN-λ1 versions. We were unable to observe any differences between IFN-λ1 N188 and IFN-λ1 D188 based on biological activity or secretion that could account for the positive selection.
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Affiliation(s)
- Michelle Møhlenberg
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Hans Henrik Gad
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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46
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Moghimi M, Tavakoli F, Doosti M, Ahmadi-Vasmehjani A, Akhondi-Meybodi M. Correlation between interleukin-28 gene polymorphism with interleukin-28 cytokine levels and viral genotypes among HCV patients in Yazd, Iran. BMC Res Notes 2019; 12:626. [PMID: 31551080 PMCID: PMC6760063 DOI: 10.1186/s13104-019-4651-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Recent studies using genome-wide association studies (GWAS) have shown the strong association between polymorphisms near the interleukin-28B (IL-28B) gene and spontaneous clearance of hepatitis C virus (HCV). The present study was designed to evaluate the association of interleukin-28 gene polymorphism with interleukin-28 cytokine levels in different viral genotypes among HCV patients in Yazd, Iran. RESULT The most prevalent genotype in chronic cases was genotype 3a, and the lowest one was 2/3a. There were statistically significant differences in genotype frequency between the two studied groups for IL-28B rs12979860C/T. The frequency of CC genotype of IL-28B at rs12979860 SNP was higher in spontaneously cleared patients in comparison with chronic HCV patients. Significant association was found when serum levels of IL28B were compared to various IL-28 genotypes. There was a significant difference between IL-28 polymorphism and HCV genotypes (p = 0.003).
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Affiliation(s)
- Mansour Moghimi
- Department of Pathology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Forough Tavakoli
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Doosti
- Infectious and Tropical Diseases Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abbas Ahmadi-Vasmehjani
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Akhondi-Meybodi
- Gastroentrology Department, Shahid Sadoughi Hospital, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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47
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Thoens C, Heinold A, Lindemann M, Horn PA, Chang DI, Scherbaum N, Timm J, Heinemann FM. A Single-Nucleotide Polymorphism Upstream of the HLA-C Locus Is Associated With an Anti-Hepatitis C Virus-Seronegative State in a High-Risk Exposed Cohort. J Infect Dis 2019; 218:2016-2019. [PMID: 30102364 DOI: 10.1093/infdis/jiy492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
In this study, we examined the impact of the rs9264942 single-nucleotide polymorphism, previously shown to be associated with human immunodeficiency virus infection status and HLA-C expression, on the hepatitis C virus status in 359 people who inject drugs (PWID). The linkage of rs9264942 alleles to HLA-C antigens assigned to different expression levels was confirmed. Multivariate analysis revealed the age (P = .003) and the rs9264942 genotype (P = .006) to be independent factors for the classification to the PWID groups. Our study showed that the presence of the rs9264942 C/C genotype was associated with persistent seronegativity.
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Affiliation(s)
- Christine Thoens
- Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University, Germany
| | - Andreas Heinold
- Institute for Transfusion Medicine, University Hospital Essen, Germany
| | - Monika Lindemann
- Institute for Transfusion Medicine, University Hospital Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, Germany
| | - Dae-In Chang
- LVR-Hospital Essen, Department of Addictive Behaviour and Addiction Medicine, Medical Faculty, University of Duisburg-Essen, Germany
| | - Norbert Scherbaum
- LVR-Hospital Essen, Department of Addictive Behaviour and Addiction Medicine, Medical Faculty, University of Duisburg-Essen, Germany
| | - Joerg Timm
- Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University, Germany
| | - Falko M Heinemann
- Institute for Transfusion Medicine, University Hospital Essen, Germany
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48
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Chaturvedi N, Svarovskaia ES, Mo H, Osinusi AO, Brainard DM, Subramanian GM, McHutchison JG, Zeuzem S, Fellay J. Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes. eLife 2019; 8:e42542. [PMID: 31478832 PMCID: PMC6721370 DOI: 10.7554/elife.42542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and response to interferon-based treatment. Here, we evaluate associations between IFN-λ polymorphism and HCV variation in 8729 patients (Europeans 77%, Asians 13%, Africans 8%) infected with various viral genotypes, predominantly 1a (41%), 1b (22%) and 3a (21%). We searched for associations between rs12979860 genotype and variants in the NS3, NS4A, NS5A and NS5B HCV proteins. We report multiple associations in all tested proteins, including in the interferon-sensitivity determining region of NS5A. We also assessed the combined impact of human and HCV variation on pretreatment viral load and report amino acids associated with both IFN-λ polymorphism and HCV load across multiple viral genotypes. By demonstrating that IFN-λ variation leaves a large footprint on the viral proteome, we provide evidence of pervasive viral adaptation to innate immune pressure during chronic HCV infection.
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Affiliation(s)
- Nimisha Chaturvedi
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Hongmei Mo
- Gilead Sciences IncFoster CityUnited States
| | | | | | | | | | | | - Jacques Fellay
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Precision Medicine UnitLausanne University HospitalLausanneSwitzerland
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49
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Ansari MA, Aranday-Cortes E, Ip CL, da Silva Filipe A, Lau SH, Bamford C, Bonsall D, Trebes A, Piazza P, Sreenu V, Cowton VM, Hudson E, Bowden R, Patel AH, Foster GR, Irving WL, Agarwal K, Thomson EC, Simmonds P, Klenerman P, Holmes C, Barnes E, Spencer CC, McLauchlan J, Pedergnana V. Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife 2019; 8:42463. [PMID: 31478835 PMCID: PMC6721795 DOI: 10.7554/elife.42463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly variable pathogen that frequently establishes chronic infection. This genetic variability is affected by the adaptive immune response but the contribution of other host factors is unclear. Here, we examined the role played by interferon lambda-4 (IFN-λ4) on HCV diversity; IFN-λ4 plays a crucial role in spontaneous clearance or establishment of chronicity following acute infection. We performed viral genome-wide association studies using human and viral data from 485 patients of white ancestry infected with HCV genotype 3a. We demonstrate that combinations of host genetic variants, which determine IFN-λ4 protein production and activity, influence amino acid variation across the viral polyprotein - not restricted to specific viral proteins or HLA restricted epitopes - and modulate viral load. We also observed an association with viral di-nucleotide proportions. These results support a direct role for IFN-λ4 in exerting selective pressure across the viral genome, possibly by a novel mechanism.
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Affiliation(s)
- M Azim Ansari
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Camilla Lc Ip
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Siu Hin Lau
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Connor Bamford
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - David Bonsall
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Vattipally Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | | | - Emma Hudson
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Graham R Foster
- Blizard Institute, Queen Mary University, London, United Kingdom
| | - William L Irving
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine and the Oxford NIHR BRC, University of Oxford, Oxford, United Kingdom
| | - Chris Ca Spencer
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Glasgow, United Kingdom
| | - Vincent Pedergnana
- Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.,Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM), Montpellier, France
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50
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IFNL4 haplotype, linkage disequilibrium and their influence on virological response to hepatitis C virus infection in Indian population. Virusdisease 2019; 30:344-353. [DOI: 10.1007/s13337-019-00535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022] Open
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