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Matic S, Milovanovic D, Mijailovic Z, Djurdjevic P, Sazdanovic P, Stefanovic S, Todorovic D, Popovic S, Vitosevic K, Vukicevic V, Vukic M, Vukovic N, Milivojevic N, Zivanovic M, Jakovljevic V, Filipovic N, Baskic D, Djordjevic N. IFNL3/4 polymorphisms as a two-edged sword: An association with COVID-19 outcome. J Med Virol 2023; 95:e28506. [PMID: 36655749 DOI: 10.1002/jmv.28506] [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: 10/08/2022] [Revised: 12/14/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) has been ranked among the most fatal infectious diseases worldwide, with host's immune response significantly affecting the prognosis. With an aim to timely predict the most likely outcome of SARS-CoV-2 infection, we investigated the association of IFNL3 and IFNL4 polymorphisms, as well as other potentially relevant factors, with the COVID-19 mortality. This prospective observational case-control study involved 178 COVID-19 patients, hospitalized at Corona Center or Clinic for Infectious Diseases of University Clinical Centre Kragujevac, Serbia, followed up until hospital discharge or in-hospital death. Demographic and clinical data on all participants were retrieved from the electronic medical records, and TaqMan assays were employed in genotyping for IFNL3 and IFNL4 single nucleotide polymorphisms (SNPs), namely rs12980275, rs8099917, rs12979860, and rs368234815. 21.9% and 65.0% of hospitalized and critically ill COVID-19 patients, respectively, died in-hospital. Multivariable logistic regression analysis revealed increased Charlson Comorbidity Index (CCI), N/L, and lactate dehydrogenase (LDH) level to be associated with an increased likelihood of a lethal outcome. Similarly, females and the carriers of at least one variant allele of IFNL3 rs8099917 were almost 36-fold more likely not to survive SARS-CoV-2 infection. On the other hand, the presence of at least one ancestral allele of IFNL4 rs368234815 decreased more than 15-fold the likelihood of mortality from COVID-19. Our results suggest that, in addition to LDH level, N/L ratio, and CCI, IFNL4 rs368234815 and IFNL3 rs8099917 polymorphisms, but also patients' gender, significantly affect the outcome of COVID-19.
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Affiliation(s)
- Sanja Matic
- Department of Pharmacy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Dragan Milovanovic
- Department of Pharmacology and Toxicology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Department of Clinical Pharmacology, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Zeljko Mijailovic
- Department of Infectious Diseases, Serbia, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Infectious Diseases Clinic, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Predrag Djurdjevic
- Department of Internal medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Clinic for Haematology, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Predrag Sazdanovic
- Department of Anatomy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Gynecology and Obstetrics Clinic, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Srdjan Stefanovic
- Department of Pharmacy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Danijela Todorovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Suzana Popovic
- Centre for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Katarina Vitosevic
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Vukicevic
- Corona Centre, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Milena Vukic
- Department of Chemistry, Faculty of Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Nenad Vukovic
- Department of Chemistry, Faculty of Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Nevena Milivojevic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Marko Zivanovic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Jakovljevic
- Department of Physiology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Deprtment of Human Pathology, 1st Moscow Medical Unuversity "I. M. Sechenov", Moscow, Russia
| | - Nenad Filipovic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
| | - Dejan Baskic
- Centre for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Institute of Public Health Kragujevac, Kragujevac, Serbia
| | - Natasa Djordjevic
- Department of Pharmacology and Toxicology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
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Redondo N, Rodríguez-Goncer I, Parra P, Albert E, Giménez E, Ruiz-Merlo T, López-Medrano F, San Juan R, González E, Sevillano Á, Andrés A, Navarro D, Aguado JM, Fernández-Ruiz M. Impact of polymorphisms in genes orchestrating innate immune responses on replication kinetics of Torque teno virus after kidney transplantation. Front Genet 2022; 13:1069890. [DOI: 10.3389/fgene.2022.1069890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Torque teno virus (TTV) DNAemia has been proposed as a surrogate marker of immunosuppression after kidney transplantation (KT), under the assumption that the control of viral replication is mainly exerted by T-cell-mediated immunity. However, Tthe impact on post-transplant TTV kinetics of single genetic polymorphisms (SNPs) in genes orchestrating innate responses remains unknown. We aimed to characterize the potential association between 14 of these SNPs and TTV DNA levels in a single-center cohort of KT recipients.Methods: Plasma TTV DNAemia was quantified by real-time PCR in 221 KT recipients before transplantation (baseline) and regularly through the first 12 post-transplant months. We performed genotyping of the following SNPs: CTLA4 (rs5742909, rs231775), TLR3 (rs3775291), TLR9 (rs5743836, rs352139), CD209 (rs735240, rs4804803), IFNL3 (rs12979860, rs8099917), TNF (rs1800629), IL10 (rs1878672, rs1800872), IL12B (rs3212227) and IL17A (rs2275913).Results: The presence of the minor G allele of CD209 (rs4804803) in the homozygous state was associated with undetectable TTV DNAemia at the pre-transplant assessment (adjusted odds ratio: 36.96; 95% confidence interval: 4.72–289.67; p-value = 0.001). After applying correction for multiple comparisons, no significant differences across SNP genotypes were observed for any of the variables of post-transplant TTV DNAemia analyzed (mean and peak values, areas under the curve during discrete periods, or absolute increments from baseline to day 15 and months 1, 3, 6 and 12 after transplantation).Conclusion: The minor G allele of CD209 (rs4804803) seems to exert a recessive protective effect against TTV infection in non-immunocompromised patients. However, no associations were observed between the SNPs analyzed and post-transplant kinetics of TTV DNAemia. These negative results would suggest that post-transplant TTV replication is mainly influenced by immunosuppressive therapy rather than by underlying genetic predisposition, reinforcing its clinical application as a biomarker of adaptive immunity.
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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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Bhushan A, Chinnaswamy S. Identifying causal variants at the interferon lambda locus in case-control studies: Utilizing non-synonymous variant rs117648444 to probe the role of IFN-λ4. Gene 2018; 664:168-180. [PMID: 29705128 DOI: 10.1016/j.gene.2018.04.076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/19/2018] [Accepted: 04/25/2018] [Indexed: 02/08/2023]
Abstract
Genetic variants at the interferon lambda (IFNL) locus have been associated with several human phenotypes in both disease and health. In chronic hepatitis C virus (HCV) infections, where the IFNL variants were first identified to be associated with response to interferon-α-ribavirin therapy, the available data clearly suggests that the causal variant could be the dinucleotide polymorphism rs368234815 that causes an open reading frame-shift in the IFNL4 gene resulting in expression of a functional IFN-λ4, a new type III IFN. In other human diseases/phenotypes where IFNL variants have been recently associated with, the causal mechanism remains unclear. In vitro evidence has shown that other IFNL variants (rs28416813, rs4803217) may regulate expression of another type III IFN, IFN-λ3. Therefore, expression of a functional IFN-λ4 and quantitative differences in IFN-λ3 expression are two potential causal mechanisms behind the observed phenotypes. Since these two potential causal mechanisms involve features of mutual exclusivity and overlapping functions, it is difficult to differentiate one from the other, in vivo, in absence of other implicating evidences. In addition, the strong linkage disequilibrium (LD) observed in many populations at the IFNL locus makes it difficult to tease out the actual functional/causal variants responsible for the phenotypes. The non-synonymous single nucleotide polymorphism rs117648444 that alters the activity of IFN-λ4 and the LD structure in the IFNL region which leads to a confounding effect of rs117648444 on other IFNL variants, provide us with additional tools in case-control studies to probe the role of IFN-λ4.
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Affiliation(s)
- Anand Bhushan
- 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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Backus LI, Shahoumian TA, Belperio PS, Winters M, Prokunina-Olsson L, O'Brien TR, Holodniy M. Impact of IFNL4-∆G genotype on sustained virologic response in hepatitis C genotype 1 patients treated with direct-acting antivirals. Diagn Microbiol Infect Dis 2018; 92:34-36. [PMID: 29866411 DOI: 10.1016/j.diagmicrobio.2018.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/10/2018] [Accepted: 04/08/2018] [Indexed: 12/12/2022]
Abstract
In direct acting antiviral (DAA)-treated HCV genotype 1, the sustained virologic response rate with the ∆G/∆G genotype of IFNL4 rs368234815 (86.8%) was significantly lower than with ∆G/TT (95.9%, P = 0.03) or TT/TT (98.6%, P = 0.01). The SVR odds ratio for ∆G/∆G compared to TT/TT was 0.10 (P = 0.03). IFNL4 genotype might predict DAA-response.
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Affiliation(s)
- Lisa I Backus
- Population Health Services, Department of Veterans Affairs, Palo Alto, CA 94304, USA.
| | - Troy A Shahoumian
- Population Health Services, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Pamela S Belperio
- Population Health Services, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Mark Winters
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Holodniy
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Office of Public Health Surveillance & Research, Department of Veterans Affairs, Palo Alto, CA 94304, USA
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Enache EL, Sin A, Enache LS, Bancu L. Triplex High-Resolution Melting Assay for the Simultaneous Assessment of IFNL3 rs12979860, ABCB11 rs2287622, and RNF7 rs16851720 Genotypes in Chronic Hepatitis C Patients. J Mol Diagn 2017; 19:857-869. [PMID: 28860020 DOI: 10.1016/j.jmoldx.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/14/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high-resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IFNL3 rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classic therapy. The assay showed excellent reproducibility and 100% accuracy, sensitivity, and specificity against the gold standard Sanger sequencing. When added to routine examination data, genotype information significantly improved their performance for prediction of advanced liver fibrosis and sustained virological response (P = 0.041 and P = 0.011, respectively). Correspondingly, the full models had area under the receiver operating characteristic curve values of 0.842 (95% CI, 0.773-0.911) and 0.921 (95% CI, 0.870-0.972) and integrated discrimination improvements of 7.5% (95% CI, 2.5%-12.5%; P = 0.003) and 11.5% (95% CI, 5.8%-17.2%; P < 0.001), respectively. This is the first report on a diagnostic test for simultaneous genotyping of IFNL3, ABCB11, and RNF7 in CHC patients. Reliable and inexpensive, the assay should provide useful information for the clinical management of CHC, like identification of patients at risk of rapid disease progression or with high chances of response to classic therapy.
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Affiliation(s)
- Elena L Enache
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy Tirgu Mures, Tirgu Mures
| | - Anca Sin
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy Tirgu Mures, Tirgu Mures; Pathology Department, Emergency County Clinical Hospital Tirgu Mures, Tirgu Mures, Romania
| | - Liviu S Enache
- Department of Cell and Molecular Biology, University of Medicine and Pharmacy Tirgu Mures, Tirgu Mures; Clinical Laboratory, Emergency County Clinical Hospital Tirgu Mures, Tirgu Mures, Romania.
| | - Ligia Bancu
- Department of Internal Medicine 2, University of Medicine and Pharmacy Tirgu Mures, Tirgu Mures; Internal Medicine Department 2, Emergency County Clinical Hospital Tirgu Mures, Tirgu Mures, Romania
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Kandoussi N, Elannaz H, Melloul M, Tagajdid Mohamed R, Abi R, Elalaoui My A, Alaoui Amine S, Touil N, Elfahime E, Elkabbaj S, Zouhdi M, Mrani S. Genetic variation in interleukin 28B rs8099917 and response to antiviral therapy in Moroccan patients with chronic hepatitis C. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Trinks J, Caputo M, Hulaniuk ML, Corach D, Flichman D. Hepatitis C virus pharmacogenomics in Latin American populations: implications in the era of direct-acting antivirals. Pharmgenomics Pers Med 2017; 10:79-91. [PMID: 28405170 PMCID: PMC5378445 DOI: 10.2147/pgpm.s125452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In recent years, great progress has been made in the field of new therapeutic options for hepatitis C virus (HCV) infection. The new direct-acting antiviral agents (DAAs) represent a great hope for millions of chronically infected individuals because their use may lead to excellent cure rates with fewer side effects. In Latin America, the high prevalence of HCV genotype 1 infection and the significant association of Native American ancestry with risk predictive single-nucleotide polymorphisms (SNPs) in IFNL4 and ITPA genes highlight the need to implement new treatment regimens in these populations. However, the universal accessibility to DAAs is still not a reality in the region as their high cost is one of the major, although not the only, limiting factors for their broad implementation. Therefore, under these circumstances, could the assessment of host genetic markers be a useful tool to prioritize DAA treatment until global access to these new drugs can be achieved? This review will summarize the scientific evidences and the potential implications of HCV pharmacogenomics in this rapidly evolving era of anti-HCV drug development.
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Affiliation(s)
- Julieta Trinks
- Basic Science and Experimental Medicine Institute (ICBME), University Institute of the Italian Hospital of Buenos Aires
- Scientific and Technological National Research Council (CONICET)
| | - Mariela Caputo
- Scientific and Technological National Research Council (CONICET)
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica
| | - María L Hulaniuk
- Basic Science and Experimental Medicine Institute (ICBME), University Institute of the Italian Hospital of Buenos Aires
| | - Daniel Corach
- Scientific and Technological National Research Council (CONICET)
- Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica
| | - Diego Flichman
- Scientific and Technological National Research Council (CONICET)
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
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