Towards a Systems Immunology Approach to Understanding Correlates of Protective Immunity Against HCV

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2021 Sep 28

PMID 34578451

Citations 5

Authors

Naglaa H Shoukry

Affiliations

Soon will be listed here.

Abstract

Over the past decade, tremendous progress has been made in systems biology-based approaches to studying immunity to viral infections and responses to vaccines. These approaches that integrate multiple facets of the immune response, including transcriptomics, serology and immune functions, are now being applied to understand correlates of protective immunity against hepatitis C virus (HCV) infection and to inform vaccine development. This review focuses on recent progress in understanding immunity to HCV using systems biology, specifically transcriptomic and epigenetic studies. It also examines proposed strategies moving forward towards an integrated systems immunology approach for predicting and evaluating the efficacy of the next generation of HCV vaccines.

Citing Articles

Immunological Monitoring in Hepatitis C Virus Controlled Human Infection Model.

Shoukry N, Cox A, Walker C Clin Infect Dis. 2023; 77(Suppl 3):S270-S275.

PMID: 37579206 PMC: 10425133. DOI: 10.1093/cid/ciad359.

Studying T Cell Responses to Hepatotropic Viruses in the Liver Microenvironment.

Lopez-Scarim J, Nambiar S, Billerbeck E Vaccines (Basel). 2023; 11(3).

PMID: 36992265 PMC: 10056334. DOI: 10.3390/vaccines11030681.

Correlates of vaccine protection against sub-species infection revealed in a transcriptomic study of responses in Gudair vaccinated sheep.

Purdie A, Plain K, Pooley H, Begg D, de Silva K, Whittington R Front Vet Sci. 2022; 9:1004237.

PMID: 36504842 PMC: 9729357. DOI: 10.3389/fvets.2022.1004237.

Hepatic iNKT cells produce type 2 cytokines and restrain antiviral T cells during acute hepacivirus infection.

Raus S, Lopez-Scarim J, Luthy J, Billerbeck E Front Immunol. 2022; 13:953151.

PMID: 36159876 PMC: 9501689. DOI: 10.3389/fimmu.2022.953151.

Mesenchymal stem cells-based therapy in liver diseases.

Han H, Jin W, Li X Mol Biomed. 2022; 3(1):23.

PMID: 35895169 PMC: 9326420. DOI: 10.1186/s43556-022-00088-x.

References

Bolen C, Robek M, Brodsky L, Schulz V, Lim J, Taylor M . The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response. J Interferon Cytokine Res. 2012; 33(1):15-23. PMC: 3539252. DOI: 10.1089/jir.2012.0037. View

Haque A, Engel J, Teichmann S, Lonnberg T . A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med. 2017; 9(1):75. PMC: 5561556. DOI: 10.1186/s13073-017-0467-4. View

Martin B, Hennecke N, Lohmann V, Kayser A, Neumann-Haefelin C, Kukolj G . Restoration of HCV-specific CD8+ T cell function by interferon-free therapy. J Hepatol. 2014; 61(3):538-43. DOI: 10.1016/j.jhep.2014.05.043. View

Bengsch B, Ohtani T, Khan O, Setty M, Manne S, OBrien S . Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 2018; 48(5):1029-1045.e5. PMC: 6010198. DOI: 10.1016/j.immuni.2018.04.026. View

Gaucher D, Therrien R, Kettaf N, Angermann B, Boucher G, Filali-Mouhim A . Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med. 2008; 205(13):3119-31. PMC: 2605227. DOI: 10.1084/jem.20082292. View

Bowen D, Walker C . Mutational escape from CD8+ T cell immunity: HCV evolution, from chimpanzees to man. J Exp Med. 2005; 201(11):1709-14. PMC: 2213256. DOI: 10.1084/jem.20050808. View

Kasprowicz V, Kang Y, Lucas M, Schulze Zur Wiesch J, Kuntzen T, Fleming V . Hepatitis C virus (HCV) sequence variation induces an HCV-specific T-cell phenotype analogous to spontaneous resolution. J Virol. 2009; 84(3):1656-63. PMC: 2812309. DOI: 10.1128/JVI.01499-09. View

Cunningham E, Hajarizadeh B, Amin J, Hellard M, Bruneau J, Feld J . Reinfection Following Successful Direct-acting Antiviral Therapy for Hepatitis C Virus Infection Among People Who Inject Drugs. Clin Infect Dis. 2020; 72(8):1392-1400. DOI: 10.1093/cid/ciaa253. View

Hensel N, Gu Z, Sagar , Wieland D, Jechow K, Kemming J . Memory-like HCV-specific CD8 T cells retain a molecular scar after cure of chronic HCV infection. Nat Immunol. 2021; 22(2):229-239. DOI: 10.1038/s41590-020-00817-w. View

10.

Chen L, Borozan I, Feld J, Sun J, Tannis L, Coltescu C . Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection. Gastroenterology. 2005; 128(5):1437-44. DOI: 10.1053/j.gastro.2005.01.059. View

11.

Tsang J, Schwartzberg P, Kotliarov Y, Biancotto A, Xie Z, Germain R . Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell. 2014; 157(2):499-513. PMC: 4139290. DOI: 10.1016/j.cell.2014.03.031. View

12.

Longo S, Guo M, Ji A, Khavari P . Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat Rev Genet. 2021; 22(10):627-644. PMC: 9888017. DOI: 10.1038/s41576-021-00370-8. View

13.

Wieland D, Kemming J, Schuch A, Emmerich F, Knolle P, Neumann-Haefelin C . TCF1 hepatitis C virus-specific CD8 T cells are maintained after cessation of chronic antigen stimulation. Nat Commun. 2017; 8:15050. PMC: 5418623. DOI: 10.1038/ncomms15050. View

14.

Kared H, Fabre T, Bedard N, Bruneau J, Shoukry N . Galectin-9 and IL-21 mediate cross-regulation between Th17 and Treg cells during acute hepatitis C. PLoS Pathog. 2013; 9(6):e1003422. PMC: 3688567. DOI: 10.1371/journal.ppat.1003422. View

15.

Richard H, Schulz M, Sultan M, Nurnberger A, Schrinner S, Balzereit D . Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 2010; 38(10):e112. PMC: 2879520. DOI: 10.1093/nar/gkq041. View

16.

Nakaya H, Pulendran B . Vaccinology in the era of high-throughput biology. Philos Trans R Soc Lond B Biol Sci. 2015; 370(1671). PMC: 4527391. DOI: 10.1098/rstb.2014.0146. View

17.

Page K, Melia M, Veenhuis R, Winter M, Rousseau K, Massaccesi G . Randomized Trial of a Vaccine Regimen to Prevent Chronic HCV Infection. N Engl J Med. 2021; 384(6):541-549. PMC: 8367093. DOI: 10.1056/NEJMoa2023345. View

18.

Peterson V, Zhang K, Kumar N, Wong J, Li L, Wilson D . Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol. 2017; 35(10):936-939. DOI: 10.1038/nbt.3973. View

19.

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

20.

Abdel-Hakeem M, Bedard N, Murphy D, Bruneau J, Shoukry N . Signatures of protective memory immune responses during hepatitis C virus reinfection. Gastroenterology. 2014; 147(4):870-881.e8. PMC: 4170061. DOI: 10.1053/j.gastro.2014.07.005. View