TP21: Metabolic regulation of the virus-specific T cell response in viral hepatitis

T cells require energy to fight and eliminate viral infection. In chronic hepatitis virus infection, virus-specific CD8 T cells become “exhausted” and are unable to clear the infection. We found that this exhaustion is connected to a metabolic dysfunction with reduced glycolysis, reduced enolase expression and dysregulated mitochondria. In this project we will analyse if related metabolic dysregulation occurs in HBV/HDV coinfection, whether it can be reversed by antiviral therapy, and investigate the epigenetic mechanisms. Moreover, we will explore if microanatomical liver niches regulate T cell dysfunction in different stages of chronic HBV infection.

Prof. Dr. Dr. Bertram Bengsch

Bengsch B, Johnson AL, Kurachi M, Odorizzi PM, Pauken KE, Attanasio J, Stelekati E, McLane LM, Paley MA, Delgoffe GM, Wherry EJ. (2016) Bioenergetic Insufficiencies Due to Metabolic Alterations Regulated by the Inhibitory Receptor PD-1 Are an Early Driver of CD8(+) T Cell Exhaustion. Immunity. 45, 358-373. doi:10.1016/j.immuni.2016.07.008.

Edwards-Hicks J, Apostolova P, Buescher JM, Maib H, Stanczak MA, Corrado M, Klein Geltink RI, Maccari ME, Villa M, Carrizo GE, Sanin DE, Baixauli F, Kelly B, Curtis JD, Haessler F, Patterson A, Field CS, Caputa G, Kyle RL, Soballa M, Cha M, Paul H, Martin J, Grzes KM, Flachsmann L, Mitterer M, Zhao L, Winkler F, Rafei-Shamsabadi DA, Meiss F, Bengsch B, Zeiser R, Puleston DJ, O'Sullivan D, Pearce EJ, Pearce EL. (2023) Phosphoinositide acyl chain saturation drives CD8(+) effector T cell signaling and function. Nat Immunol. 24, 516-530. doi:10.1038/s41590-023-01419-y.

Hensel N, Gu Z, Sagar, Wieland D, Jechow K, Kemming J, Llewellyn-Lacey S, Gostick E, Sogukpinar O, Emmerich F, Price DA, Bengsch B, Boettler T, Neumann-Haefelin C, Eils R, Conrad C, Bartenschlager R, Grun D, Ishaque N, Thimme R, Hofmann M. (2021) Memory-like HCV-specific CD8(+) T cells retain a molecular scar after cure of chronic HCV infection. Nat Immunol. 22, 229-239. doi:10.1038/s41590-020-00817-w.

Bengsch B, Martin B, Thimme R. (2014) Restoration of HBV-specific CD8+ T cell function by PD-1 blockade in inactive carrier patients is linked to T cell differentiation. J Hepatol. 61, 1212-1219. doi:10.1016/j.jhep.2014.07.005.

Heim K, Binder B, Sagar, Wieland D, Hensel N, Llewellyn-Lacey S, Gostick E, Price DA, Emmerich F, Vingerhoet H, Kraft ARM, Cornberg M, Boettler T, Neumann-Haefelin C, Zehn D, Bengsch B, Hofmann M, Thimme R. (2020) TOX defines the degree of CD8+ T cell dysfunction in distinct phases of chronic HBV infection. Gut. 70, 1550-1560. doi:10.1136/gutjnl-2020-322404.

Winkler F, Hipp AV, Ramirez C, Martin B, Villa M, Neuwirt E, Gorka O, Aerssens J, Johansson SE, Rana N, Llewellyn-Lacey S, Price DA, Panning M, Gross O, Pearce EL, Hermann CM, Schumann K, Hannibal L, Neumann-Haefelin C, Boettler T, Knolle P, Hofmann M, Wohlleber D, Thimme R, Bengsch B. (2023) Enolase represents a metabolic checkpoint controlling the differential exhaustion programmes of hepatitis virus-specific CD8(+) T cells. Gut. doi:10.1136/gutjnl-2022-328734.

Schwabenland M, Salie H, Tanevski J, Killmer S, Lago MS, Schlaak AE, Mayer L, Matschke J, Puschel K, Fitzek A, Ondruschka B, Mei HE, Boettler T, Neumann-Haefelin C, Hofmann M, Breithaupt A, Genc N, Stadelmann C, Saez-Rodriguez J, Bronsert P, Knobeloch KP, Blank T, Thimme R, Glatzel M, Prinz M, Bengsch B. (2021) Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions. Immunity. 54, 1594-1610 e1511. doi:10.1016/j.immuni.2021.06.002.

Boettler T, Csernalabics B, Salie H, Luxenburger H, Wischer L, Salimi Alizei E, Zoldan K, Krimmel L, Bronsert P, Schwabenland M, Prinz M, Mogler C, Neumann-Haefelin C, Thimme R, Hofmann M, Bengsch B. (2022) SARS-CoV-2 vaccination can elicit a CD8 T-cell dominant hepatitis. J Hepatol. 77, 653-659. doi:10.1016/j.jhep.2022.03.040.

Barsch M, Salie H, Schlaak AE, Zhang Z, Hess M, Mayer LS, Tauber C, Otto-Mora P, Ohtani T, Nilsson T, Wischer L, Winkler F, Manne S, Rech A, Schmitt-Graeff A, Bronsert P, Hofmann M, Neumann-Haefelin C, Boettler T, Fichtner-Feigl S, van Boemmel F, Berg T, Rimassa L, Di Tommaso L, Saeed A, D'Alessio A, Pinato DJ, Bettinger D, Binder H, Wherry JE, Schultheiss M, Thimme R, Bengsch B. (2022) T-cell exhaustion and residency dynamics inform clinical outcomes in hepatocellular carcinoma. J Hepatol. 77, 397-409. doi:10.1016/j.jhep.2022.02.032.

Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ. (2018) Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 48, 1029-1045 e1025. doi:10.1016/j.immuni.2018.04.026.

Project in detail +

T cell exhaustion is a major driver of impaired CD8+ T cell responses in chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. We had previously observed a major regulation of cellular metabolism connected to the exhaustion program in the LCMV model of chronic infection. In the last funding period we therefore performed a comprehensive evaluation of the virus-specific CD8+ T cell metabolism in chronic HBV and HCV infection and observed that metabolic regulation is linked to the severity of CD8+ T cell exhaustion in both infections. Specifically, HCV-specific CD8+ T cells were enriched for severe mitochondrial dysfunction, a finding connected to their advanced exhaustion program. In HBV, the metabolic state differed between different epitope-specific responses. In particular, HBV-polymerase-specific CD8+ T cells displayed significant exhaustion and related mitochondrial dysfunction, and their frequency correlated with patient HBsAg levels, suggesting a direct role of antigen recognition in driving the exhaustion and metabolic program. This notion is supported by the improvement of HCV-specific CD8+ T cell metabolism observed after initiation of DAA therapy. Moreover, we identified enolase as a glycolytic regulator of cellular metabolism and virus-specific effector function. Based on our previous findings, in the next funding period, we plan to test the hypothesis that the metabolic program of exhausted CD8+ T cells is also modified by antiviral therapy in HBV and HBV-/HDV-co-infection. We will use our established im-munometabolic profiling approach to address this important hypothesis together with Neumann-Haefelin/Luxenburger, Hofmann, Urban/Nkongolo and Thimme by using patient cohorts treated with the entry inhibitor Bulevirtide, nucleos(t)ide analogues and interferon. To understand the connection of metabolism and epigenetics in regulating hepatitis virus-specific T cells, together with Z02, we will employ single-cell sequencing (RNA-Seq and ATAC-Seq) combined with single-cell histone modification profiling using mass cytometry (EpiTOF) for the analysis of virus-specific CD8+ T cells isolated from patients in different clinical stages of chronic HBV infection and in HBV/-HDV co-infection. We will also compare acute and chronic infection and distinguish different epitope-specific responses. These experiments will provide in-sights into key metabolic and epigenetic regulators responsible for regulating antiviral effector function. Together with Böttcher we will extend this analysis to MAIT cells and with Böttler to CD4+ T cell responses. We also plan to investigate non-metabolic “moonlighting” functions of Enolase 1 such as a direct effect on transcriptional regulation and the impact of this activity on T cell effector-, memory- and -exhaustion-related gene expression and mitochondrial genes and function. Finally, we will use a spatial approach to understand the intrahepatic niches involved in immune escape from the HBV-specific immune response during chronic HBV infection. Together with Z02 and Z03, we will take advantage of the spatially resolved multiomics (highly multiplexed imaging, spatial transcriptomics and spatial proteomics) cell atlas of HBV infected livers to identify microanatomic, metabolic and distinct immunovirological niches as well as cellular and molecular interaction partners of CD8+ T cells regulating T cell metabolism in different stages of HBV infection. Together with Knolle, Protzer/Wettengel and Wohlleber, we will correlate this data to murine models of HBV infection.