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

Exhausted virus-specific T cells with reduced antiviral function are enriched during unsuccessful immune responses in patients with chronic Hepatitis B and C infection. Our previous work suggest that this is due to regulation of cellular metabolism. In this project, we aim to understand by a combination of cytometry and metabolic analyses how changes in T cell metabolism influence the T cell response in viral hepatitis. We hypothesize that different metabolic programming secondary to differences in antigen recognition and inflammation determine the severity of T cell exhaustion.

Prof. Dr. Dr. Bertram Bengsch

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, Herrmann CM, Schumann K, Hannibal L, Neumann-Haefelin C, Boettler T, Knolle P, Hofmann M, Wohlleber D, Thimme R, Bengsch B. Enolase represents a metabolic checkpoint controlling the differential exhaustion programs of hepatitis virus-specific CD8+ T cells. Gut accepted (TP01, TP02, TP04, TP05, TP13, TP20, TP21, Z03)

Luxenburger H, Reeg D, Lang-Meli J, Reinscheid M, Eisner M, Bettinger D, Oberhardt V, Alizei ES, Wild K,Graeser A, Karl V, Sagar, Emmerich F, Klein F, Panning M, Huzly D, Bengsch B, Boettler T, Elling R, Thimme R, Hofmann M, Neumann-Haefelin C. (2023) Boosting compromised SARS-CoV-2-specific immunity with mRNA vaccination in liver transplant recipients. J Hepatol. 78(5):1017-1027. doi: 10.1016/j.jhep.2023.02.007.

Reinscheid M, Luxenburger H, Karl V, Graeser A, Giese S, Ciminski K, Reeg DB, Oberhardt V, Roehlen N, Lang-Meli J, Heim K, Gross N, Baum C, Rieg S, Speer C, Emmerich F, Breisinger S, Steinmann D, Bengsch B, Boettler T, Kochs G, Schwemmle M, Thimme R, Neumann-Haefelin C, Hofmann M. (2022) COVID-19 mRNA booster vaccine induces transient CD8+ T effector cell responses while conserving the memory pool for subsequent reactivation. Nat Commun. 13(1):4631. doi: 10.1038/s41467-022-32324-x.

Barsch M, Salié 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(2):397-409. doi: 10.1016/j.jhep.2022.02.032.

Lang-Meli J, Luxenburger H, Wild K, Karl V, Oberhardt V, Salimi Alizei E, Graeser A, Reinscheid M, Roehlen N, Reeg DB, Giese S, Ciminski K, Götz V, August D, Rieg S, Waller CF, Wengenmayer T, Staudacher D, Huzly D, Bengsch B, Kochs G, Schwemmle M, Emmerich F, Boettler T, Thimme R, Hofmann M, Neumann-Haefelin C. (2022) SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals. Nat Microbiol. 7(5):675-679. doi: 10.1038/s41564-022-01106-y.

Boettler T, Csernalabics B, Salié H, Luxenburger H, Wischer L, Alizei ES , 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(3):653-659 https://doi.org/10.1016/j.jhep.2022.03.040.

Wild K, Smits M, Killmer S, Strohmeier S, Neumann-Haefelin C, Bengsch B, Krammer F, Schwemmle M, Hofmann M, Thimme R, Zoldan K, Boettler T. (2021) Pre-existing immunity and vaccine history determine hemagglutinin-specific CD4 T cell and IgG response following seasonal influenza vaccination. Nat Commun. 18;12(1):6720. doi: 10.1038/s41467-021-27064-3.

Schulien I, Kemming J, Oberhardt V, Wild K, Seidel LM, Killmer S, Sagar, Daul F, Salvat Lago M, Decker A, Luxenburger H, Binder B, Bettinger D, Sogukpinar O, Rieg S, Panning M, Huzly D, Schwemmle M, Kochs G, Waller CF, Nieters A, Duerschmied D, Emmerich F, Mei HE, Schulz AR, Llewellyn-Lacey S, Price DA, Boettler T, Bengsch B, Thimme R, Hofmann M, Neumann-Haefelin C. (2021) Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells. Nat Med. 27(1):78-85. doi: 10.1038/s41591-020-01143-2.

Oberhardt V, Luxenburger H, Kemming J, Schulien I, Ciminski K, Giese S, Csernalabics B, Lang-Meli J, Janowska I, Staniek J, Wild K, Basho K, Marinescu MS, Fuchs J, Topfstedt F, Janda A, Sogukpinar O, Hilger H, Stete K, Emmerich F, Bengsch B, Waller CF, Rieg S, Sagar, Boettler T, Zoldan K, Kochs G, Schwemmle M, Rizzi M, Thimme R, Neumann-Haefelin C, Hofmann M. (2021) Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine. Nature. 597(7875):268-273. doi: 10.1038/s41586-021-03841-4.

Rennert C, Tauber C, Fehrenbach P, Heim K, Bettinger D, Sogukpinar Ö, Schuch A, Zecher BF, Bengsch B, Lang SA, Bronsert P, Björkström NK, Fichtner-Feigl S, Schultheiss M, Thimme R, Hofmann M. (2021) Adaptive subsets limit the anti-tumoral NK-cell activity in hepatocellular carcinoma. Cells. 2;10(6):1369. doi: 10.3390/cells10061369.

Schwabenland M, Salié H, Tanevski J, Killmer S, Lago MS, Schlaak AE, Mayer L, Matschke J, Püschel 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. 13;54(7):1594-1610.e11. doi: 10.1016/j.immuni.2021.06.002.

Basho K, Zoldan K, Schultheiss M, Bettinger D, Globig A-M, Bengsch B, Neumann-Haefelin C, Klocperk A, Warnatz K, Hofmann M, Thimme R, Boettler T. (2021) IL-2 contributes to cirrhosis-associated immune dysfunction by impairing follicular T helper cells in advanced cirrhosis. J Hepatol. 74(3):649-660. doi: 10.1016/j.jhep.2020.10.012.

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, Grün 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(2):229-239. doi: 10.1038/s41590-020-00817-w.

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(8): 1550–1560. doi: 10.1136/gutjnl-2020-322404

Schulien I, Kemming J, Oberhardt V, Wild K, Seidel LM, Killmer S, Sagar, Daul F, Salvat Lago M, Decker A, Luxenburger H, Binder B, Bettinger D, Sogukpinar O, Rieg S, Panning M, Huzly D, Schwemmle M, Kochs G, Waller CF, Nieters A, Duerschmied D, Emmerich F, Mei HE, Schulz AR, Llewellyn-Lacey S, Price DA, Boettler T, Bengsch B, Thimme R, Hofmann M, Neumann-Haefelin C. Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells. Nat Med. 2020 Nov 12. doi: 10.1038/s41591-020-01143-2. (TP01, TP02, TP11, TP20, TP21)

Schuch A, Salimi Alizei E, Heim K, Wieland D, Kiraithe MM, Kemming J, Llewellyn-Lacey S, Sogukpinar Ö, Ni Y, Urban S, Zimmermann P, Nassal M, Emmerich F, Price DA, Bengsch B, Luxenburger H, Neu-mann-Haefelin C, Hofmann M, Thimme R. 2019. Phenotypic and functional differences of HBV core-specific versus HBV polymerase-specific CD8+ T cells in chronically HBV-infected patients with low vi-ral load. Gut. 68(5):905-915.

Qiu J, Villa M, Sanin DE, Buck MD, O'Sullivan D, Ching R, Matsushita M, Grzes KM, Winkler F, Chang CH, Curtis JD, Kyle RL, Van Teijlingen Bakker N, Corrado M, Haessler F, Alfei F, Edwards-Hicks J, Maggi LB Jr, Zehn D, Egawa T, Bengsch B, Klein Geltink RI, Jenuwein T, Pearce EJ, Pearce EL. 2019. Acetate Promotes T Cell Effector Function during Glucose Restriction. Cell Rep. 27(7):2063-2074.e5

Manske K, Kallin N, König V, Schneider A, Kurz S, Bosch M, Welz M, Cheng RL, Bengsch B, Steiger K, Protzer U, Thimme R, Knolle PA, Wohlleber D. 2018. Outcome of anti-viral immunity in the liver is shaped by the level of antigen expressed in infected hepatocytes. Hepatology. 68(6):2089-2105

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(5):1029-1045.e5.

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 are an early driver of CD8 T cell exhaustion. Immunity. 45(2):358-73.

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(6):1212-9

Seigel B, Bengsch B, Lohmann V, Bartenschlager R, Blum HE, Thimme R. 2013. Factors That Determine the Antiviral Efficacy of HCV-Specific CD8(+) T Cells Ex Vivo. Gastroenterology. 144(2):426-36.

Bengsch B*, Jo J*, Seigel B*, Rau SJ*, Schmidt J, Bisse E, Aichele P, Aichele U, Joeckel L, Royer C, Ferreira KS, Borner C, Baumert TF, Blum HE, Lohmann V, Fischer R, Thimme R. 2012. Low perforin ex-pression of early differentiated HCV-specific CD8+ T cells limits their hepatotoxic potential. J Hepatol 57(1):9-16

Bengsch B*, Seigel B*, Ruhl M, Timm J, Kuntz M, Blum HE, Pircher H, Thimme R. 2010. Coexpression of PD-1, 2B4, CD160 and KLRG1 on exhausted HCV-specific CD8+ T cells is linked to antigen recogni-tion and T cell differentiation. PLoS Pathog 6:e1000947.

Boettler T, Panther E, Bengsch B, Nazarova N, Spangenberg HC, Blum HE, Thimme R. 2006. Expres-sion of the interleukin-7 receptor alpha chain (CD127) on virus-specific CD8+ T cells identifies function-ally and phenotypically defined memory T cells during acute resolving hepatitis B virus infection. J Virol 80(7):3532-40

Project in detail +

Accumulation of exhausted virus-specific CD8+ T cells (TEX) with impaired antiviral function is a major fea-ture of unsuccessful immune responses in patients with chronic hepatitis B and C virus (HBV and HCV) in-fection. We previously identified a major role for the control of cellular metabolism downstream of inhibitory receptor signalling (i.e. via PD-1) in the development of TEX in murine models of chronic infection that in-volved regulation of glucose metabolism, induction of mitochondrial depolarization and ROS production (Bengsch et al 2016). Importantly, reversion of mitochondrial dysfunction resulted in increased T cell effec-tor function. Understanding the metabolic regulation of HCV- and HBV-specific TEX will be important for a better understanding of T cell dysfunction and should reveal novel targets for immune-based therapy ap-proaches. In preliminary work, we have profiled metabolic hallmarks of virus-specific T cells ex vivo in pa-tients with chronic HBV and HCV infection. These results indicate that unlike in mice, glucose uptake is maintained in HBV- and HCV-specific TEX, while mitochondrial dysfunction occurs in both settings. However, our data also indicate that the metabolic profile differs significantly between HBV and HCV. We hypothesize that the differential metabolic programming of virus-specific T cells determines the severity of exhaustion and is linked to differences in antigen recognition and inflammation.
We therefore plan to perform a detailed characterization of the metabolism of HBV- and HCV-specific CD8 T cells to understand the metabolic determinants of functional vs. exhausted hepatitis virus-specific T cells in different settings of viral hepatitis and viral control. We will use a comprehensive approach with high-parametric metabolic single-cell profiling using flow cytometry and mass cytometry, analysis of metabolic pathways on the transcriptional level using low-input RNA-Seq (with help from Z02 and Z03N) and metabolic flux studies. The comparison of different hepatitis virus infections (focus on HBV and HCV infection, exten-sion in collaboration to HDV, HEV) and animal models of hepatitis virus infections is possible due to the collaborations with Thimme, Neumann-Haefelin, Boettler, Hofmann, Urban, Heikenwälder and Wohlleber and will allow us to dissect the effects of different conditions of successful and dysfunctional immune respons-es (e.g., acute infection, spontaneous clearance vs. chronic infection). A high-dimensional exhaustion-directed phenotypic and functional assessment using mass cytometry will be used with help of Z02 to de-termine the differences in the degree and differentiation of TEX subsets linked to different metabolic states and clinical outcomes. In selected samples, we will attempt to correlate cytometry of peripheral blood phe-notypes to liver histology together with Z02. We will then seek to understand the impact of metabolic altera-tions and manipulations on the function of the antiviral T cell response by antagonizing immunomodulatory pathways regulating TEX (e.g., PD-1 or CD39) and promote metabolic pathways identified as deficient (such as via stimulation of metabolic regulators or provision of anaplerotic nutrient sources). Moreover, to under-stand how antigen and therapy impact on TEX metabolism, we will test samples from patients with chronic HCV infection undergoing direct acting antiviral (DAA) therapy and compare them to patients that underwent interferon-based therapy. Similarly, we will test patients with chronic HBV and HDV infection undergoing antiviral therapy with standard therapy (nucleos(t)ide analogues, interferon treatment) or the novel entry in-hibitor MyrcludexB. These ex vivo analyses will be combined with in vitro assays testing the effects of inter-ferons on T cell metabolism and inhibition of viral replication in T cell – hepatocyte co-cultures in collabora-tion with Bartenschlager, Heikenwälder and Lohmann. In collaboration, we will test specific results, such as candidate metabolic checkpoints in the glycolytic pathway, in murine models of viral hepatitis in collabora-tion with Wohlleber. Together, the planned experiments will shed light on the metabolic underpinnings of the dysfunctional antiviral T cell response in chronic viral hepatitis and reveal novel metabolism-based targets that could be harnessed to enhance T cell function.