TP01: Fate and function of memory-like virus-specific CD8+ T cells in chronic viral hepatitis

TP01 is based on the hypothesis that duration of antigen recognition might be a central determinant of the transcriptional profile of virus-specific CD8+ T cells. Hence, a transcriptional profile characteristic for persisting antigen recognition is inherent to memory-like virus-specific CD8+ T cells that emerge during chronic viral hepatitis and that are maintained after viral clearance. With the proposed work program we aim to define the fate, the biological role and the translational value of memory-like virus-specific CD8+ T cells in chronic viral hepatitis. We will therefore assess molecular determinants, driving immunological factors and the memory potential of memory-like virus-specific CD8+ T cells.

Prof. Dr. Robert Thimme

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. 72(10):1971-1984. doi: 10.1136/gutjnl-2022-328734. (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.

Kemming J, Gundlach S, Panning M, Huzly D, Huang J, Lütgehetmann M, Pischke S, Schulze zur Wiesch J, Emmerich F, Llewellyn-Lacey S, Price DA, Tanriver Y, Warnatz K, Boettler T, Thimme R, Hofmann M, Fischer N, Neumann-Haefelin C. (2022) Mechanisms of CD8+ T-cell failure in chronic hepatitis E virus infection. J Hepatol. 77(4):978-990. https://doi.org/10.1016/j.jhep.2022.05.019.

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.

Oberhardt V, Hofmann M, Thimme R, Neumann-Haefelin C. (2022) Adaptive immune responses, immune escape and immune-mediated pathogenesis during HDV infection. Viruses. 20;14(2):198. doi: 10.3390/v14020198.

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.

Salimi Alizei E, Hofmann M, Thimme R, Neumann-Haefelin C. (2021) Mutational escape from cellular immunity in viral hepatitis: variations on a theme. Curr Opin Virol. 50:110-118. doi: 10.1016/j.coviro.2021.08.002.

Zoldan K, Ehrlich S, Killmer S, Wild K, Smits M, Russ M, Globig AM, Hofmann M, Thimme R, Boettler T. (2021) Th1-biased Hepatitis C virus-specific follicular T helper-like cells effectively support B cells after antiviral therapy. Front Immunol. 30;12:742061. doi: 10.3389/fimmu.2021.742061.

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.

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. (2021) Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses. Nat Commun. 12;12(1):4882. doi: 10.1038/s41467-021-25218-x.

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.

Dudek M, Pfister D, Donakonda S, ....Thimme R, Böttler T, Tacke F, Dufour J-F, Haller D, Murray PJ, Heeren R, Zehn D, Böttcher JP, Heikenwälder M, Knolle PA. (2021) Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH. Nature. 592, 444–449. doi: 10.1038/s41586-021-03568-2.

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.

Thimme R. (2021) T cell immunity to hepatitis C virus: Lessons for a prophylactic vaccine. J Hepatol. 74(1):220-229. doi: 10.1016/j.jhep.2020.09.022.

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

Basho K, Zoldan K, Schultheiss M, Bettinger D, Globig AM, Bengsch B, Neumann-Haefelin C, Klocperk A, Warnatz K, Hofmann M, Thimme R, Boettler T. (2020) IL-2 contributes to cirrhosis-associated immune dysfunction by impairing follicular T helper cells in advanced cirrhosis. J Hepatol. 24:S0168-8278(20)33692-8. doi: 10.1016/j.jhep.2020.10.012.

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)

Kemming J, Thimme R, Neumann-Haefelin C. Adaptive Immune Response against Hepatitis C Virus. Int J Mol Sci. 2020 Aug 6;21(16):5644. doi: 10.3390/ijms21165644. (TP01, TP02)

Smits M, Zoldan K, Ishaque N, Gu Z, Jechow K, Wieland D, Conrad C, Eils R, Fauvelle C, Baumert TF, Emmerich F, Bengsch B, Neumann-Haefelin C, Hofmann M, Thimme R, Boettler T. 2020. Follicular T helper cells shape the HCV-specific CD4 T cell repertoire after viral elimination. J Clin Invest. 130(2):998-1009. (TP01, TP01A, TP02, TP04, Z02)Winkler F, Bengsch B. 2020. Use of Mass Cytometry to Profile Human T Cell Exhaustion. Front Immunol. 10:3039. (TP01A) Review.

Binder B, Thimme R. CD4+ T cell responses in human viral infection: lessons from hepatitis C. J Clin Invest. 2020 Feb 3;130(2):595-597. doi: 10.1172/JCI133222. (TP01, TP11)

A. Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, Utzschneider DT, Hösslin M, Cullen J, Fan Y, Eisenberg V, Wohlleber D, Steiger K, Merkler D, Delorenzi M, Knolle PA, Cohen C, Thimme R*, Youngblood B*, Zehn D*. 2019. Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection. Nature. 2019 571(7764):265-269* co-corresponding au-thors

B. Karimzadeh H*, Kiraithe MM*, Oberhardt V*, Salimi Alizei E, Bockmann J, Schulze Zur Wiesch J, Budeus B, Hoffmann D, Wedemeyer H, Cornberg M, Krawczyk A, Rashidi-Alavijeh J, Rodríguez-Frías F, Casillas R, Buti M, Smedile A, Alavian SM, Heinold A, Emmerich F, Panning M, Gostick E, Price DA, Timm J, Hofmann M, Raziorrouh B, Thimme R, Protzer U, Roggendorf M, Neumann-Haefelin C. 2019. Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8+ T Cells and Evolve at the Population Level. Gastroenterology. 156(6):1820-1833 *equal contribution

C. Jacobi FJ, Wild K, Smits M, Zoldan K, Csernalabics B, Flecken T, Lang J, Ehrenmann P, Emmerich F, Hofmann M, Thimme R, Neumann-Haefelin C, Boettler T. 2019. OX40 stimulation and PD-L1 blockade synergistically augment HBV-specific CD4 T cells in patients with HBeAg-negative infection. J Hepatol. pii: S0168-8278(19)30131-X. doi: 10.1016/j.jhep.2019.02.016.

D. Schuch A, Salimi Alizei E*, Heim K*, Wieland D, Kiraithe MM, Kemming J, Llewellyn-Lacey S, Soguk-pinar Ö, Ni Y, Urban S, Zimmermann P, Nassal M, Emmerich F, Price DA, Bengsch B, Luxenburger H, Neumann-Haefelin C, Hofmann M*, Thimme R*. 2019a. Phenotypic and functional differences of HBVcore- versus HBVpolymerase-specific CD8+ T cells in chronically HBV-infected patients with low viral load. GUT. 68(5) *equal contribution

E. Schuch A, Zecher BF, Müller PA, Correia MP, Daul F, Rennert C, Tauber C, Schlitt K, Böttler T, Neumann-Haefelin C, Hengel H, Pircher H, Cerwenka A, Thimme R, Hofmann M. 2019b. NK-cell re-sponses are based towards CD16-mediated effector functions in chronic hepatitis B virus infection. J Hepatol. 70(3):351-360

F. 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 Antiviral Immunity in the Liver Is Shaped by the Level of Antigen Expressed in Infected Hepatocytes. Hepatology. 68(6):2089-2105

G. Grünvogel O, Colasanti O, Lee JY, Klöss V, Belouzard S, Reustle A, Esser-Nobis K, Hesebeck-Brinckmann J, Mutz P, Hoffmann K, Mehrabi A, Koschny R, Vondran FWR, Gotthardt D, Schnitzler P, Neumann-Haefelin C, Thimme R, Binder M, Bartenschlager R, Dubuisson J, Dalpke AH, Lohmann V. 2018. Secretion of Hepatitis C Virus Repilcation Intermediates Reduces Activation of Toll-Like Recep-tor 3 in Hepatocytes. Gastroenterology. 154(8):2231-2251.

H. Utzschneider DT, Delpoux A, Wieland D, Huang X, Lai CY, Hofmann M, Thimme R, Hedrick SM. 2018. Active Maintenance of T Cell Memory in Acute and Chronic Viral Infection Depends on Continu-ous Expression of FOXO1. Cell Rep. 22(13):3454-3467

I. Wieland D, Kemming J, Schuch A, Emmerich F, Knolle P, Neumann-Haefelin C, Held W, Zehn D, Hofmann M*, Thimme R*. 2017. TCF1+ hepatitis C virus-specific CD8+ T cells are maintained after cessation of chronic antigen stimulation. Nat Commun. 8:15050 *equal contribution

J. Utzschneider DT, Charmoy M, Chennupati V, Pousse L, Ferreira DP, Calderon-Copete S, Danilo M, Alfei F, Hofmann M, Wieland D, Pradervand S, Thimme R, Zehn D, Held W. 2016. T Cell Factor 1-Expressing Memory-like CD8(+) T Cells Sustain the Immune Response to Chronic Viral Infections. Immunity. 45(2):415-2

Project in detail +

Virus-specific CD8+ T cells play an important role in the outcome and pathogenesis of viral hepatitis. Chron-ic viral hepatitis is associated with the presence of dysfunctional namely exhausted virus-specific CD8+ T cells that are characterized by the expression of multiple inhibitory receptors, such as PD1. In the first fund-ing period, we demonstrated that exhausted virus-specific CD8+ T cells obtained from patients with chronic hepatitis B virus (HBV) or chronic hepatitis C virus (HCV) infection are not homogeneous, but rather consist of more severely/terminally exhausted and memory-like subsets (Wieland et al., 2017; coll. Knolle, Neumann-Haefelin); Schuch et al., 2019, coll. Urban, Nassal, Bengsch, Neumann-Haefelin). The memory-like subsets exhibit a superior proliferative capacity, maintain the pool of virus-specific CD8+ T cells during chronic in-fection, survive independently of antigen and provide recall responses after cessation of chronic antigen stimulation. These characteristics render memory-like virus-specific CD8+ T cells promising targets for im-munotherapeutic approaches during chronic hepatitis virus infection and to combat re-infection. In the pro-posed next funding period, we therefore aim to further define the key determinants and the memory poten-tial of this clinically relevant virus-specific CD8+ T-cell subset. For this, we will explore regulatory molecular circuits of the memory-like virus-specific CD8+ T-cell fate including master regulators, transcription factor networks, metabolic characteristics and epigenetic fingerprints (Protzer, Wohlleber, Knolle, Bartenschlager, Lohmann, Z03N). Furthermore, we will also investigate how immunological factors like antigen recognition and the inflammatory microenvironment impact on the establishment and functional capacity of the memory-like virus-specific CD8+ T-cell subsets in chronic viral hepatitis. For our analyses we will make use of our large Hepatologic Biobank of the University hospital in Freiburg (HBUF) that contains samples from patients exhibiting an acute, resolved (spontaneous or therapy-induced) or chronic viral hepatitis (Bengsch, Böttler, Hofmann, Neumann-Haefelin, Z02). Our experimental setups will comprise high-dimensional FACS and mass cytometry (CyTOF), low input/single cell RNAseq and ATACseq as well as in vitro gene knock-down and overexpression followed by functional assays in cell culture. Hence, our proposed research program will generate important novel insights into molecular and immunological determinants of memory-like cells in viral hepatitis that may be relevant for the design of memory-like virus-specific T cell-based immunothera-peutic interventions and prevention strategies.

Milestones of the first funding period:
- Definition of molecular determinants of exhausted and restored HCV-specific CD8+ T cells
- Dissecting the impact of viral antigen on virus-specific CD8+ T-cell exhaustion and restoration
- Identification of immunological factors that determine CD8+ T-cell exhaustion and restoration
- Definition of molecular determinants of NK-cell alterations in chronic viral hepatitis and their impact on CD8+ T-cell exhaustion and restoration