CD8 T cells with classical and NK-like cytotoxic gene expression programs mediate control of HBV replication and functional cure

Lattouf, E. I.; Feuerherd, M.; Bartsch, L. M.; Drescher, H. K.; Dijkstra, S.; Villanueva, M. A.; Hoogeveen, R. C.; Lieb, D.; Van Den Berge, K.; De Troyer, E.; Subudhi, S.; Genshaft, A. S.; Conceicao-Neto, N.; Traunbauer, A. K.; Alrubayyi, A.; Crain, C. R.; Salimzadeh, L.; Damasio, M.; Beudeker, B. J.; La, D. P.; Sanchez Vasquez, J. D.; Cheney, J. A.; Moreno-Cheek, M. V.; Shah, S.; Aneja, J.; Waring, M. T.; Alatrakchi, N.; Kim, A. Y.; de Knegt, R. J.; Lewis-Ximenez, L. L.; Aerssens, J.; Bollekens, J.; Hacohen, N.; Gaiha, G. D.; Chung, R. T.; Feld, J. J.; Janssen, H. L.; Shalek, A. K.; Boonstra,

doi:10.64898/2026.06.27.732784

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bioRxiv · 10.64898/2026.06.27.732784

CD8 T cells with classical and NK-like cytotoxic gene expression programs mediate control of HBV replication and functional cure

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Abstract

Chronic hepatitis B is characterized by a decades-long evolving engagement between host immunity and the hepatitis B virus (HBV). Understanding the molecular characteristics of HBV-specific CD8 T cells linked to control of viral replication and antigenemia is essential to design effective immunotherapeutic modalities. Here we show that HBV-specific CD8 T cells, even during infection stages with extremely high viral loads, lack the features of terminally exhausted CD8 T cells observed in chronic HCV and HIV infection or cancer. Instead, we observe emerging gene expression programs over disease stages that correlate with increasing HBV control, which include a bona fide cytotoxic and T-cell localization program associated with low levels of viral replication, and a second NK-like T-cell program that combines expression of classical NK markers (KIRs, KLRs, FCGR3A, TYROBP, IKZF2) with cytotoxic genes (GZMB, GNLY, PRF1), which emerges with complete control of HBV viremia and antigenemia. We also found enrichment of both CD8 T-cell programs in HIV-specific CD8 T cells from HIV elite controllers, supporting a conserved role in controlling persistent viral infections with viral reservoirs.

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Lattouf, E. I., Feuerherd, M., Bartsch, L. M., Drescher, H. K., Dijkstra, S., Villanueva, M. A., Hoogeveen, R. C., Lieb, D., Van Den Berge, K., De Troyer, E., Subudhi, S., Genshaft, A. S., Conceicao-Neto, N., Traunbauer, A. K., Alrubayyi, A., Crain, C. R., Salimzadeh, L., Damasio, M., Beudeker, B. J., La, D. P., Sanchez Vasquez, J. D., Cheney, J. A., Moreno-Cheek, M. V., Shah, S., Aneja, J., Waring, M. T., Alatrakchi, N., Kim, A. Y., de Knegt, R. J., Lewis-Ximenez, L. L., Aerssens, J., Bollekens, J., Hacohen, N., Gaiha, G. D., Chung, R. T., Feld, J. J., Janssen, H. L., Shalek, A. K., Boonstra,. 2026-06-29. CD8 T cells with classical and NK-like cytotoxic gene expression programs mediate control of HBV replication and functional cure. https://doi.org/10.64898/2026.06.27.732784

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