Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Levan, J.; Vaaben, A. V.; Tsui, J.; Davidson, B. R.; Olive, M. E.; Callaway, P. C.; Nguyen, C. B. T.; Ilala, M.; Patel, R. K.; Hunter, R. D.; Fragiadakis, G. K.; Combes, A. J.; Nankya, F.; Dorsey, G.; Kakuru, A.; Muhindo, M.; Feeney, M. E.

doi:10.1101/2025.11.20.689355

bioRxiv · 10.1101/2025.11.20.689355

Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Levan, J.·Vaaben, A. V.·Tsui, J.·Davidson, B. R.·Olive, M. E.·Callaway, P. C.·Nguyen, C. B. T.·Ilala, M.·Patel, R. K.·Hunter, R. D.·Fragiadakis, G. K.·Combes, A. J.·Nankya, F.·Dorsey, G.·Kakuru, A.·Muhindo, M.·Feeney, M. E.

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Abstract

Gamma delta T cells ({gamma}{delta} T cells) emerge early during human gestation and are uniquely equipped to protect the fetus and infant following in utero infection with viruses such as cytomegalovirus (CMV). Previous research showed that fetal {gamma}{delta} T cells in early gestation are transcriptionally pre-programmed for effector functions in the thymus. Infants with congenital CMV infection (cCMV) exhibit expansions of {gamma}{delta} T cells with CMV-reactive TCRs; however, the functional and transcriptional programming of these innate-like effector cells has not been characterized. Here, we analyzed cord blood mononuclear cells from cCMV+ and uninfected neonates in Uganda using flow cytometry and single-cell RNA and TCR sequencing. We find that {gamma}{delta} T cells in cCMV+ neonates are more differentiated, activated, cytotoxic, and proliferative. TCR repertoires of cCMV+ infants exhibit oligoclonal expansions with an enrichment of {gamma}{delta}TCRs that possess shorter CDR3 lengths and fewer N additions, which suggest they arise from early fetal progenitor cells. These expanded {gamma}{delta} T cell clonotypes in cCMV+ infants are more frequently public and exhibit cytotoxic transcriptional programming. These findings demonstrate that cCMV infection drives an oligoclonal expansion of highly cytotoxic effector {gamma}{delta} T cells with fetal-like TCR features, underscoring their specialized roles in early-life immunity.

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Levan, J., Vaaben, A. V., Tsui, J., Davidson, B. R., Olive, M. E., Callaway, P. C., Nguyen, C. B. T., Ilala, M., Patel, R. K., Hunter, R. D., Fragiadakis, G. K., Combes, A. J., Nankya, F., Dorsey, G., Kakuru, A., Muhindo, M., Feeney, M. E.. 2025-11-21. Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors. https://doi.org/10.1101/2025.11.20.689355

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