Circadian misalignment underlies immune escape in breast cancer

Liang, C.; Liu, Z.; Xu, X.; Xu, Z.; Zhang, Q.; Zhang, T.; Mangan, R. J.; Xiu, B.; Wu, G.; Akhshi, T.; Sandusky, Z. M.; Gray, G. K.; Zhang, N.; Kuziel, G.; Traphagen, N. A.; Fass, S. B.; Grayson, A.; Ho, L.-L.; Gu, S. S.; Wang, S.; Sheng, Z. Z.; Zhang, Y.; Adib, E.; Chen, T.; Jeselsohn, R.; Kellis, M.; Brown, M.

doi:10.64898/2026.05.26.726543

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bioRxiv · 10.64898/2026.05.26.726543

Circadian misalignment underlies immune escape in breast cancer

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Abstract

Circadian regulation shapes tissue physiology, yet how it organizes cellular and molecular dynamics within the tumor microenvironment (TME) and influences tumor immunity remains unclear. Using temporal single-nucleus multiomic profiling of mouse breast tumors, we uncovered extensive circadian programs that are both cell-type-specific and shared across the TME, governing proliferation and immune responses. Notably, cancer epithelial cells exhibited global acrophase misalignment relative to immune populations. This intercellular desynchrony manifests as temporal decoupling between tumor proliferation and immune activation, discordant antigen presentation and T cell recognition with intrinsic activation-exhaustion overlap in T cells, and asynchronous PD-1/PD-L1 oscillations that sustain checkpoint-mediated suppression. Similar patterns were observed in human triple-negative breast cancer (TNBC). Together, these findings establish intercellular circadian misalignment as a mechanism of tumor immune evasion and position the circadian architecture of the tumor-immune ecosystem as a previously underappreciated determinant of tumor development and therapeutic response. HIGHLIGHTSO_LISingle-cell multiomics maps circadian regulation of tumor-immune programs. C_LIO_LICircadian regulation in cancer epithelial cells is misaligned with immune cell populations. C_LIO_LITumor-immune temporal misalignment undermines antitumor immunity. C_LIO_LICircadian misalignment in human TNBC suggests relevance for immunotherapy timing. C_LI

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Liang, C., Liu, Z., Xu, X., Xu, Z., Zhang, Q., Zhang, T., Mangan, R. J., Xiu, B., Wu, G., Akhshi, T., Sandusky, Z. M., Gray, G. K., Zhang, N., Kuziel, G., Traphagen, N. A., Fass, S. B., Grayson, A., Ho, L.-L., Gu, S. S., Wang, S., Sheng, Z. Z., Zhang, Y., Adib, E., Chen, T., Jeselsohn, R., Kellis, M., Brown, M.. 2026-05-29. Circadian misalignment underlies immune escape in breast cancer. https://doi.org/10.64898/2026.05.26.726543

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