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BCL11B predetermines a persister state in breast cancer that is reversed by TNFα

Qi, Z.;Gulati, G.;Kuo, A.;Sikandar, S.;Ho, W.;Qian, D.;Dirbas, F.;Newman, A.;Cai, S.;Clarke, M.

2026-06-11 Cancer Biology
10.64898/2026.06.09.731253 bioRxiv
Show abstract

The frequent development of chemoresistance in cancer presents a significant clinical challenge, yet the underlying causes for heterogeneous drug responses remain largely elusive. Here, we systematically assessed the cellular differentiation status of human breast cancer cells utilizing single-cell atlases and identified a distinct population of immature basal-like cancer cells marked by BCL11B. Notably, higher levels of BCL11B+ cancer cells are significantly associated with early relapse in breast cancer patients who received chemotherapy. Functioning as a central regulator, BCL11B delineates an immature cell state that preferentially transitions to a drug-resistant persister state during treatment through multiple pre-existing and adaptive drug-resistance programs. Importantly, the cytokine tumor necrosis factor alpha (TNF) is revealed as a natural inhibitor of BCL11B and can directly reverse the emergence of chemoresistant persister cells. Therefore, we identify BCL11B as an unappreciated pre-determinant of drug response and a therapeutic target for a subset of breast cancer patients at high risk of developing chemoresistance.

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