Abstract LB093: Circadian misalignment between cancer cells and immune cells drives immune escape

Abstract The circadian clock profoundly influences cancer biology, including tumor progression, immune dynamics, and therapeutic efficacy. However, a comprehensive understanding of circadian regulation within the tumor microenvironment (TME) remains elusive. To address this gap and elucidate the diurnal cancer cell-immune interaction landscape of the TME, we generated a temporal single-cell epigenomic and transcriptomic atlas from mouse breast tumors sampled at four time points across a 24-hour cycle with a total of more than 100,000 cells with both modalities. We identified 6 main cell types including epithelial, mesenchymal, plasmablasts, T/NK cells, B cells and myeloid cells, and further classified into 14 cell subclasses and 36 cell subtypes. Significant time-of-day-dependent fluctuations in immune cell infiltration were observed, with T cells predominating in the TME during nighttime, accompanied by a decrease in macrophage populations. We characterized the rhythmic genes across cell subclasses including Cancer epithelial cells, Cancer-associated fibroblasts, CD4+/CD8+T cells, B cells, Macrophages/Monocytes, Neutrophils, and Natural killer T cells. Integrated analysis of circadian gene modules revealed cell subclass-specific regulatory patterns characterized by variations in amplitude and acrophase. Mechanistic analysis further highlighted a circadian misalignment between Cancer epithelial cells and immune cells, wherein the peak phases of cell cycle and antigen-processing activities in cancer epithelial cells were desynchronized with the activation, antigen recognition, and anti-tumor cytotoxicity peak phases of immune cells. These misalignments indicate a potential mechanism by which Cancer epithelial cells evade immune surveillance. Our findings provide a single-cell multiomic atlas of circadian regulation in breast cancer TME, uncovering rhythmic tumor-immune interactions and providing translational perspective on combining chronotherapy with immunotherapy. Citation Format: Chuqian Liang, Zunpeng Liu, Qi Zhang, Tao Zhang, Bingqiu Xiu, Gongwei Wu, Stuart Benjamin Fass, Li-Lun Ho, Manolis Kellis, Myles Brown. Circadian misalignment between cancer cells and immune cells drives immune escape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB093.