Abstract 778: Profiling the immune landscape of CDK4/6 inhibitor intrinsic resistance among metastatic HR+ breast cancer
Authors: Haoting Shi, Zheshen Han, Xue Wang, Yufei Wang, Chao Hu, Ruixin Pan, Xiaosong Chen, Qing Qu, Rong Cai, Kunwei Shen
Journal: Cancer Research (2025)

Abstract Cyclin-dependent kinases 4/6 (CDK4/6) inhibitor is a standard-of-care for hormone receptor-positive/human epidermal growth factor receptor 2 negative metastases breast cancer (HR+/HER2- mBC), while substantial proportion of patients suffer from intrinsic resistance (IR), and the mechanism at the spatial level remains unclear. A total of 10 eligible HR+/HER2- mBC patients (age: median age 63, range 40-67 years) with liver metastases who underwent liver biopsies and received CDK4/6 inhibitor were included. The majority (N = 7, 70%) were of first-line treatment at metastatic disease settings and in combination with fulvestrant (N = 9, 90%). After a median follow-up of 22.2 months, four patients were determined as IR, with a median PFS of 4.2 months. We collected formalin-fixed paraffin-embedded samples from these patients and spatially profiled the expression of more than 570 proteins across tumor (panCK+), immune (CD45+), and cancer-associated fibroblast region (CAF, α-SMA+) regions, respectively using the GeoMx Digital Spatial Profiler (DSP) platform. The differentially expressed proteins (DEPs) were identified and GSEA analyses were performed. Elevated expression of MHC I proteins (HLA B7 and HLA E), extracellular matrix (ECM)-associated protein (FAK, Fibronectin, and Periostin), antioxidant-associated proteins (NQO1 and G6PD), and mucin-related proteins (Muc5AC and Muc1) were observed in tumor regions (all FDR &amp;lt; 0.05) among IR patients. Similarly, HLA B7, Fibronectin, MucAC5 and NQO1 were found to be overexpressed in CAF region. The proteins associated with the target of CDK4/6 inhibitor were down-regulated among IR patients [NF-kB p105, CK8 (phosphor S431), and Cyclin D1], suggesting that the IR could be partially explained by loss-of- drug-target. Meanwhile, downregulation of Caveolin-1 and CD63 were identified in CAF regions, while downregulation of HLA-DR and MHC II proteins were observed in immune regions. GSEA results showed that MHC I antigen presentation pathway was significantly upregulated in CAF regions (NES 1.87, FDR 0.016), while TGF-beta pathway and autophagy pathway were significantly downregulated in CAF regions (NES -1.77 [FDR 0.016] and -1.84 [FDR 0.040], respectively). These findings suggested that IR might be driven by the immune escape associated with CAFs. Our results showed that Bcl-2 expression in tumor region has the highest value in predicting IR (AUROC 0.989). Leveraging high-plex spatial proteomics data from HR+/HER2- mBC patients, the IR of CDK4/6 inhibitor might be associated with loss-of-target in tumor cells, immune escape driven by CAFs, and alterations in the ECM. Citation Format: Haoting Shi, Zheshen Han, Xue Wang, Yufei Wang, Chao Hu, Ruixin Pan, Xiaosong Chen, Qing Qu, Rong Cai, Kunwei Shen. Profiling the immune landscape of CDK4/6 inhibitor intrinsic resistance among metastatic HR+ breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 778.