Abstract 6618: Longitudinal, multimodal profiling of metastatic ER+ breast cancer on CDK4/6 inhibitor therapy
Authors: Creason Allison L. , Egger Julian , Watson Cameron , Sivagnanam Shamilene , Lin Jia-Ren , Chin Koei , Sorger Peter K. , Coussens Lisa M. , Mitri Zahi I. , Gray Joe W. , Mills Gordon B. , Goecks Jeremy 
Published: June 2023

Abstract
Introduction: Use of CDK4/6 inhibitors (CDK4/6i) in combination with endocrine therapy has transformed treatment and greatly improved outcome for ER+ breast cancer (BC) patients. However, many BC patients eventually progress on therapy. To understand how ER+ metastatic BC (mBC) tumors become refractory to CDK4/6i, we have created a multimodal, longitudinal tumor atlas to investigate tumor mechanisms of therapeutic resistance, as part of the NCI Cancer Moonshot Human Tumor Atlas Network. By deeply profiling individual patients, we identified a wide variety of putative tumor intrinsic and extrinsic mechanisms of resistance to CDK4/6i.
Methods: mBC ER+ patients (n=5) enrolled in the Knight Cancer Institute SMMART Trials program underwent biopsies before treatment and on progression with combination CDK4/6i and endocrine therapy. Biopsies were profiled using: clinical imaging, bulk genomics (WES), transcriptomics (RNAseq), and proteomics (RPPA), multiplex tissue imaging (mIHC, cycIF), single-cell genomics (scDNAseq) and epigenomics (sci-ATAC-seq).
Results: Upon progression, patients displayed dysregulated tumor-intrinsic activity via upregulation of gene expression in cell cyclins and kinases as well as genomic copy loss of regulatory factors, such as Rb. On-progression biopsies exhibited increased expression and pathway activity of IL-Jak-Stat and Interferon signaling and changes in tumor microenvironment immune cell composition, including elevated immune cytotoxicity; however, a subset of CD8 T cells expressed LAG3, Tbet, and TIM3, indicating signs of immune activation trending toward exhaustion. Patients also exhibited increased M2 Macrophage and T regulatory cell infiltration, suggesting compensatory feedback to dampen immune activity. Analysis of spatial organization identified cellular neighborhoods recurring across all samples with changes after therapy observed primarily in neighborhoods associated with epithelial-stromal density and immune reactivity/suppression.
Conclusion: Findings from this mBC ER+ cohort highlight heterogenous molecular and cellular changes that occur after treatment with a CDK4/6i. We observed multiple tumor intrinsic and extrinsic factors, including modulation of proliferation in neoplastic cells and tumor microenvironment composition, that are suggested to play a role in acquired resistance. We hypothesize a set of patients that initially respond to CDK4/6i therapy may initially display immune activation, but the sustained activation and long-term exposure to therapy may lead to chronic inflammation and immunosuppression. These observations suggest combining CDK4/6i therapy with immunotherapy may provide benefit. We also observed recurrent spatial cellular patterns that recapitulate known biological structures in these tissues; future work will explore association of spatial organization with therapeutic response.
Citation Format: Allison L. Creason, Julian Egger, Cameron Watson, Shamilene Sivagnanam, Jia-Ren Lin, Koei Chin, Peter K. Sorger, Lisa M. Coussens, Zahi I. Mitri, Joe W. Gray, Gordon B. Mills, Jeremy Goecks. Longitudinal, multimodal profiling of metastatic ER+ breast cancer on CDK4/6 inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6618.