“Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers”

CDK4/6 inhibitors (CDK4/6i) have transformed the treatment of hormone receptor-positive (HR+), HER2-negative (HR+) breast cancers as they are effective across all clinicopathological, age, and ethnicity subgroups for metastatic HR+ breast cancer. In metastatic ER+ breast cancer, CDK4/6i lead to strong and consistent improvement in survival across different lines of therapy. To understand how metastatic HR+ breast cancers become refractory to CDK4/6i, we have created a multimodal and longitudinal tumor atlas to investigate therapeutic adaptations in malignant cells and in the tumor immune microenvironment. This atlas is part of the NCI Cancer Moonshot Human Tumor Atlas Network and includes seven pairs of pre- and on-progression biopsies from five metastatic HR+ breast cancer patients treated with CDK4/6i. Biopsies were profiled with bulk genomics, transcriptomics, and proteomics as well as single-cell ATAC-seq and multiplex tissue imaging for spatial, single-cell resolution. These molecular datasets were then linked with detailed clinical metadata to create an atlas for understanding tumor adaptations during therapy. Analysis of our atlas datasets revealed a diverse but tractable set of tumor adaptations to CDK4/6i therapy. Malignant cells adapted to therapy via mTORC1 activation, cell cycle bypass, and increased replication stress. The tumor immune microenvironment displayed evidence of both immune activation and immune suppression, including increased PD-1 expression, features of T cell dysfunction, and CD163+ macrophage infiltration. Together, our metastatic ER+ breast cancer atlas represents a rich multimodal resource to understand tumor therapeutic adaptations to CDK4/6i therapy. ### Competing Interest Statement G.B.M. is a SAB member or Consultant: for Amphista, Astex, AstraZeneca, BlueDot, Chrysallis Biotechnology, Ellipses Pharma, GSK, ImmunoMET, Infinity, Ionis, Leapfrog Bio, Lilly, Medacorp, Nanostring, Nuvectis, PDX Pharmaceuticals, Qureator, Roche, Signalchem Lifesciences, Tarveda, Turbine, Zentalis Pharmaceuticals. G.B.M. has Stock/Options/Financial relationships with: Bluedot, Catena Pharmaceuticals, ImmunoMet, Nuvectis, SignalChem, Tarveda, and Turbine. G.B.M. has Licensed Technology: HRD assay to Myriad Genetics, DSP patents with Nanostring. G.B.M. has Sponsored research with AstraZeneca.J.W.G. has licensed technologies to Abbott Diagnostics; has ownership positions in Convergent Genomics, Health Technology Innovations, Zorro Bio, and PDX Pharmaceuticals; serves as a paid consultant to New Leaf Ventures; has received research support from Thermo Fisher Scientific (formerly FEI), Zeiss, Miltenyi Biotech, Cepheid (Danaher), Quantitative Imaging, Health Technology Innovations, and Micron Technologies; and owns stock in Abbott Diagnostics, AbbVie, Alphabet, Amazon, Amgen, Apple, General Electric, Gilead, Intel, Microsoft, Nvidia, and Z.I.M.mer Biomet. L.M.C. has received reagent support from Cell Signaling Technologies, Syndax Pharmaceuticals, Inc., ZielBio, Inc., and Hibercell, Inc.; holds sponsored research agreements with Syndax Pharmaceuticals, Hibercell, Inc., Prospect Creek Foundation, Lustgarten Foundation for Pancreatic Cancer Research, Susan G. Komen Foundation, and the National Foundation for Cancer Research; is on the Advisory Board for Carisma Therapeutics, Inc., CytomX Therapeutics, Inc., Shasqi, Kineta, Inc., Hibercell, Inc., Cell Signaling Technologies, Inc., Alkermes, Inc., Raska Pharma, Inc., NextCure, Guardian Bio, AstraZeneca Partner of Choice Network (OHSU Site Leader), Genenta Sciences, Pio Therapeutics Pty Ltd., and Lustgarten Foundation for Pancreatic Cancer Research Therapeutics Working Group, Inc. A.C.A. is an author on licensed patents that cover one or more aspects of the single-cell ATAC-seq technologies utilized in this study.P.K.S. is a co-founder and member of the BOD of Glencoe Software, a member of the BOD for Applied Biomath, and a member of the SAB for RareCyte, NanoString, and Montai Health; he holds equity in Glencoe, Applied Biomath, and RareCyte. P.K.S. is a consultant for Merck, and the Sorger lab has received research funding from Novartis and Merck in the past five years. Z.I.M. has a consulting/advisory role with AstraZeneca, Gilead Sciences and Daiichi Sankyo. He has also received research funding for his institution from Seattle Genetics, Novartis, AstraZeneca, Radius Health, Daiichi Sankyo, Lilly, GlaxoSmithKline, and Olema Oncology.