Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, here we perform single cell RNA-sequencing of 26,515 cells (including 8433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-γ and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4648 BC patients reveals that treatment with metformin (an indirect PPAR-γ signaling activator) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-γ link for BC treatment.

Aarhus University of Advanced Studies Aarhus University Aarhus 8000 Denmark

Center for Biotechnology Khalifa University of Science and Technology Abu Dhabi United Arab Emirates

Department of Biomedicine Aarhus University Aarhus 8000 Denmark

Department of General Medical Oncology and Multidisciplinary Breast Centre University Hospitals Leuven Leuven Belgium

Department of Gynaecologic Oncology Leuven Cancer Institute University Hospital Leuven KU Leuven Leuven Belgium

Department of Pathology University Hospitals Leuven Leuven Belgium

Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Vestec Prague West Czech Republic

Laboratory for Translational Breast Cancer Research Department of Oncology KU Leuven Leuven Belgium

Laboratory of Angiogenesis and Vascular Heterogeneity Department of Biomedicine Aarhus University Aarhus 8000 Denmark

Laboratory of Angiogenesis and Vascular Metabolism Center for Cancer Biology KU Leuven Leuven 3000 Belgium

Laboratory of Translational Cell and Tissue Research Department of Imaging and Pathology KU Leuven Leuven 3000 Belgium

Laboratory of Tumor Inflammation and Angiogenesis Center for Cancer Biology Department of oncology KU Leuven Leuven 3000 Belgium

Laboratory of Tumor Inflammation and Angiogenesis Center for Cancer Biology VIB Leuven 3000 Belgium

Lars Bolund Institute of Regenerative Medicine Qingdao Europe Advanced Institute for Life Sciences BGI Shenzhen Qingdao 266555 China

Multidisciplinary Breast Centre and Department of Surgical Oncology University Hospitals Leuven KU Leuven Leuven Belgium

National Center for Cancer Immune Therapy Department of Oncology University of Copenhagen Herlev Denmark

State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat Sen University 510275 Guangzhou Guangdong People's Republic of China

Steno Diabetes Center Aarhus Aarhus University Hospital Aarhus 8000 Denmark

Translational Cancer Research Unit GZA Hospitals Sint Augustinus Antwerp Belgium and Center for Oncological Research University of Antwerp Antwerp Belgium

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