The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

Daniela Nachmanson; Adam Officer; Hidetoshi Mori; Jonathan Gordon; Mark F Evans; Joseph Steward; Huazhen Yao; Thomas O'Keefe; Farnaz Hasteh; Gary S Stein; Kristen Jepsen; Donald L Weaver; Gillian L Hirst; Brian L Sprague; Laura J Esserman; Alexander D Borowsky; Janet L Stein; Olivier Harismendy

doi:10.1038/s41523-021-00365-y

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

NPJ Breast Cancer. 2022 Jan 13;8(1):6. doi: 10.1038/s41523-021-00365-y.

Authors

Daniela Nachmanson¹, Adam Officer^{1

2}, Hidetoshi Mori³, Jonathan Gordon^{4

5}, Mark F Evans^{4

6}, Joseph Steward⁷, Huazhen Yao⁸, Thomas O'Keefe⁹, Farnaz Hasteh^{7

10}, Gary S Stein^{4

5}, Kristen Jepsen⁸, Donald L Weaver^{4

6}, Gillian L Hirst¹¹, Brian L Sprague^{4

12}, Laura J Esserman¹¹, Alexander D Borowsky³, Janet L Stein^{4

5}, Olivier Harismendy^{13

14}

Affiliations

¹ Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
² Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
³ Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA.
⁴ University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA.
⁵ Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA.
⁶ Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
⁷ Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
⁸ Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
⁹ Department of Surgery, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
¹⁰ Department of Pathology, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
¹¹ Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA.
¹² Department of Surgery, University of Vermont, Burlington, VT, 05405, USA.
¹³ Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA. oharismendy@ucsd.edu.
¹⁴ Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA. oharismendy@ucsd.edu.

Abstract

Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.

Abstract

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