Ductal carcinoma in situ develops within clonal fields of mutant cells in morphologically normal ducts

Abstract Mutations are abundantly present in tissues of healthy individuals, including the breast epithelium. Yet it remains unknown whether mutant cells directly induce lesion formation or first spread, leading to a field of mutant cells that is predisposed towards lesion formation. To study the clonal and spatial relationships between morphologically normal breast epithelium adjacent to pre‐cancerous lesions, we developed a three‐dimensional (3D) imaging pipeline combined with spatially resolved genomics on archival, formalin‐fixed breast tissue with the non‐obligate breast cancer precursor ductal carcinoma in situ (DCIS). Using this 3D image‐guided characterization method, we built high‐resolution spatial maps of DNA copy number aberration (CNA) profiles within the DCIS lesion and the surrounding normal mammary ducts. We show that the local heterogeneity within a DCIS lesion is limited. However, by mapping the CNA profiles back onto the 3D reconstructed ductal subtree, we find that in eight out of 16 cases the healthy epithelium adjacent to the DCIS lesions has overlapping structural variations with the CNA profile of the DCIS. Together, our study indicates that pre‐malignant breast transformations frequently develop within mutant clonal fields of morphologically normal‐looking ducts. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.