Abstract

Ductal Carcinoma in Situ (DCIS) management is challenged by the absence of reliable markers predictive of radiotherapy (RT) response, leading to both overtreatment of indolent disease and inadequate treatment for aggressive cases. Through whole-exome sequencing of 147 DCIS cases, we characterized the genomic landscape and identified markers for disease prognosis - specifically the risk of local recurrence (in situ or invasive) within 10 years after diagnosis. Our analysis revealed that pure DCIS is characterized by frequent mutations in genes governing tissue architecture, with established cancer drivers (PIK3CA, TP53) present at lower frequencies (∼10%) than in invasive disease. These early driver mutations, while potentially conferring fitness advantages to pre-malignant cells, lack prognostic value, suggesting they may act as fitness enhancers rather than direct drivers of progression. A subset of younger patients exhibited distinct mutational processes with increased mutational burden, though this was not associated with recurrence risk. We identified twelve mutually exclusive genes significantly associated with early recurrence risk across the entire cohort, functioning in cytoskeleton and vesicle dynamics (MYO7A, STON1), signal transduction (NPFFR1), and DNA/RNA regulation. In RT-treated patients specifically, we identified 27 co-occurring variants in genes controlling cytoskeletal organization (SORBS1, KRT1), cell polarity (WWC1, PATJ), and extracellular matrix interactions (COL5A3, RELN) that were also associated with early local recurrence (within 3 years). Copy number analyses revealed that pure DCIS already harbors molecular subtype-specific patterns characteristic of invasive disease with novel recurrence-associated alterations including gains at 11q11-12 and 5p14, containing genes involved in cell adhesion. These findings suggest that certain DCIS lesions harbor genetic alterations that may compromise tissue homeostasis and create an epithelial microenvironment conducive to disease relapse, some specifically associated as following RT-induced stress, providing novel biomarkers for treatment optimization in DCIS patients.