Abstract

Background Managing Ductal Carcinoma in Situ (DCIS) remains challenging due to the lack of reliable biomarkers to predict radiotherapy (RT) response, leading to both overtreatment of indolent disease and undertreatment of aggressive cases. Results Through whole-exome sequencing of 147 DCIS cases, we characterized the genomic landscape of pure DCIS and identified genetic alterations associated with the risk of recurrence, either in-situ or invasive. DCIS lesions harbored frequent mutations in established cancer drivers (PIK3CA, TP53) and genes regulating tissue architecture, which likely enhanced pre-invasive cell fitness but lacked prognostic value. A subset of younger patients exhibited distinct mutational processes characterized by high mutational burden, though these were not linked to recurrence risk. Across the cohort, five mostly mutually exclusive genes (SH2B2, PDZD8, MYO7A, MUCL3, DNASE2B), involved in cell adhesion, membrane organization, and DNA degradation, were significantly associated with early recurrence (within 5 years). In RT-treated patients, we identified 27 additional mutated genes uniquely associated with recurrence, along with SH2B2 and MUCL3, which were also identified in the whole cohort. Most of these genes are involved in cytoskeletal regulation, cell adhesion, and cell-environment interactions. Mutations in two metabolic regulators (MGAM2 and AADACL3), as well as REV1, a key player in DNA damage tolerance, may impair cellular responses to RT-induced stress or genomic stability. Copy number analyses revealed that pure DCIS exhibits molecular subtype-specific patterns characteristic of invasive disease, with novel recurrence-associated alterations, including three non-adjacent gains and 12 losses in regions harboring oncogenes, tumor suppressor genes, and genes regulating structural integrity, cell-cell adhesion and interactions. Conclusions Our findings identify key genetic alterations associated with local recurrence and RT resistance. While TP53, PIK3CA, and recurrent copy number alterations represent early events in tumorigenesis, they lack prognostic value in pure DCIS, underscoring the need for alternative biomarkers. By uncovering mutations associated with cytoskeletal integrity, cell adhesion, and cel-cell interactions, our study provides insights into DCIS recurrence and RT response, with potential to guide personalized therapeutic strategies.