Early metabolic and differentiation remodeling in BRCA1/2 high-risk fallopian tube epithelium revealed by single-cell multi-omics

Germline mutations in BRCA1 and BRCA2 greatly increase the risk of developing high-grade serous carcinoma (HGSC), yet the earliest molecular events driving malignant transformation in the fallopian tube epithelium, the likely site of origin, remain poorly understood. Defining these early alterations is essential for improving risk prediction and informing preventive strategies for BRCA -associated ovarian cancer.To investigate the initial cellular and molecular perturbations in high-risk individuals, we performed single-cell transcriptomic and multi-omic profiling on fallopian tube fimbrial samples obtained through exfoliative cytology brushings and conventional tissue specimens. Single-cell RNA sequencing was conducted on 14 brushings from BRCA1/2 mutation carriers, 3 brushings from average-risk individuals, and 12 tissue samples from average-risk controls. In parallel, single-cell multi-omic analysis was applied to short-term epithelial cultures derived from 4 high-risk and 2 average-risk individuals, enabling an integrated assessment of transcriptional states, chromatin accessibility, and gene regulatory programs.Brushings were enriched for epithelial and immune populations, facilitating high-resolution characterization of epithelial differentiation. Cells from BRCA1/2 mutation carriers exhibited disrupted secretory-ciliated differentiation trajectories, accompanied by upregulation of mitochondrial respiration and oxidative phosphorylation genes, suggesting early mitochondrial and metabolic remodeling in high-risk epithelia. Multi-omic integration further identified a distinct epithelial cluster enriched in BRCA1/2 carriers characterized by increased RUNX3 transcription factor activity. Although these cells remain transcriptionally aligned with secretory epithelium, RUNX3 -associated programs indicate a partial or intermediate differentiation state-potentially reflecting early lineage instability preceding malignant transformation. Subtle alterations in immune-related pathways were also observed, pointing to microenvironmental changes that may support a permissive niche for tumor initiation.Together, these data reveal early transcriptomic, metabolic, and gene-regulatory remodeling in the fallopian tube epithelium of BRCA mutation carriers. By defining epithelial states and pathways perturbed prior to neoplasia, this work provides new mechanistic insight into hereditary ovarian cancer predisposition and highlights potential biomarkers for early detection and prevention.