Abstract PR011: Breakage of chromosome 3p initiates clear cell renal cell carcinoma evolution

Abstract Clear cell renal cell carcinoma (ccRCC) is characterized by a near-universal loss of chromosome 3p arising early in life, which is then followed by inactivating tumor suppressor mutations occurring decades later. Given the deleterious consequences of chromosome loss on cellular fitness, it is unclear how non-transformed renal epithelial cells tolerate 3p loss during early tumorigenesis. Here we show by large-scale sequencing that ccRCC tumors exhibit a wide spectrum of 3p structural alterations that range from simple arm-level deletions to complex rearrangements surrounding a terminal breakpoint, a pattern we term breakpoint-confined chromothripsis. We modeled these events in human renal proximal tubule epithelial cells by engineering Cas9-induced DNA breaks on chromosome 3p. Although 3p loss rapidly induces senescence, a rare subset of cells characterized by high levels of nuclear SOD3 bypassed senescence and underwent clonal expansion. Ongoing genomic evolution further drove the emergence of subclonal DNA copy number changes that recapitulated recurrent alterations in ccRCC, including chromosome 5q gain and 14q loss. These secondary alterations synergized with 3p loss to restore cellular fitness, enable metabolic reprogramming, and drive subcutaneous tumor formation in vivo. Lastly, we propose a breakage-fusion-bridge model that explains the mechanistic origin of breakpoint-confined chromothripsis involving 3p. Our findings demonstrate that a single DNA break is sufficient to trigger ccRCC evolution and initiate renal cell tumorigenesis. Citation Format: Rashmi Dahiya, Ianthe Van. Belzen, Chengheng Liao, Yu-Fen Lin, Emilija Aleksandrovic, Angad Kumar, Ahyeon Ko, James Brugarolas, Siyuan Zhang, Qing Zhang, Isidro Cortés-Ciriano, Peter Ly. Breakage of chromosome 3p initiates clear cell renal cell carcinoma evolution [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr PR011.