The fanconi anemia pathway restrains MLL-rearranged leukemogenesis through suppressing NHEJ-mediated genomic instability

Abstract Genetic rearrangements involving the mixed lineage leukemia (MLL) gene give rise to MLL-rearranged (MLL-r) leukemia, which compromise approximately 10% of all acute leukemia, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). The risk of developing devastating AML is markedly elevated in individuals with Fanconi anemia (FA), a hereditary genetic disorder marked by defective DNA damage repair (DDR) and genomic instability. Despite their individual contributions to leukemogenesis, the mechanistic interplay between these MLL-r and FA pathway deficiency remains poorly understood. Using murine models and human MLL-r leukemia cells, here we demonstrate that FA pathway exerts a critical tumor-suppressive role by curbing error-prone non-homologous end joining (NHEJ)-mediated genomic instability. Genetic ablation of FA components profoundly accelerates leukemogenesis, drives leukemic stem cell (LSC) expansion, and leads to excessive DNA damage accumulation through hyperactive NHEJ. Notably, pharmacological inhibition of NHEJ selectively compromises the survival and clonal propagation of FA-deficient MLL-r leukemia cells, uncovering a synthetic lethal interaction that can be exploited using existing chemotherapy agents. Transcriptomic and clinical analysis of primary patient samples further reveal that reduced FA pathway gene expression correlates with poor prognosis and increased sensitivity to NHEJ inhibition. Mechanistically, FA proteins inhibit the recruitment of NHEJ machinery to the N-terminal region of the MLL fusion protein, thereby restraining aberrant NHEJ activity in MLL-r leukemia. Together, these findings identify a previously unrecognized role for the FA pathway in safeguarding genomic integrity in MLL-r leukemia and establish NHEJ blockade as a compelling and targeted therapeutic strategy for treating high-risk MLL-r leukemias.