Bhowmik, M. C. | bioRxiv Science

bioRxiv2026

KDM7B-mediated demethylation of RNF113A regulates small cell lung cancer sensitivity to alkylation damage

Chemoresistance remains a major obstacle to effective cancer treatment, often driven by enhanced DNA repair mechanisms that enable tumor cells to withstand genotoxic therapies. One such pathway involves the atypical DNA damage repair complex ALKBH3-ASCC, activated by the E3 ligase RNF113A in response to alkylation damage. We previously showed that SMYD3-dependent methylation of RNF113A stimulates this pathway, enhancing DNA repair and promoting resistance. Here, we identify KDM7B/PHF8 as the bona fide RNF113A demethylase, establishing one of the first functional examples of a dynamic, reversible non-histone methylation event regulating genome integrity. KDM7B antagonizes SMYD3 activity by maintaining low levels of methylated RNF113A, thereby limiting ASCC activation and sensitizing cancer cells to alkylating agents. To dissect this regulation in depth, we focused on small cell lung cancer (SCLC), a particularly aggressive malignancy characterized by limited therapeutic options and rapid acquisition of resistance. In SCLC, high KDM7B levels correlate with improved patient prognosis, whereas xenografts with reduced expression exhibit diminished responses to alkylating treatment. Moreover, CRISPR-based on/off modulation of KDM7B in genetically engineered SCLC mouse models demonstrates its central role in determining tumor response to chemotherapy. Our findings position the RNF113A-ASCC axis as a central modulator of chemoresistance, regulated through a post-translational methylation switch representing an innovative therapeutic vulnerability that could be exploited to enhance the efficacy of alkylating agents. Targeting this pathway may provide new opportunities to overcome chemoresistance, with KDM7B levels serving as a predictive biomarker to guide treatment in SCLC.

cell biology↗

bioRxiv2025

Human MutLa activates methylpurine DNA glycosylase to induce alkylation damage cytotoxicity

Alkylation chemotherapy is commonly used against tumors such as glioblastoma, yet resistance often develops through downregulation of mismatch repair (MMR). Previous work has established that loss of MMR prevents the excision of the thymine-containing strand across O6meG-T mismatches. Thus, MMR dysfunction is advantageous because it prevents a vicious cycle of attempted repair that leads to cell death. Here, we provide an alternative explanation to this prevailing mechanism of alkylation chemoresistance by MMR loss. We find that the MMR protein MutL physically and functionally interacts with the base excision repair (BER) enzyme methylpurine DNA glycosylase (MPG), which processes common alkylation adducts, such as 7meG and 3meA. Biochemical reconstitution demonstrates that MutL activates MPG glycosylase activity at least partly by promoting MPG substrate binding. This glycosylase stimulation requires ATP hydrolysis as well as the MLH1-interacting region on MPG. Both MutL or its ability to interact with MPG promote the generation of alkylation-induced abasic sites in cells, which contribute to the cytotoxicity of methyl methanesulfonate (MMS), an SN2 alkylating agent which does not produce O6meG. Our results provide new insight into the mechanism of alkylation chemoresistance and uncover an unappreciated crosstalk between MMR and base excision repair.

biochemistry↗