Abstract A018: KDM4C histone demethylase connects redox balance to chromatin remodeling via histone H3 tail clipping
Authors: Li Zheqi , Peluffo Guillermo , Stevens Laura E. , Qiu Xintao , Egri Shawn B. , Papanastasiou Malvina , Kingston Natalie , D'Santos Clive S. , Papachristou Eva , Evans Kyle , Seo Ji-Heui , Clement Kendell , Temko Daniel , Ekram Muhammad , Simeonov Anton , Kales Stephen C. , Rai Ganesha , Lal-Nag Madhu , Maloney David J. , Jadhav Ajit , Michor Franziska , Meissner Alex , Carroll Jason S. , Freedman Matthew L. , Long Henry W. , Jaffe Jacob D. , Polyak Kornelia 
Published: December 2022

Abstract
Triple-negative breast cancer (TNBC) is a subtype accounting for 20-30% all breast cancer cases and is a highly aggressive disease with inferior prognosis. The acquired resistance is a major obstacle for efficient therapy and discovery of novel clinically-actionable targets has become an urgent need. In this study, we carried out an in-depth functional characterization of histone demethylase KDM4C in TNBC and uncovered a novel mechanism underlying KDM4C-driven tumorigenesis. KDM4C is the second most frequently amplified histone demethylase in TNBC. Genetic knockdown or pharmacological inhibition of KDM4C in two amplified basal breast cancer cell lines, SUM149 and HCC1954, drastically suppressed primary tumor growth in vitro and in vivo. Transcriptomic analysis underlined oxidative phosphorylation impairment as functional consequences of KDM4C blockade. Surprisingly, integrating series of histone ChIP-seq and ATAC-seq showed that KDM4C suppression caused accessible chromatin remodeling without substantial changes of its canonical substrates H3K9me3 and H3K36me3. Rather KDM4C loss caused proteolytic cleavage at histone 3 N-terminus (Ala21 site) identified by histone mass spectrometry. Protease inhibitor array pointed out cathepsin L (CTSL) as the endopeptidase mediating this procedure. KDM4C blockade induced CTSL activation and promoted H3 tail clipping at around 30% CTSL binding sites, which was associated with restricted chromatin accessibility and transcriptomic reprogramming. Proteomic interactome profiling revealed that grainyhead like transcription factor 2 (GRHL2) tightly binds to CTSL. In addition, GRHL2 knockout induced nearly complete loss of CTSL chromatin binding, demonstrating its role as a recruiter of CTSL to the chromatin. KDM4C serves as either a direct or indirect suppressor for CTSL-mediated H3 cleavage. The latter one was largely mediated by redox imbalance. Metabolomic profiling showed that KDM4C inhibition strongly dampened intracellular glutathione (GSH) levels and hence produced more reactive oxygen species (ROS) and alleviated mitochondrial respiration. This procedure was grounded on the mechanism that KDM4C blockade decreased expression of GSH synthesis rate-limiting enzyme glutamate-cysteine ligase catalytic subunit (GCLC) via CTSL-mediated H3 tail clipping. Knockout of CTSL rescued KDM4C blockade-associated metabolic dysfunction, confirming KDM4C links redox homeostasis and chromatin remodeling. Finally, we found KDM4C-CTSL-GSH axis was associated with cisplatin resistance in TNBC patients. Co-targeting KDM4C and GSH production efficiently improved cisplatin response in TNBC cells. Our study provided detailed and unbiased evidence supporting a novel non-canonical role of KDM4C in preventing CTSL-mediated histone clipping and maintaining redox balance, opening up possibilities to improve chemotherapy through targeting this circus.
Citation Format: Zheqi Li, Guillermo Peluffo, Laura E. Stevens, Xintao Qiu, Shawn B. Egri, Malvina Papanastasiou, Natalie Kingston, Clive S. D'Santos, Eva Papachristou, Kyle Evans, Ji-Heui Seo, Kendell Clement, Daniel Temko, Muhammad Ekram, Anton Simeonov, Stephen C. Kales, Ganesha Rai, Madhu Lal-Nag, David J. Maloney, Ajit Jadhav, Franziska Michor, Alex Meissner, Jason S. Carroll, Matthew L. Freedman, Henry W. Long, Jacob D. Jaffe, Kornelia Polyak. KDM4C histone demethylase connects redox balance to chromatin remodeling via histone H3 tail clipping. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A018.