Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4.

Introduction: KDM2B encodes a JmjC domain-containing histone lysine demethylase, which functions as an oncogene in several types of tumors, including TNBC. This study was initiated to address the cancer relevance of the results of our earlier work, which had shown that overexpression of KDM2B renders mouse embryonic fibroblasts (MEFs) resistant to oxidative stress by regulating antioxidant mechanisms.
Methods: We mainly employed a multi-omics strategy consisting of RNA-Seq, quantitative TMT proteomics, Mass-spectrometry-based global metabolomics, ATAC-Seq and ChIP-seq, to explore the role of KDM2B in the resistance to oxidative stress and intermediary metabolism. These data and data from existing patient datasets were analyzed using bioinformatic tools, including exon-intron-split analysis (EISA), FLUFF and clustering analyses. The main genetic strategy we employed was gene silencing with shRNAs. ROS were measured by flow cytometry, following staining with CellROX and various metabolites were measured with biochemical assays, using commercially available kits. Gene expression was monitored with qRT-PCR and immunoblotting, as indicated.
Results: The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors. To address the mechanism of GSH regulation, we knocked down KDM2B in MDA-MB-231 cells and we examined the effects of the knockdown, using a multi-omics strategy. The results showed that KDM2B, functioning in the context of ncPRC1.1, regulates a network of epigenetic and transcription factors, which control a host of metabolic enzymes, including those involved in the SGOC, glutamate, and GSH metabolism. They also showed that KDM2B enhances the chromatin accessibility and expression of MYC and ATF4, and that it binds in concert with MYC and ATF4, the promoters of a large number of transcriptionally active genes, including many, encoding metabolic enzymes. Additionally, MYC and ATF4 binding sites were enriched in genes whose accessibility depends on KDM2B, and analysis of a cohort of TNBCs expressing high or low levels of KDM2B, but similar levels of MYC and ATF4 identified a subset of MYC targets, whose expression correlates with the expression of KDM2B. Further analyses of basal-like TNBCs in the same cohort, revealed that tumors expressing high levels of all three regulators exhibit a distinct metabolic signature that carries a poor prognosis.
Conclusions: The present study links KDM2B, ATF4, and MYC in a transcriptional network that regulates the expression of multiple metabolic enzymes, including those that control the interconnected SGOC, glutamate, and GSH metabolic pathways. The co-occupancy of the promoters of many transcriptionally active genes, by all three factors, the enrichment of MYC binding sites in genes whose chromatin accessibility depends on KDM2B, and the correlation of the levels of KDM2B with the expression of a subset of MYC target genes in tumors that express similar levels of MYC, suggest that KDM2B regulates both the expression and the transcriptional activity of MYC. Importantly, the concerted expression of all three factors also defines a distinct metabolic subset of TNBCs with poor prognosis. Overall, this study identifies novel mechanisms of SGOC regulation, suggests novel KDM2B-dependent metabolic vulnerabilities in TNBC, and provides new insights into the role of KDM2B in the epigenetic regulation of transcription.
Competing Interests: Declaration of competing interest PNT is a co-founder of “Epi-Cure” which specializes on demethylase inhibitors. Strengths: a) Showed that KDM2B is a critical new player, in the regulation of SGOCP, a pathway with major roles in stem cell self-renewal, inflammation, angiogenesis, development and cancer, providing new insights into how KDM2B may regulate these processes; b) Showed that KDM2B has global effects on metabolism, and identified KDM2B-dependent pathways other than SGOCP; c) Provided evidence that KDM2B not only regulates the expression of MYC and ATF4, two factors with established roles in cancer and other processes, but may also regulate their function; d) Omics data provided insights into epigenetic regulation of transcription and perhaps other chromatin-regulated process. They are also a valuable resource for future studies. Weaknesses: The major weakness is that rescue experiments with wild-type and demethylase mutants of KDM2B have not been performed yet. Such experiments were delayed when we observed that the canonical KDM2B isoform has low demethylase activity, apparently because of autoinhibitory N-terminal sequences [65]. However, there are KDM2B isoforms with different N-termini, encoded by RNAs transcribed from different promoters, whose relative activity may be signal- and context-dependent. Determining the demethylase activity of different isoforms, and the conditions regulating their relative expression, is a prerequisite for meaningful rescue experiments. Translational potential: a) Identified KDM2B-dependent metabolic vulnerabilities of cancer cells, some of which, like the sensitivity to DUB inhibitors, ROS inducers and GSH-targeting molecules were confirmed; b) Linked the KDM2B/ncPRC1.1-MYC-ATF4 axis to the MPS2 subtype of TNBCs, which is associated with higher tumor grade, increased proliferation, and poor prognosis [43]. Targeting this axis can be a therapeutic strategy for these tumors; c) SGOCP plays a critical role in most cancer-types. Our data may therefore suggest therapeutic opportunities in cancers other than BRCA.
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