Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistance

Abstract

Lysine demethylase 5A (KDM5A/RBP2/JARID1A) is a histone lysine demethylase that is overexpressed in several human cancers including lung, gastric, breast and liver cancers. It plays key roles in important cancer processes including tumorigenesis, metastasis, and drug tolerance, making it a potential cancer therapeutic target. Chemical tools to analyze KDM5A demethylase activity are extremely limited as available inhibitors are not specific for KDM5A. Here, we characterized KDM5A using a homogeneous luminescence-based assay and conducted a screen of about 9,000 small molecules for inhibitors. From this screen, we identified several 3-thio-1,2,4-triazole compounds that inhibited KDM5A with low μM in vitro IC50 values. Importantly, these compounds showed great specificity and did not inhibit its close homologue KDM5B (PLU1/JARID1B) or the related H3K27 demethylases KDM6A (UTX) and KDM6B (JMJD3). One compound, named YUKA1, was able to increase H3K4me3 levels in human cells and selectively inhibit the proliferation of cancer cells whose growth depends on KDM5A. As KDM5A was shown to mediate drug tolerance, we investigated the ability of YUKA1 to prevent drug tolerance in EGFR-mutant lung cancer cells treated with gefitinib and HER2+ breast cancer cells treated with trastuzumab. Remarkably, this compound hindered the emergence of drug-tolerant cells, highlighting the critical role of KDM5A demethylase activity in drug resistance. The small molecules presented here are excellent tool compounds for further study of KDM5A's demethylase activity and its contributions to cancer.

An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting

“…KDM5 family proteins, KDM5A (RBP2), KDM5B (PLU1), KDM5C (SMCX) and KDM5D (SMCY), are mammalian demethylases for trimethylated lysine 4 of histone H3 (H3K4me3), an epigenetic mark associated with transcriptional activation (46–49). KDM5D is located on the Y chromosome, so only KDM5A, 5B and 5C H3K4me3 demethylases are present in cells isolated from females.…”

Hypoxia Promotes Resistance to EGFR Inhibition in NSCLC Cells via the Histone Demethylases, LSD1 and PLU-1

“…Histone demethylases and their associated chromatin modulations have been linked to EGFR TKIs resistance in NSCLC cells (24,25). In addition, PLU-1 has been reported to promote drug resistance in melanomas (26) and to drive metastasis and EMT in hepatocellular cancer cells (27), while LSD1 has been shown to promote invasion and metastasis through facilitating EMT in many cancer cell types (28–30).…”

KDM5 lysine demethylases are involved in maintenance of 3′UTR length

“…6D), supporting the notion that the demethylase activity of KDM5 family members is involved in APA regulation of DICER1 . To determine which KDM5(s) contribute to this regulation, we deleted KDM5A, KDM5B, and KDM5C individually using an inducible CRISPR (clustered regularly interspaced short palindromic repeats) system ( 51 , 52 ) and found that deletion of KDM5A or KDM5B, but not KDM5C, decreased 3′UTR length of DICER1 (Fig. 6E), suggesting that both KDM5A and KDM5B are involved in APA regulation.…”