title: DNA-intercalators causing rapid re-expression of methylated and silenced genes in cancer cells.
abstract: Epigenetic inactivation of tumor-suppressor and other regulatory genes plays a critical role in carcinogenesis. Transcriptional silencing is often maintained by DNA methyl transferase (DNMT)-mediated hypermethylation of CpG islands in promoter DNA. Nucleoside analogs including azacytidine and decitabine have been used to inhibit DNMT and re-activate genes, and are clinically used. Their shortcomings include a short half-life and a slow onset of action due to required nucleotide incorporation during DNA replication, which may limit clinical utility. It might be useful to begin to identify lead compounds having novel properties, specifically distinct and fast-acting gene desilencing. We previously identified chemicals augmenting gene expression in multiple reporter systems. We now report that a subset of these compounds that includes quinacrine re-expresses epigenetically silenced genes implicated in carcinogenesis. p16, TFPI2, the cadherins E-cadherin and CDH13, and the secreted frizzle-related proteins (SFRPs) SFRP1 and SFRP5 were desilenced in cancer cell lines. These lead compounds were fast-acting: re-expression occurred by 12-24 hours. Reactivation of silenced genes was accompanied by depletion of DNMT1 at the promoters of activated genes and demethylation of DNA. A model compound, 5175328, induced changes more rapidly than decitabine. These gene desilencing agents belonged to a class of acridine compounds, intercalated into DNA, and inhibited DNMT1 activity in vitro. Although to define the mechanism would be outside the scope of this initial report, this class may re-activate silenced genes in part by intercalating into DNA and subsequently inhibiting full DNMT1 activity. Rapid mechanisms for chemical desilencing of methylated genes therefore exist.
authors.affiliation: Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: M Zulfiquer
authors.initials: MZ
authors.lastname: Hossain
authors.forename: Megan A
authors.initials: MA
authors.lastname: Healey
authors.forename: Calvin
authors.initials: C
authors.lastname: Lee
authors.forename: Weijie
authors.initials: W
authors.lastname: Poh
authors.forename: Sashidhar R
authors.initials: SR
authors.lastname: Yerram
authors.forename: Kalpesh
authors.initials: K
authors.lastname: Patel
authors.forename: Nilofer S
authors.initials: NS
authors.lastname: Azad
authors.forename: James G
authors.initials: JG
authors.lastname: Herman
authors.forename: Scott E
authors.initials: SE
authors.lastname: Kern
mesh_terms: D000166:Acridines / Q000494:pharmacology; D000818:Animals; D016466:CHO Cells; D045744:Cell Line, Tumor; D006224:Cricetinae; D003412:Cricetulus; D004247:DNA / Q000187:drug effects; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000037:antagonists & inhibitors / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects*; D057890:Epigenomics; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D020868:Gene Silencing / Q000187:drug effects*; D016147:Genes, Tumor Suppressor / Q000187:drug effects*; D045325:HCT116 Cells; D006801:Humans; D007364:Intercalating Agents / Q000494:pharmacology*
chemical_list: D000166:Acridines; D007364:Intercalating Agents; D004247:DNA; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; C000619380:DNMT1 protein, human