Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach

Abstract

We tested the hypothesis that the effects on gene expression of altered DNA methylation by 5-aza-2'-deoxycytidine (5-aza-CdR) and genetic (DNMT knockout) manipulation of DNA are similar, and distinct from Trichostatin A (TSA)-induced chromatin decondensation. Surprisingly, the effects of 5-aza-CdR were more similar to those of TSA than to DNMT1, DNMT3B, or double DNMT somatic cell knockout. Furthermore, the effects of 5-aza-CdR were similar at one and five days exposure, suggesting active demethylation or direct influence of both drugs on the stability of methylation and/or chromatin marks. Agents that induce gene activation through hypomethylation may have unintended consequences, since nearly as many genes were downregulated as upregulated after demethylation. In addition, a 75 kb cluster of metallothionein genes was coordinately regulated.

Cigarette smoke induces demethylation of prometastatic oncogene synuclein-γ in lung cancer cells by downregulation of DNMT3B

“…Altered expressions of DNMTs have been linked to the cancer-associated hypermethylation of TSGs (Gius et al, 2004;Suzuki et al, 2004;Pruitt et al, 2005;Oka et al, 2006), as well as the hypomethylation of melanoma antigen gene MAGE-A1 (Loriot et al, 2006). We sought to determine which DNMT was involved in CSE-induced changes in the methylation pattern of SNCG.…”

Epigenetic silencing of HSulf-1 in ovarian cancer:implications in chemoresistance

“…Two chemical agents commonly used to modulate the expression of silenced genes in cancer cells are 5-aza-2 0 -deoxycytitdine (5-aza-dC), which is an inhibitor of DNA methylation and trichostatin A (TSA), an inhibitor of histone deacetylation (Marks et al, 2001;Johnstone, 2002;Yamashita et al, 2002). Gene expression studies revealed that the effects of 5-aza-dC are similar to those of TSA exposure than either of the somatic cell DNA methyltransferase knockouts (DNMT knockouts), implying a converging mechanism for these agents (Gius et al, 2004).…”

Epigenetic regulation of protein tyrosine phosphatases: potential molecular targets for cancer therapy

“…51 Second, recent microarray analysis of human colon cancer cells (HCT116) revealed alterations in the gene expression profiles of 5-AzaC-treated cells irrespective of growth stage. 57 It also appears that among three DNMTs only DNMT1 is the target of 5-AzaC. Since gene expression profile of the inhibitor-treated HCT116 cells is similar to that of DNMT1 null cells, DNMT1 is likely to be the preferential target of 5-azaC.…”

“…Since gene expression profile of the inhibitor-treated HCT116 cells is similar to that of DNMT1 null cells, DNMT1 is likely to be the preferential target of 5-azaC. 57 This observation is consistent with our earlier report that DNMT1 is selectively and rapidly degraded in animal cells following exposure to 5-azaC. 58 Recent study in our laboratory has shown that this selective degradation of DNMT1 is mediated by the proteasomal pathway (K Ghoshal and S Jacob, unpublished data), which offers an alternative mechanism of action for these potent anticancer drugs.…”

“…58 In this study, the synergistic effects of the two classes of drugs in the MT-I re-expression was found to be due to promoter demethylation, altered association of different factors that leads to reorganization of the chromatin, and the resultant increase in accessibility of the promoter to the activated transcription factor MTF-1. 58 It is noteworthy that the whole MT locus comprising of MT-IV, MT-III, MT-IIA and several isoforms of MT-I on human chromosome 16q13 are reactivated upon treatment with this drug, 57 probably due to open chromatin structure.…”