Transcriptional alterations of protein coding and noncoding RNAs in triple negative breast cancer in response to DNA methyltransferases inhibition

Abstract

Background DNA methylation plays a crucial role in multiple cellular processes such as gene regulation, chromatin stability, and genetic imprinting. In mammals, DNA methylation is achieved by DNA methyltransferases (DNMTs). A number of studies have associated alterations in DNMT activity to tumorigenesis; however, the exact role of DNMTs in shaping the genome in triple negative breast cancer (TNBC) is still being unraveled. Methods In the current study, we employed two DNMT inhibitors (Decitabine and 5-Azacytidine), two TNBC models (MDA-MB-231 and BT-549) and whole transcriptome RNA-Seq and characterized the transcriptional alterations associated with DNMT inhibition. Colony forming unit (CFU), flow cytometry, and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. Ingenuity pathway analysis (IPA) was used for network and pathway analyses. Results Remarkably, DNMT inhibition induced the expression of genes involved in endoplasmic reticulum response to stress, response to unfolder protein, as well as cobalamin metabolic processes. In contrast, suppression of cellular processes related to cell cycle and mitosis were hallmarks of DNMT inhibition. Concordantly, DNMT inhibition led to significant inhibition of TNBC cell proliferation, G2-M cell cycle arrest and induction of cell death. Mechanistically, DNMT inhibition activated TP53, NUPR1, and NFkB (complex) networks, while RARA, RABL6, ESR1, FOXM1, and ERBB2 networks were suppressed. Our data also identified the long noncoding RNA (lncRNA) transcriptional portrait associated with DNMT inhibition and identified 25 commonly upregulated and 60 commonly downregulated lncRNAs in response to Decitabine and 5-Azacytidinec treatment in both TNBC models. TPT1-AS1 was the most highly induced (6.3 FC), while MALAT1 was the most highly suppressed (− 7.0 FC) lncRNA in response to DNMT inhibition. Conclusions Taken together, our data provides a comprehensive view of transcriptome alterations in the coding and noncoding transcriptome in TNBC in response to DNMT inhibition.

Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome

“…3G). In cells treated with either AZA or CL alone, a signi cant reduction in global 5mC levels was observed as expected 43 , but when NO was present during either CL or AZA treatment, 5mC levels remained elevated (Fig. 3H).…”

The lncRNA TPT1-AS1 promotes the survival of neuroendocrine prostate cancer cells by facilitating autophagy

“…Our previous study involving REST knockdown transcriptomic analysis combined with siRNA screening also identified TPT1-AS1 as another potential REST-repressed neuroendocrineassociated lncRNA [24]. TPT1-AS1 has been Am J Cancer Res 2024;14(5):2103-2123 studied extensively and is recognized as a tumor-associated lncRNA with varying expression levels in different types of cancer [38][39][40][41][42][43][44][45][46][47]63]. To comprehensively assess its expression in various cancers, we analyzed TPT1-AS1 levels in clinical samples from the TCGA database.…”

BUB1 regulates non-homologous end joining pathway to mediate radioresistance in triple-negative breast cancer

“…Although, we have not confirmed the mechanism of pDNAPKcs stabilization by BUB1, we are tempted to speculate that known (RNF144A (54), MARCH5 (55), CRL4ADTL (56)) or yet unrelated E3-ubiquitin ligase(s) may be involved. Although tumor suppressor protein P53 (p53) has been linked to BUB1 expression (57), the data has been lacking that demonstrated BUB1 protein regulation by radiotherapy. Our cycloheximide chase assays clearly demonstrates that BUB1 is stabilized upon RT while pretreatment with BUB1i or DNAPKi reverses this and causes BUB1 degradation after irradiation ( Fig.…”