Epigenetic Silencing of PTEN and Epi-Transcriptional Silencing of MDM2 Underlied Progression to Secondary Acute Myeloid Leukemia in Myelodysplastic Syndrome Treated with Hypomethylating Agents

Abstract

In myelodysplastic syndrome (MDS), resistance to hypomethylating agents (HMA) portends a poor prognosis, underscoring the importance of understanding the molecular mechanisms leading to HMA-resistance. In this study, P39 and Kasumi-1 cells and their azacitidine-resistant and decitabine-resistant sublines were evaluated comparatively with transcriptomic and methylomic analyses. Expression profiling and genome-wide methylation microarray showed downregulation of PTEN associated with DNA hypermethylation in P39 cell lines resistant to azacitidine and decitabine. This pattern of PTEN dysregulation was also confirmed in a cohort of patients failing treatment with HMA. DNA hypomethylation of MDM2 was detected with downregulation of MDM2 in HMA resistant cell lines. Long-read sequencing revealed significant RNA hypomethylation of MDM2 resulting in alternative splicing and production of a truncated MDM2 transcript in azacitidine-resistant P39 cells. The expression of this MDM2 truncated transcript was also significantly increased in HMA-resistant patients compared with HMA-responsive patients. In conclusion, epigenetic and epi-transcriptomic dysregulation of PTEN and MDM2 were associated with resistance to hypomethylating agents.

Contingent Synergistic Interactions between Non-Coding RNAs and DNA-Modifying Enzymes in Myelodysplastic Syndromes

“…Recently HOTAIR-lncRNA was shown to positively influence DNMT3B activity and increase methylation levels of Phosphatase and Tensin-Like protein's gene PTEN and HOAX5 in AML [77,78]. PTEN has been shown to be associated with HMA resistance in MDS and progression to AML, suggesting that it might represent a potential target for treatment in combination with HMAs [79]. Another homeobox (HOX) antisense transcript, HOTAIRM1-lncRNA, has been implicated to cell autophagy and enhanced cell proliferation in leukemic cells and has been associated with adverse prognosis in adult NPM1 (nucleophosmin)-mutated AML [80,81].…”

“…Additionally, miRNA-29b, down-regulates indirectly and directly DNMT1 and DNMT3A/3B expression respectively in AML patients [96] and along with miRNA-29a cooperatively target DNMT3A/3B expression in lung cancer [97], while they are both down-regulated in AML [98]. MiR-185 and miR-152, act by suppressing DNMT1 activity in hepatocellular carcinoma cells [99] and prostate cancer respectively [100], promoting PTEN expression, also shown to be associated with HMA resistance in MDS [79]. Another DNMT1-inhibitor examined in prostate cancer cells [101], miRNA-342, is downregulated in AML [102].…”

Adding the epigenomic signature to the prognostic jigsaw of myelodysplastic neoplasm?

“…Whether the long‐term hypomethylating effects of HMA induce activation of proto‐oncogenes driving disease progression or preferentially select resistant leukaemic clones remains largely unanswered. Furthermore, the impact of HMA on RNA modification that has shown to be associated with HMA resistance 8 has not be comprehensively assessed.…”