RNA epigenetic and mitochondrial signatures of azacitidine response in higher-risk myelodysplastic syndromes

ABSTRACT: Azacytidine (AZA) treatment for higher-risk myelodysplastic syndromes (HR-MDS) has been extensively used in the clinic but its role goes beyond the DNA de-methylation and reactivation of critical genes silenced by DNA methylation. Among other mechanisms implicated to AZA mechanism of action, the documented partial restoration of chromatin structure and the recombinational repair, mainly attributed to the enhanced expression of long-noncoding RNAs highlight more stimulated epigenetic signatures. We present novel AZA effects in the epigenome that discriminate Responders from Non-Responders. Specific miRNA families significantly suppressed or upregulated, which promote the restoration of several critical cell pathways as a consequence; prostaglandin synthesis and regulation, ribosomal protein synthesis and function, glycolysis as well as response to starvation regression, offering overall unique benefits to MDS clinical phenotype of AZA Responders. Also, a trend for reduction of 2'-O-Methylguanosine (Gm) RNA modification in AZA Responders and differentiated expression patterns of other kinds of chemical modifications studied, such as methyladenosine (m6A), 5-Methylcytidine (5mC) and N1-Methyladenosine (m1A), between Responders and Non-Responders. Finally, AZA treatment significantly reduced copies of mitochondrial DNA (mtDNA) in both HR-MDS patient groups. Liquid chromatography combined with mass spectrometry (LC-MS/MS) was employed for the accurate assessment of various RNA modifications, mapping of AZA treatment-responsive regulatory pathways was performed by miRNA-NGS followed by a multi-layered bioinformatic pipeline integrating miRNA differential expression, gene set enrichment and network analysis. The precise number of mtDNA copies was evaluated by digital PCR assays. Our results support epigenetic and mitochondrial mechanisms of re-directing MDS neoplastic hematopoietic stem and progenitor cells (HSPCs) upon hypomethylating agents’ (HMA) therapy. In patients who respond to AZA, HSPCs adapt by shifting toward glycolytic metabolism and restoring ribosomal activity while reducing mtDNA content and oxidative phosphorylation (OXPHOS) dependence, supporting survival and suppression of malignant progression. Non-Responders, however, despite experiencing mtDNA depletion, seem unable to coordinate metabolic reprogramming and consequently remain metabolically disadvantaged and less responsive to AZA-therapy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE315656 | GEO | 2026/08/05

REPOSITORIES: GEO