Deciphering ceRNA Networks in AML Focused on NPM۱ Mutation

Acute Myeloid Leukemia (AML) is characterized by multiple mutations, with NPM۱ gene mutations being the most frequent. These mutations, particularly cytoplasmic dislocation variations, contribute to leukemogenesis by altering cellular pathways and are associated with distinct clinical features. NPM۱ mutations affect prognosis and provide insights for new therapies. They cause aberrant cytosolic localization of NPM۱ protein, leading to misfolding and loss of standard functions. This study uses in-silico transcriptomics analysis and computational methods to interpret NPM۱ mutation profile datasets, focusing on structural and functional consequences and implications for disease pathogenesis and clinical outcomes. Methods: Through Differential Expressed Genes (DEG), miRNAs (DEM), and lncRNAs (DElncRNAs) analysis, significant genes and non-coding RNAs were identified based on mutated and wild-type NPM۱ groups. We investigated Competitive endogenous RNA (ceRNA) networks, intricates interplay between lncRNAs, miRNAs, and mRNAs, focusing on the NPM۱ mutation associated with key RNA molecules in AML development. Additionally, we identified significant miRNA-lncRNA interaction’s binding site using TargetScanHuman web tool. To understand the biological relevance of hub genes targeted by central miRNAs, functional annotation and enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, as well as Gene Set Enrichment Analysis (GSEA) were conducted. Protein-protein interaction (PPI) network based on hub DEGs was conducted and analyzed by MCODE algorithm in Cytoscape. Prognostic survival risk analysis was conducted using COX regression. Results: Our findings reveal hsa-miR-۴۶۶ plays a central role in the ceRNA network significantly, which is defined by centrality parameters including MCC, Degree, Betweenness, and Closeness, representing as a central source node interacting to more targets with high degree and centrality scores. Besides, we identified lncRNA MIR۱۹۱۵HG as a crucial lncRNA within ceRNA network with high centrality rank, showing significant down-regulated expression in samples with mutated NPM۱. We identified binding site of MIR۱۹۱۵HG ‒hsa-miR-۴۶۶ interaction as a conserved ۸mer target site (۳' UTR: AUGUGUAA). Significant functional enrichment annotations of hub gene targets of hsa-miR-۴۶۶, and hub proteins, released from MCODE PPI module, demonstrated Neutrophil Extracellular Traps (NETs) formation, and aspects of DNA/protein structure and interactions based on mutated NPM۱ samples (p.value < ۰.۰۵). In survival prognosis analysis, NPM۱ mutation showed low survival rates of patients with mutation and the patients’ number decreased drastically during the time more than non-mutation groups. Furthermore, down-regulated key gene H۲BC۱۴ in the ceRNA network (key protein HIST۱H۲BM in PPI network) in samples with NPM۱ mutation represented a significant effect on survival rates and revealed very poor prognosis associated with high risk of death (p.value=۰.۰۲). Conclusion: To sum up, our research provides insights into the complex ceRNA network in AML and highlights the potential roles of crucial genes, miRNAs, and lncRNAs in AML development and progression. Our study also sheds light on the effects of NPM۱ mutation on altering cellular pathways and influencing clinical outcomes. We found that NPM۱ mutations are associated with lower survival rates and poorer prognosis. These findings underscore the significance of NPM۱ mutations in AML and suggest potential avenues for innovative targeted therapy.

کلیدواژه ها:

NPM۱ ، transcriptomics ، AML ، non-coding RNA ، ceRNA network