Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profile in Myelodysplastic Syndromes

Background Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid malignancies. The incidence of MDS is gradually increasing, but the pathogenesis is still not very clear. Studies have shown that long non-coding RNAs (lncRNAs) play a critical role in both oncogenic and tumor-suppressive pathways. However, the function of lncRNAs in MDS is still unknown. The purpose of this study was to investigate the expression profiles and biological function of the aberrantly expressed lncRNAs and mRNAs in MDS. Methods We downloaded two data sets (GSE4619 and GSE19429) from the Gene Expression Omnibus database and obtained differentially expressed (DE) lncRNAs and DE-mRNAs between MDS cases and healthy controls. Then we performed systematic bioinformatics analysis to know the biological function of DE-lncRNAs and DE-mRNAs in MDS. Results We identified 40 DE-lncRNAs and 643 DE-mRNAs between MDS cases and healthy controls. Gene Ontology (GO) and pathway analysis revealed that DE-lncRNAs and DE-mRNAs were mainly involved in necroptosis, apoptosis, immunodeficiency, p53 and FoxO signaling pathways. LncRNA-mRNA co-expression and lncRNA functional similarity network showed that twelve down-regulated lncRNAs co-regulated the same target gene and they were similar in function. Conclusions The comprehensive analysis of lncRNA and mRNA is helpful in understanding the pathogenesis of MDS, and the synergistically down-regulated lncRNAs may contribute to the development of new diagnostic and therapeutic strategies.