Identification of novel long noncoding RNA with distinct expression patterns in different subtypes of multiple myeloma

Evidence has accumulated regarding the association of some types of long noncoding RNA (lncRNAs) with severity and progression of multiple myeloma (MM). In this study, we explore the expression of novel lncRNA in different molecular subtypes of MM and examine their correlation with the prognosis of the patient. Whole transcriptome RNA sequencing of 643 newly diagnosed MM samples was performed. De novo and reference guided transcript assembly pipelines were used for RNA-seq data processing and discovery of novel lncRNAs in MM. We identified 8,556 potentially novel lncRNA transcripts expressed in patients with MM. Of these, 1,264 novel transcripts showed significant differential expression between the different molecular subtypes of MM. Through bioinformatic analysis, we identify their potential targets and roles in MM. Functional enrichment analysis of nearby coexpressed genes was used to predict involved pathways. The function was also inferred by comparing the k-mer content with known lncRNAs. Two of the novel lncRNAs had a significant association with progression free survival and/or overall survival. In conclusion, we identified many novel lncRNAs, describe their expression pattern among different genetic subtypes of MM and provide evidence of their potential role in the pathogenesis, progression, and prognosis of the disease.