lncRNAs with specific tissue expression involved in the diagnosis and prognosis of various cancers

lncRNAs have been shown to be involved in cellular processes. One of their prominent features is the special and specific expression of tissue. In present study, using RNAseq data from the TCGA database for ۱۹ most common cancers, we identified lncRNAs with specific expression for each cancer as good candidates for diagnosis and prognosis for respective cancer. Therefore, RNAseq data for all ۱۹ common cancers were downloaded as raw data (HTSeq-count) and initial preprocessing and data normalization were performed with limma, edgeR and NOIseq packages. A CPM criterion of less than ۰.۵ was chosen to filter out genes with zero expression(Abbas-Aghababazadeh F et al, ۲۰۱۸). A list of all lncRNAs was obtained from the HGNC database and all the lncRNAs expressed in each cancer were extracted. The expression network showed that there are a large number of lncRNAs that have specific expression only in specific cancer, such as: breast, cervix, kidney, liver, lung, prostate, and thyroid. Also, the expression level differences between them compared to counterpart normal samples. Many of them had high diagnostic potency in distinguishing cancer samples from normal ones. Such as breast, colon, kidney, liver, lung (AUC> ۰.۹ and P <۰.۰۰۱). Also, some of them were related to the survival of patients in terms of expression, such as breast, neck and neck, kidney, liver, lung, prostate and thyroid (HR> ۱, HR <۱, P <۰.۰۰۱). Taken together, these lncRNAs could be used as a diagnostic and prognostic biomarkers. They can also be good candidates for identifying specific and common pathways in cancers and can be a good therapeutic target in cancer treatment.

کلیدواژه ها:

Bioinformatics ، R software ، cytoscape ، Prism ، Long non coding RNA