Identification of deregulated lncRNAs incervical cancer using RNA-Seq data analysis

Background: Long non-coding RNAs (lncRNAs) are a groupof RNAs with more than ۲۰۰ nucleotides involved in geneexpression regulation at different levels including chromatinremodeling, epigenetics, transcription, and translation. Theexpression profile of lncRNAs alters in cervical cancer. Theinvestigation of deregulated lncRNAs helps the identificationof new biomarkers for the diagnosis and treatment of cervicalcancer. In this study, deregulated lncRNAs in cervical cancerwere identified by RNA-Seq data analysis.Materials and Methods: The raw sequence RNA-Seq dataof ۱۲ samples including ۶ pairs of cervical tumor (SquamousCell Carcinoma (SCC)) and their matched normal tissue fromGSE۱۴۷۰۰۹ dataset was downloaded from SRA database andconverted to fastq files using SRA Toolkit. After quality controlusing FastQC, trimming of raw NGS data was carried out usingthe Trim-Galore tool. The alignment was performed usingHISAT۲ aligner and its index file and Sam files were obtained.Annotation GTF file downloaded from GENCODE databaseand Sam files were used for the preparation of lncRNA countfiles. Analysis of count files was performed in the RStudioprogram using the DESeq۲ package and deregulated lncRNAswere detected.Results: RNA-Seq data analysis indicated the down-regulationof ۴۰۹ lncRNAs and the up-regulation of ۴۵۸ lncRNAs. TheLINC۰۲۰۴۲ had the highest up-regulation (log۲FoldChange =۶.۹۵, padj = ۰.۰۰۰۰۵), and the AC۰۱۵۸۴۹.۱۳ had the highestdown-regulation (log۲FoldChange = -۶.۶۳, padj = ۰.۰۰۴۷) incervical cancer.Conclusion: LINC۰۲۰۴۲ and AC۰۱۵۸۴۹.۱۳ can be potentialbiomarkers and therapeutic targets for cervical cancer

کلیدواژه ها:

LINC۰۲۰۴۲ ، AC۰۱۵۸۴۹.۱۳ ، Biomarker ، RNA-Seq ، lncRNAs