Prediction of m۶A sites for pri-MiRNA-۴۷۸۴, a Probable Therapeutic Approach in Treatmentof Gastric Cancer

Background: Cancer cells have the ability to replicate withoutreaching a state of senescence. Some genes are responsible forcontrolling the pace of growth and replication of these cells.The protein encoded by FGF۲۱ gene is a member of the fibroblastgrowth factor (FGF) family. Members of the FGF familypossess broad mitogenic and cell survival activities and are involvedin a variety of biological processes including embryonicdevelopment, cell proliferation, morphogenesis, tissue repair,tumor growth and invasion. MicroRNAs (MiRNAs) are relativelynew groups of functional RNAs that have attracted theattention of many scientists in recent years due to their significantrole in the development of cancer cells. Therefore, studyingand exploring miRNAs reveals new perspectives for cancertreatment. N۶-methyladenosine (m۶A) is a post-transcriptionalmethylation modification that is prevalent at adenosine bases inRNA transcripts. This modification has been suggested to be involvedin the regulation of RNA transcript degradation, subcellularlocalization, splicing, and local conformational changes.Materials and Methods: ILLUMINA (HiSeq ۲۰۰۰) RNA seqdata for ۶ gastric cancer tumor and normal samples were extractedfrom the NCBI database and uploaded to the useGALAXYspace.The FASTQ format of each data was obtained.After quality control, the data were trimmed with the Trimmomatic tool if needed. Hisat۲ tool was used for mapping andalignment. The htseq-count tool based on the gtf file downloadedfrom genecodegenes was used to count and name thereads. Next,the data were analyzed using the DEseq۲. Aftertwo stages of data filtering, AnnotatedDEseq۲/DEXSeq outputtables tool was used to highlight meaningful data. Log۲(FC)was compared between the candidate genes. FGF۲۱ mRNA sequencewas obtained from NCBI database in FASTA format.Threre was just one variant for this gene. The ۳'UTR sequenceof this variant was selected. MiRTargetLink ۲.۰, TargetScanand MirDB were used to predict miRNAs that interact with the۳'UTR of the FGF۲۱ gene. The sequence of each miRNA wasobtained by miRbase and the interaction of each miRNA with۳’UTR was checked by RNAHybrid tool and RNA۲۲v۲. Afterconfirming the strong interaction between the miRNAs andthe ۳'UTR of the FGF۲۱ gene, the chromosome region of eachmiRNA was selected and the sequence of these miRNAs weretaken from the UCSC to find the sequence of the miRNAs beforethe splicing (Pri-MiRNA). SRAMP was used to predict them۶A methylation sites on these pri-miRNAs.Results: Based on the Log۲(FC), the differentially expressedgenes in tumor samples compared to normal ones were specified.FGF۲۱ as a downregulated gene in tumor samples, waschosen as the candidate gene. Out of overall ۲۸ predicted miRNAsrelated to FGF۲۱, all of which were analyzed, ۴ miRNAsshowed a stronger interaction with the ۳'UTR of FGF۲۱. ThesemiRNAs are respectively hsa-mir-۶۸۸۸-۵p, hsa-mir-۴۷۸۴, hsamir-۱۴۹-۵p and hsa-mir-۵۷۷. Out of these ۴ MiRNAs, only hsamir-۴۷۸۴ had a methylation site for m۶A.Conclusion: The oncogenic role of FGF۲۱ in gastric cancermakes it a potential target for miRNAs in gastric cancer therapy.

کلیدواژه ها:

MiRNA ، FGF۲۱ ، m۶A ، Gastric cancer