Identification of prognostic biomarkersand therapeutic targets in sigmoid and descending colon cancer for personalized medicine

Background: Colorectal cancer (CRC) is the third most commoncancer in males and the second most common in females,with approximately ۱.۹ million new cases and ۰.۹ million deathsin ۲۰۲۰ worldwide (۱). CRC incidence has increased in recentyears. It represents approximately ۱۰% of all cancers and is thesecond most frequent cause of cancer deaths (۲,۳). Therefore,CRC is a global public health challenge in terms of morbidity,mortality, and utilization of health care services, includingincreasingly high medical costs (۴). The aim of this study is todetect biomarkers in sigmoid and descending colon cancer fortherapeutic targets in personalized medicine.Materials and Methods: SRP۲۶۸۱۴۴ dataset was downloadedfrom NCBI>SRA, the sra file was converted to two fastq pairedfiles with sratoolkit.۲.۱۱.۳-ubuntu۶۴ software under Linux.Quality control of fastq files was performed with FASTQC software,and low quality reads were trimmed with Trimmomaticsoftware and we mapped the trimmed file to GRCH۳۸_genomeusing Hisat۲ software and a sam file was obtained. In the nextstep, we converted the sam file to counts files using hg۳۸.ncbi.refseq.gtf and finally, DEGs were identified using the DESeq۲package in R Studio software by threshold (log۲foldchange>۱).Results: Based on the results, in the sigmoid colon cancer comparedto descending colon cancer, upregulated genes includes:SLIT۳-AS۲, FGF۳, FAHD۲CP, LAMP۵-AS۱, KRT۴۳P anddownregulated genes includes: CTTNBP۲, CFAP۷۴, MGAM,TRIML۱, LOC۱۰۵۳۷۲۶۵۷.Conclusion: Due to the important role of SLIT۳-AS۲ andCTTNBP۲ in cell proliferation, differentiation, apoptosis andsignaling pathways, genes that up and down expression in thesigmoid colon cancer and descending colon cancer, were usedfor prevention, diagnosis and treatment in patients with coloncancer.