• Identification of DEGs in colon adenocarcinoma with peroxiredoxin2 enzyme siRNA transfected to HT29 and SW480 cells using RNA-Seq data
  • Seyed Taleb Houseini,1 Saeedeh saderi oskoiee,2 arash sattari,3 Mansoureh Azadeh,4 Roya BishehKolaei,5 Farkhondeh Nemati,6,*
    1. Department of Biology, Faculty of Basic sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
    2. Department of Medical science, Faculty of medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
    3. Department of Medical laboratory sciences, Faculty of medical sciences, Gorgan Brach, Islamic Azad University, Gorgan, Iran
    4. ZistFanavari Novin Biotechnology Institute, Isfahan, Iran
    5. Department of Biology, Faculty of Basic sciences, Qaemshahr Bransch, Islamic Azad University, Mazandaran, Iran
    6. Department of Biology, Faculty of Basic sciences, Qaemshahr Bransch, Islamic Azad University, Mazandaran, Iran


  • Introduction: Colorectal cancer (CRC) is a common malignant disease with high morbidity and mortality. Many researches have demonstrated that PRDX2 play an important part in various biological functions, such as the protection effects for intracellular lipids and proteins and the mediation role for cellular signaling pathways associated with cell proliferation, apoptosis and differentiation. In addition, overexpression of PRDX2 has been reported in various cancer tissues and cells, which is essential for tumor maintenance and survival by protecting cells against ROS injury and apoptosis. The aim of this study was to evaluate the expression of genes in the presence and absence of peroxiredoxin2 enzyme in HT29 and SW480 cells.
  • Methods: SRP075061 dataset was downloaded from NCBI>SRA, the sra file was converted to two fastq paired files with sratoolkit.2.11.3-ubuntu64 software under Linux. Quality control of fastq files was done with FASTQC software, and low quality reads were trimmed with Trimmomatic software and we mapped the trimmed file to hg38_genome using Hisat2 software and a sam file was obtained. In the next step, we converted the sam file to counts files using hg38.ncbi.refseq.gtf and finally, DEGs were identified using the DESeq2 package in R Studio software by threshold(FDR:0.05 and log2foldchange>1)
  • Results: Based on the results, in the HT29 cell line (control and siRNA transfected), upregulated genes include: ATL2, SNX2O, NSL1 and downregulated genes include: ND5, COX1, ATP6. In cell line SW480 (control and siRNA transfected) SLC9A3, SLC9A3-AS1, IL7R are upregulated genes and NECAP1, HMGCS1, KRT1 are downregulated genes.
  • Conclusion: Due to the important role of peroxiredoxin2 enzyme in cell proliferation, differentiation, apoptosis and signaling pathways, genes that up and down expression in the presence and absence of peroxiredoxin2 enzyme in cell, were used for prevention, diagnosis and treatment in patients with colorectal cancer.
  • Keywords: Colorectal cancer, peroxiredoxin2 enzyme, HT29, SW480