en Molecular Genetics & Genomics Molecular Genetics & Genomics مقاله کامل Full Length/Original Article <div style="text-align: justify;"><span style="font-family:Times New Roman;"><span style="font-size:11pt"><span style="line-height:normal"><span sans-serif=""><b><span style="font-size:10.5pt"><span new="" roman="" times="">Background: </span></span></b><span style="font-size:10.5pt"><span new="" roman="" times="">Hypoxic tumor microenvironment is one of the important impediments for conventional cancer therapy. This study aimed to computationally identify hypoxia-related messenger RNA (mRNA) signatures in nine hypoxic-conditioned cancer cell lines and investigate their role during hypoxia. </span></span><br> <b><span style="font-size:10.5pt"><span new="" roman="" times="">Methods: </span></span></b><span style="font-size:10.5pt"><span new="" roman="" times="">Nine </span></span><span lang="EN-GB" style="font-size:10.5pt"><span new="" roman="" times="">RNA sequencing</span></span><span style="font-size:10.5pt"><span new="" roman="" times=""> (RNA-Seq) expression data sets were retrieved from the Gene Expression Omnibus database. D</span></span><span lang="EN-GB" style="font-size:10.5pt"><span new="" roman="" times="">i</span></span><span lang="EN-GB" style="font-size:10.5pt">ff</span><span lang="EN-GB" style="font-size:10.5pt"><span new="" roman="" times="">erentially expressed genes</span></span><span style="font-size:10.5pt"><span new="" roman="" times=""> (DEGs) were identified in each cancer cell line. Then 23 common DEGs were selected by comparing the gene lists across the nine cancer cell lines. </span></span><span lang="EN-GB" style="font-size:10.5pt"><span new="" roman="" times="">Reverse transcription-quantitative PCR</span></span><span style="font-size:10.5pt"><span new="" roman="" times=""> (qRT-PCR) was performed to validate the identified DEGs.&nbsp; </span></span><br> <b><span style="font-size:10.5pt"><span new="" roman="" times="">Results: </span></span></b><span style="font-size:10.5pt"><span new="" roman="" times="">By comparing the data sets, GAPDH, LRP1, ALDOA, EFEMP2, PLOD2, CA9, EGLN3, HK, PDK1, KDM3A, UBC, and P4HA1 were identified as hub genes. In addition, miR-335-5p, miR-122-5p, miR-6807-5p, miR-1915-3p, miR-6764-5p, miR-92-3p, miR-23b-3p, miR-615-3p, miR-124-3p, miR-484, and miR-455-3p were determined as common micro RNAs. Four DEGs were selected for mRNA expression validation in cancer cells under normoxic and hypoxic conditions with qRT-PCR. The results also showed that the expression levels determined by qRT-PCR were consistent with RNA-Seq data. </span></span><br> <b><span style="font-size:10.5pt"><span new="" roman="" times="">Conclusion: </span></span></b><span style="font-size:10.5pt"><span new="" roman="" times="">The identified </span></span><span lang="EN-GB" style="font-size:10.5pt"><span new="" roman="" times="">protein-protein interaction</span></span><span style="font-size:10.5pt"><span new="" roman="" times=""> network of common DEGs could serve as potential hypoxia biomarkers and might be helpful for improving therapeutic strategies.</span></span></span></span></span></span><span style="font-size:11pt"><span style="line-height:normal"><span sans-serif="" style="font-family:Calibri,"><span style="font-family:"Times New Roman","serif""></span></span></span></span></div> Hypoxia, MicroRNA, RNAseq 23 33 http://ibj.pasteur.ac.ir/browse.php?a_code=A-10-4885-2&slc_lang=en&sid=1 Sara Shayan sarashayaan@gmail.com 0000-0002-8110-0489 No Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran Golnaz Bahramali gbhramali@gmail.com 0000-0002-1762-4907 No Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, Tehran, Iran Arash Arashkia arash.arashkia@gmail.com 0000-0002-3117-3217 No Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran Kayhan Azadmanesh k.azadmanesh@gmail.com 0000-0002-7165-9043 Yes Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran