Evaluation of Epithelial-Mesenchymal Transition Genes Involved in Iranian Gastric Cancer Patients via Transcriptome Analysis

Abstract

Background: Gastric cancer is one of the most frequent cancers among men and women. Patients with gastric cancer are mostly diagnosed in advanced stages because of asymptomatic progression. Due to the heterogeneity and poor prognosis of this cancer, a comprehensive study at the transcriptome level gene expression is needed to find the various genes and mechanisms involved in gastric cancer. Differentially expressed genes (DEG) derived from high-throughput RNA-sequencing could lead to the achievement of new molecular biomarkers. Objectives: In this study, after transcriptome reanalysis, we focused on the genes involved in epithelial-mesenchymal transition (EMT) via extracellular matrix (ECM). We have aimed at finding mRNA level changes in new candidate genes among Iranian patients with gastric cancer. Methods: Six gastric cancer and two normal sequencing raw sample datasets were collected from the European Nucleotide Archive (ENA). The bioinformatic pipeline was used to reanalyze raw datasets and get DEGs, using the DESeq2 package. After analyzing, THBS2, OSMR, and CHI3L1 genes were selected for validation and verification in 25 confirmed adenocarcinoma gastric cancer patients and non-malignant normal tissues from the Iranian population by real-time polymerase chain reaction (PCR). Results: The bioinformatic analysis of raw datasets revealed many upregulated and downregulated genes in gastric cancer tissues compared with normal samples. Then, real-time PCR verified the upregulation of THBS2, OSMR, and CHI3L1 genes in a group of Iranian patients with gastric cancer. Analyzing graphs showed a significant increase in the expression of targeted genes in patients with gastric cancer (P < 0.0001, P = 0.0016, and P = 0.0002, respectively). Conclusions:The results validated an obvious increase in the expression of THBS2, OSMR, and CHI3L1 genes in gastric cancer of Iranian patients. These genes are involved in EMT and may have a role in cancer invasion if tested further for their diagnostic and prognostic value in larger sample sizes.

The pseudogenes of eukaryotic translation elongation factors (EEFs): Role in cancer and other human diseases

“…), leukemia (?) 87 , 107 ' EEF1A1P30 EEF1A1 pseudogene 30 X Xq24 2354 – EEF1A1P31 108 EEF1A1 pseudogene 31 Unprocessed pseudogene X Xq28 10,389 – EEF1A1P32 EEF1A1 pseudogene 32 1 1q31.3 2156 Oral squamous cell carcinoma 74 EEF1A1P33 EEF1A1 pseudogene 33 Processed pseudogene 12 12q23.1 1662 – EEF1A1P34 EEF1A1 pseudogene 34 20 20p11.23 1464 – EEF1A1P35 EEF1A1 pseudogene 35 4 4q28.3 1646 – EEF1A1P36 EEF1A1 pseudogene 36 6 6q23.2 1431 – EEF1A1P37 EEF1A1 pseudogene 37 8 8q23.3 557 Oral squamous cell carcinoma 74 EEF1A1 EEF1A1P38 EEF1A1 pseudogene 38 Processed pseudogene 16 16p12.1 1937 Gastric cancer, oral squamous cell carcinoma 74 , 101 EEF1A1P39 EEF1A1 pseudogene 39 10 10p11.23 250 Oral squamous cell carcinoma 74 EEF1A1P40 EEF1A1 pseudogene 40 X Xq22.3 573 …”

“… 74 , 100 EEF1A1P15 70 EEF1A1 pseudogene 15 X Xq21.33 1689 – EEF1A1P16 EEF1A1 pseudogene 16 12 12p12.3 1635 Gastric cancer, Glioma (?) 101 , 102 EEF1A1P17 EEF1A1 pseudogene 17 12 12q12 1413 – EEF1A1P18 EEF1A1 pseudogene 18 11 11q13.1 467 – EEF1A1P19 103 EEF1A1 pseudogene 19 5 5p12 1645 Hepatocellular carcinoma (?) 31 EEF1A1P20 EEF1A1 pseudogene 20 5 5q21.1 1644 Nonalcoholic fatty liver disease (?)…”

“…EEF1A1 pseudogene 16 ( EEF1A1P16 ) and EEF1A1 pseudogene 38 ( EEF1A1P38 ) are both upregulated in gastric cancer patient samples. 101 Furthermore, EEF1A1P16 is also reported on glioma 102 while EEF1A1P38 is reported on oral squamous cell carcinoma (with copy gain). 74 …”

Cytotoxic Activity of Epigallocatechin and Trans-Cinnamaldehyde in Gastric Cancer Cell Line

“…Gastric cancer is one of the main causes of cancer related death all over the worlds [1]. Treatment strategies for these patients comprisesurgery and chemotherapy.…”