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Modeling Oral-Esophageal Squamous Cell Carcinoma in 3D Organoids
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Screening pathogenic genes in oral squamous cell carcinoma based on the mRNA expression microarray data.

Yang Ding1, Pengfei Liu2, Shengsheng Zhang1

  • 1Digestive Disease Center, Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University, Beijing 100010, P.R. China.

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|March 8, 2018
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This study identified key genes in oral squamous cell carcinoma (OSCC) using microarray analysis. Transglutaminase 2 (TGM2) and Islet 1 (ISL1) show potential as biomarkers for OSCC and its metastases.

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Area of Science:

  • Genomics and Molecular Biology
  • Oncology
  • Bioinformatics

Background:

  • Oral squamous cell carcinoma (OSCC) is a prevalent cancer with stagnant survival rates.
  • Identifying novel pathogenic genes is crucial for improving OSCC diagnosis and treatment.
  • Microarray analysis offers a powerful tool for comprehensive gene expression profiling.

Purpose of the Study:

  • To screen for pathogenic genes associated with oral squamous cell carcinoma (OSCC) using gene expression data.
  • To identify differentially expressed genes (DEGs) between metastatic and non-metastatic OSCC, and between OSCC and normal tissues.
  • To construct a microRNA (miRNA)-gene regulatory network for OSCC.

Main Methods:

  • Downloaded and analyzed mRNA expression microarray datasets (GSE2280, GSE3524) from the Gene Expression Omnibus (GEO) database.
  • Utilized the limma package to identify differentially expressed genes (DEGs) in OSCC samples.
  • Performed functional enrichment analyses using DAVID and constructed a miRNA-gene regulatory network with Cytoscape.

Main Results:

  • Identified 233 DEGs between metastatic and non-metastatic OSCC (DEGs-1) and 410 DEGs between OSCC and normal tissues (DEGs-2).
  • DEGs-1 were enriched in 188 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; DEGs-2 in 228 GO terms and 6 KEGG pathways.
  • Constructed a miRNA-gene network involving 126 nodes and 135 regulated pairs, highlighting potential biomarkers like TGM2 and ISL1, and pathogenic genes such as P2RY2 and RAPGEFL1.

Conclusions:

  • Transglutaminase 2 (TGM2) and Islet 1 (ISL1) are proposed as potential biomarkers for OSCC and its lymph node metastases.
  • Identified several potential pathogenic genes, including P2RY2 and RAPGEFL1, contributing to OSCC development.
  • The study provides a foundation for further investigation into the molecular mechanisms and therapeutic targets for OSCC.