Abstract

Bevacizumab combined with cytotoxic chemotherapy is the backbone of metastatic colorectal cancer (mCRC) therapy; however, its treatment efficacy is hampered by therapeutic resistance. Therefore, understanding the mechanisms underlying bevacizumab resistance is crucial to increasing the therapeutic efficacy of bevacizumab. The Gene Expression Omnibus (GEO) database (dataset, GSE86525) was used to identify the key genes and pathways involved in bevacizumab-resistant mCRC. The GEO2R web tool was used to identify differentially expressed genes (DEGs). Functional and pathway enrichment analy-ses of the DEGs were performed using the Database for Annotation, Visualization, and Integrated Discovery(DAVID). Protein-protein interaction (PPI) networks were established using the Search Tool for the Retrieval of Interacting Genes/Proteins database(STRING) and visualized using Cytoscape software. A total of 124 DEGs were obtained, 57 of which upregulated and 67 were downregulated. PPI network analysis showed that seven upregulated genes and nine downregulated genes exhibited high PPI degrees. In the functional enrichment, the DEGs were mainly enriched in negative regulation of phosphate metabolic process and positive regulation of cell cycle process gene ontologies (GOs); the enriched pathways were the phosphoinositide 3-kinase-serine/threonine kinase signaling pathway, bladder cancer, and microRNAs in cancer. Cyclin-dependent kinase inhibitor 1A(CDKN1A), toll-like receptor 4 (TLR4), CD19 molecule (CD19), breast cancer 1, early onset (BRCA1), platelet-derived growth factor subunit A (PDGFA), and matrix metallopeptidase 1 (MMP1) were the DEGs involved in the pathways and the PPIs. The clinical validation of the DEGs in mCRC (TNM clinical stages 3 and 4) revealed that high PDGFA expression levels were associated with poor overall survival, whereas high BRCA1 and MMP1 expression levels were associated with favorable progress free survival(PFS). The identified genes and pathways can be potential targets and predictors of therapeutic resistance and prognosis in bevacizumab-treated patients with mCRC.

Original languageEnglish
Article numbere0189582
JournalPLoS One
Volume13
Issue number1
DOIs
Publication statusPublished - Jan 1 2018

Fingerprint

colorectal neoplasms
Colorectal Neoplasms
Genes
prediction
genes
protein-protein interactions
Protein Interaction Maps
Proteins
Platelet-Derived Growth Factor
platelet-derived growth factor
therapeutics
metalloproteinases
Down-Regulation
breast neoplasms
Bevacizumab
Databases
Breast Neoplasms
cdc Genes
Protein Databases
Gene Ontology

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer. / Makondi, Precious Takondwa; Lee, Chia Hwa; Huang, Chien Yu; Chu, Chi Ming; Chang, Yu Jia; Wei, Po Li.

In: PLoS One, Vol. 13, No. 1, e0189582, 01.01.2018.

Research output: Contribution to journalArticle

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AU - Makondi, Precious Takondwa

AU - Lee, Chia Hwa

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AU - Chang, Yu Jia

AU - Wei, Po Li

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