Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data

Abstract

Functional analysis and interpretation of large-scale proteomics andgene expression data require effective use of bioinformatics toolsand public knowledge resources coupled with expert-guided examination.An integrated bioinformatics approach was used to analyze cellularpathways in response to ionizing radiation. ATM, or ataxia-telangiectasiamutated , a serine-threonine protein kinase, plays critical rolesin radiation responses, including cell cycle arrest and DNA repair.We analyzed radiation responsive pathways based on 2D-gel/MS proteomicsand microarray gene expression data from fibroblasts expressing wildtype or mutant ATM gene. The analysis showed that metabolism wassignificantly affected by radiation in an ATM dependent manner. Inparticular, purine metabolic pathways were differentially changedin the two cell lines. The expression of ribonucleoside-diphosphatereductase subunit M2 (RRM2) was increased in ATM-wild type cellsat both mRNA and protein levels, but no changes were detected inATM-mutated cells. Increased expression of p53 was observed 30minafter irradiation of the ATM-wild type cells. These results suggestthat RRM2 is a downstream target of the ATM-p53 pathway that mediatesradiation-induced DNA repair. We demonstrated that the integratedbioinformatics approach facilitated pathway analysis, hypothesisgeneration and target gene/protein identification.