Genomic aberrations are common in
cancers and the long arm of chromosome 1 is known for its frequent amplifications in
breast cancer. However, the key candidate genes of 1q, and their contribution in
breast cancer pathogenesis remain unexplored. We have analyzed the gene expression profiles of 1635
breast tumor samples using meta-analysis based approach and identified clinically significant candidates from chromosome 1q. Seven candidate genes including
exonuclease 1 (EXO1) are consistently over expressed in
breast tumors, specifically in high grade and aggressive
breast tumors with poor clinical outcome. We derived a EXO1 co-expression module from the
mRNA profiles of
breast tumors which comprises 1q candidate genes and their co-expressed genes. By integrative functional genomics investigation, we identified the involvement of EGFR, RAS, PI3K / AKT, MYC, E2F signaling in the regulation of these selected 1q genes in
breast tumors and
breast cancer cell lines. Expression of EXO1 module was found as indicative of elevated cell proliferation,
genomic instability, activated RAS/AKT/MYC/E2F1 signaling pathways and loss of p53 activity in
breast tumors.
mRNA-
drug connectivity analysis indicates inhibition of RAS/PI3K as a possible targeted therapeutic approach for the patients with activated EXO1 module in
breast tumors. Thus, we identified seven 1q candidate genes strongly associated with the poor survival of
breast cancer patients and identified the possibility of targeting them with EGFR/RAS/PI3K inhibitors.