Multi-Scale Genomic, Transcriptomic and Proteomic Analysis of Colorectal Cancer Cell Lines to Identify Novel Biomarkers

Abstract

Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. The objectives of this study were to establish which genes were differentially expressed with respect to treatment sensitivity and relate this to copy number in a panel of 15 CRC cell lines. Copy number variations of the identified genes were assessed in a cohort of CRCs. IC50’s were measured for 5-fluorouracil, oxaliplatin, and BEZ-235, a PI3K/mTOR inhibitor. Cell lines were profiled using array comparative genomic hybridisation, Illumina gene expression analysis, reverse phase protein arrays, and targeted sequencing of KRAS hotspot mutations. Frequent gains were observed at 2p, 3q, 5p, 7p, 7q, 8q, 12p, 13q, 14q, and 17q and losses at 2q, 3p, 5q, 8p, 9p, 9q, 14q, 18q, and 20p. Frequently gained regions contained EGFR, PIK3CA, MYC, SMO, TRIB1, FZD1, and BRCA2, while frequently lost regions contained FHIT and MACROD2. TRIB1 was selected for further study. Gene enrichment analysis showed that differentially expressed genes with respect to treatment response were involved in Wnt signalling, EGF receptor signalling, apoptosis, cell cycle, and angiogenesis. Stepwise integration of copy number and gene expression data yielded 47 candidate genes that were significantly correlated. PDCD6 was differentially expressed in all three treatment responses. Tissue microarrays were constructed for a cohort of 118 CRC patients and TRIB1 and MYC amplifications were measured using fluorescence in situ hybridisation. TRIB1 and MYC were amplified in 14.5% and 7.4% of the cohort, respectively, and these amplifications were significantly correlated (p≤0.0001). TRIB1 protein expression in the patient cohort was significantly correlated with pERK, Akt, and Caspase 3 expression. In conclusion, a set of candidate predictive biomarkers for 5-fluorouracil, oxaliplatin, and BEZ235 are described that warrant further study. Amplification of the putative oncogene TRIB1 has been described for the first time in a cohort of CRC patients.

A UBE2O-AMPKα2 Axis that Promotes Tumor Initiation and Progression Offers Opportunities for Therapy

“…UBE2O is localized in the 17q25 locus, the amplification of which is recurrent in a subset of human cancers (Briffa et al, 2015; Lin et al, 2006; Rice et al, 2011; Toffoli et al, 2014; Wang et al, 2015), and we found that in TCGA datasets from cBioPortal (www.cbioportal.org) UBE2O is upregulated in ~20% of human breast, bladder, liver and lung carcinomas (Figures 7A and 7B and Figures S7A and S7B). Previously published microarray-based gene expression analyses have also indicated a high expression rate of UBE2O in several subsets of human cancer (Figure 7C and Figure S7C).…”

“…However, in vivo evaluation of UBE2O has been limited by a lack of appropriate animal models. Intriguingly, UBE2O is localized in the 17q25 chromosome region, which is amplified in a subset of human cancers (Briffa et al, 2015; Lin et al, 2006; Rice et al, 2011; Toffoli et al, 2014; Wang et al, 2015), but its role in tumorigenesis has yet to be fully described.…”

A muscle-specific UBE2O/AMPKα2 axis promotes insulin resistance and metabolic syndrome in obesity

“…Our data demonstrate what we believe to be a previously unrecognized role for the ubiquitin-conjugating enzyme UBE2O in the regulation of energy homeostasis and insulin sensitivity in vivo. Whereas UBE2O is known to be recurrently amplified in human cancers (38)(39)(40)(41)(42), we have now shown that UBE2O is universally upregulated in animal models exhibiting insulin resistance and metabolic disorders. Whole-body knockout of Ube2o in mice reverses the gains in weight, white fat mass, and body lipid content resulting from overnutrition.…”

aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer

“…These previous reports support our results. Although the participation of other putative oncogenes involved in the sensitivity to irinotecan or resistance to oxaliplatin, such as TRIB1 [21] and POU5F1B [22], which are chromosomally located near MYC, cannot be excluded, we hypothesize that MYC is the most promising positive predictive biomarker. Further validation and functional studies from a viewpoint of chemosensitivity are required to determine the potential roles of these genes in patients with mCRC.…”