13, 14, 15 Overexpression of ERCC2 (P=0.007 in our data) is associated with cisplatin resistance in lung cancer cell lines.13 Silencing of hHR23A (P=0.022 in our data) decreases the nuclear DRP1 level and cisplatin resistance in lung adenocarcinoma cells.14 Disruption of the Fanconi anemia�CBRCA pathway promotion information is reported in cisplatin-sensitive ovarian tumors.15 Thus, this gene ontology analysis supports the clinical relevance of these DNA repair canonical pathways, which were shown to be associated with in vitro cisplatin resistance. Ingenuity Pathway Analysis functional categories enriched in poor prognosis signature were: protein synthesis, DNA replication/recombination/repair and cancer (Supplementary Table 2).

The protein synthesis category includes ribosomal subunit mRNAs (RPL13, RPL18, RPL24, RPL30, RPL38, RPL5, RPL7, RPL7A, RPL8, RPS2, RPS5) and eukaryotic translation initiation factors (EIF1, EIF2B2, EIF2B4, EIF2S1, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3H, EIF3I, EIF4A1, EIF4A3, EIF4B, EIF4EBP1, EIF5, EIF5B). This result suggests that the most prominent feature of poor prognosis signature is increased protein synthesis, presumably resulting from activation of oncogenes, such as EGFR, FGFR2 and MYC (Supplementary Table 2). MYC-induced transcriptional activation of protein synthesis-related genes is previously shown by a microarray report that the majority of genes responsive to MYC overexpression are involved in macromolecular synthesis, protein turnover and metabolism, including 30 ribosomal protein genes.

16 Infinitesimal perturbation analysis canonical pathways enriched in 648 genes in good prognosis signature were antigen presentation pathway, B-cell development and interleukin-15 production. Enriched functional categories were gastrointestinal disease, inflammatory disease and genetic disorder. Development of the three-gene predictor Although such a gene ontology analysis of the whole signature provides some insight into clinically relevant mechanisms for chemotherapy resistance, this large number of genes is not readily amenable to clinical application. Therefore, we wished to narrow down 917 genes in the whole poor prognosis signature to the smaller number of genes, which may have driven the expression of majority of genes in the signature. Focusing on such ��driver gene’ candidates would also minimize the chance of including false-positive discovery in a genomic predictor.

For this purpose, a second tier of genomic analysis was performed to identify genes that could be functionally important in gastric cancer cells. Genomic DNA from samples available from the training set patients was analyzed by array CGH to identify gene amplifications. Age, sex and overall survival were similar between the 30 patients (31.3%) whose samples Cilengitide were analyzed by array CGH and the other patients in the training set. Using very conservative criteria (average tumor/normal log2 ratio >2.

By applying ROC curve derived cut-off scores to the immunohistochemical markers selleck chemical Wortmannin in this study, we found that VEGF negative tumours were more than four times more likely to undergo a complete tumour regression than their VEGF positive counterparts. Complete pathologic response was nearly six times more likely in EGFR-positive tumours compared with EGFR-negative cases. Moreover, analysis of multi-marker phenotypes of VEGF and EGFR expression identified a subgroup of VEGF-positive and EGFR-negative tumours that were highly resistant to treatment. VEGF is a potent angiogenic promoter required for the full execution of angiogenesis. VEGF receptor signalling has been shown to have effects on endothelial cell proliferation, migration, survival and vascular permeability (Roskoski, 2007).

In addition, urokinase plasminogen activator, tissue plasminogen activator and matrix metalloproteinases are induced by upregulation of VEGF. These proteins function to degrade the basement membrane and extracellular matrix, providing a scaffold for proliferating, migrating and extravasating endothelial cells (Ferrara et al, 2003). The result of tumour angiogenesis is a newly formed vasculature with ��leaky’, disorganised vessels, increased interstitial pressure and chaotic blood flow, which decreases the efficiency of radiotherapy (Willett et al, 2006; Roskoski, 2007). In 1971, Folkman (1971) hypothesised that blocking angiogenesis in tumours could be used a method of treatment for patients with cancer.

Pharmacological agents designed to block VEGF or VEGF receptor signalling are currently in various phases of clinical trials and have demonstrating promising results (Kowanetz and Ferrara, 2006; Roskoski, 2007; Willett et al, 2007). The VEGF blockade results in ��normalisation’ of the vasculature, decreased interstitial pressure and vascular permeability, thereby potentiating the effects of radiotherapy by increasing oxygen transport to tumour cells and facilitating the delivery of chemotherapeutic agents to the target tumour (Willett et al, 2006). In our study, VEGF positivity was strongly associated with a more radio-resistant phenotype. In colorectal cancer, VEGF is associated with tumour aggressiveness, poor survival, local failure and the presence of metastatic disease (Giatromanolaki et al, 2006).

Giralt et al (2007) demonstrated that VEGF positivity is an indicator of poor disease-free survival following preoperative radiochemotherapy, while Nozue et al (2001) described an association between post-treatment VEGF overexpression and distant GSK-3 metastasis. Qiu et al (2000) found no correlation between pretreatment VEGF expression and tumour response in 72 patients undergoing long-course neoadjuvant radiotherapy. In a previous work on the same, yet smaller series of patients, we not only identified VEGF but also Bcl-2 as significant predictors of tumour regression (Zlobec et al, 2005).