Identification and validation of genes involved in gastric tumorigenesis

Abstract

BackgroundGastric cancer is one of the common cancers seen in south India. Unfortunately more than 90% are advanced by the time they report to a tertiary centre in the country. There is an urgent need to characterize these cancers and try to identify potential biomarkers and novel therapeutic targets.Materials and methodsWe used 24 gastric cancers, 20 Paired normal (PN) and 5 apparently normal gastric tissues obtained from patients with non-gastric cancers (Apparently normal - AN) for the microarray study followed by validation of the significant genes (n = 63) by relative quantitation using Taqman Low Density Array Real Time PCR. We then used a custom made Quantibody protein array to validate the expression of 15 proteins in gastric tissues (4 AN, 9 PN and 9 gastric cancers). The same array format was used to study the plasma levels of these proteins in 58 patients with gastric cancers and 18 from patients with normal/non-malignant gastric conditions.ResultsSeventeen genes (ASPN, CCL15/MIP-1δ, MMP3, SPON2, PRSS2, CCL3, TMEPAI/PMEPAI, SIX3, MFNG, SOSTDC1, SGNE1, SST, IGHA1, AKR1B10, FCGBP, ATP4B, NCAPH2) were shown to be differentially expressed between the tumours and the paired normal, for the first time. EpCAM (p = 0.0001), IL8 (p = 0.0003), CCL4/MIP-1β (p = 0.0026), CCL20/MIP-3α (p = 0.039) and TIMP1 (p = 0.0017) tissue protein levels were significantly different (Mann Whitney U test) between tumours versus AN & PN. In addition, median plasma levels of IL8, CXCL9/MIG, CCL3/MIP-1α, CCL20/MIP-3α, PDGFR-B and TIMP1 proteins were significantly different between the non-malignant group and the gastric cancer group. The post-surgical levels of EpCAM, IGFBP3, IL8, CXCL10/IP10, CXCL9/MIG, CCL3/MIP-1α, CCL20/MIP-3α, SPP1/OPN and PDGFR-B showed a uniform drop in all the samples studied.ConclusionsOur study has identified several genes differentially expressed in gastric cancers, some for the first time. Some of these have been confirmed at the protein level, as well. Some of these proteins will need to be evaluated further for their potential as diagnostic biomarkers in gastric cancers and some could be useful as follow-up markers in gastric cancer.

Intragenic DNA Methylation Concomitant with Repression of ATP4B and ATP4A Gene Expression in Gastric Cancer is a Potential Serum Biomarker

“…Our previous gene expression analysis using microarray showed that ATP4A was down regulated in tumours (Rajkumar et al, 2010). In the present study we validated the micro-array result using real-time PCR analysis for ATP4A expression in gastric tumors, PN and AN samples.…”

“…The fold changes in mRNA expression of individual samples were retrieved from our previous study (Rajkumar et al, 2010). 18/19 tumor samples showed down regulation and one sample did not show a change in the mRNA expression level.…”

“…The paraffin embedded tissue sections from the identified paraffin blocks were obtained from the Department of Pathology, Cancer Institute (WIA). The criteria for choosing apparently normal (AN), and paired normal (PN) was based on our previous report on gastric cancer (Rajkumar et al, 2010). Briefly, AN gastric tissues were obtained from patients who were admitted for treatment for other malignancies and underwent stomach resection as part of their primary surgery and did not exhibit any lesions in the stomach.…”

“…High incidence rate of gastric cancer in the region combined with majority of lesions (more than 90%) presenting in advanced stages of the disease, presents an urgent need for population based screening which can identify early lesions using bio-markers, preferably serum based. In our previous study, where we compared gene expression profile of gastric tumor with the corresponding paired normal (PN) and apparently normal (AN), we identified several genes including ATP4A and ATP4B to be repressed in gastric tumor tissues compared to PN and AN tissues (Rajkumar et al, 2010).…”

Interferon Stimulated Gene - ISG15 is a Potential Diagnostic Biomarker in Oral Squamous Cell Carcinomas

“…Hence a deregulation in the expression of ISG15 may be expected to promote carcinogenesis as ISGylated proteins remain stabilized for a sustained period. Indeed overexpression of ISG15 has been reported in many melanoma cell lines and tumor biopsies from several cancers (Padovan et al, 2002;Iacobuzio-Donahue et al, 2003;Hoek et al, 2004;Andersen et al, 2006b;Bektas et al, 2008;Rajkumar et al, 2011) including those from oral squamous cell carcinoma (OSCC) tissues in American and Chinese patients (Hui et al, 2008;Lang-Ming et al, 2009). Population genetic studies have suggested that the genetic basis of diseases in the Indian population may be different due to differences in the risk allele frequency and pattern of linkage disequilibrium.…”