An assessment of candidate genes to assist prognosis in gastric cancer

Gastric cancer (GC) is the fourth commonest cancer worldwide, with the second highest mortality rate. Its poor mortality is linked to delayed presentation. There is a drive towards non-invasive biomarker screening and monitoring of many different types of cancer, although with limited success so far. We aimed to determine if any genes from a 32-gene panel could be used to determine GC prognosis. We carried out a retrospective study on the expression of 32 genes, selected for their proven or potential links to GC, on historic formalin fixed paraffin-embedded (FFPE) GC specimens from our unit. Gene expression was measured using quantitative nuclease protection assays (qNPA) technology. Following statistical analysis of the results, immunohistochemical staining for eight genes, both discriminating and non-discriminating, was conducted in seven age and sex matched non-metastatic: metastatic GC pairings. The stained samples were reviewed by two blinded consultant histopathologists. Multivariate Cox analysis of the gene expression data revealed metastatic status, age, sex and five genes appeared to influence GC survival. Genes negatively influencing survival included and (relative risks 2.20, 3.73 and 7.53 respectively). Genes conveying survival benefit included and (relative risks 0.10 and 0.24 respectively). Immunohistochemical staining of seven age and sex matched non-metastatic: metastatic pairs revealed no association between gene expression and protein expression. Our study found several genes whose expression may affect GC prognosis. However, immunohistochemical analysis revealed no association between gene expression and protein expression. It remains to be determined whether gene expression or protein expression are reliable means of assessing GC prognosis

Gene level network analysis of transcriptome changes in motor neurons from <i>C9ORF72</i>-ALS cases.

<p>WGCNA analysis identified six gene networks which were dysregulated between <i>C9ORF72</i>-ALS and control samples. The median fold change of genes within each network and the functional enrichment of each of the gene networks is tabulated. A fold change of >1 equates to up-regulation and a fold change of <1 equates to down-regulation.</p><p>Gene level network analysis of transcriptome changes in motor neurons from <i>C9ORF72</i>-ALS cases.</p

Gene level network analysis of transcriptome changes in lymphoblastoid cell lines derived from C9ORF72-ALS cases.

<p>WGCNA analysis identified nine gene networks which were dysregulated between C9ORF72-ALS and control samples. The median fold change of genes within each network and the functional enrichment of each of the gene networks is tabulated. A fold change of >1 equates to up-regulation and a fold change of <1 equates to down-regulation.</p><p>Gene level network analysis of transcriptome changes in lymphoblastoid cell lines derived from C9ORF72-ALS cases.</p

RNA foci in lymphoblastoid cell lines derived from patients with short or long survival.

<p>RNA FISH was performed for sense and antisense RNA foci in lymphoblastoid cells. Example cells are shown derived from patients with rapid (length <2 years, Fast, upper panels) compared to slowly (length >4 years, Slow, lower panels) progressive <i>C9ORF72</i>-ALS. GGGGCC-repeat sense RNA foci are visualised (arrowheads) in the left panels whereas GGCCCC-repeat antisense RNA foci are visualised (arrowheads) in the right panels. Scale bar 10 µm.</p

Frequency of exon inclusion and exclusion events.

<p>Plots of median and 95% CI for numbers of (A) exon inclusion and (B) exon exclusion events in <i>C9ORF72</i>-ALS (+), non-<i>C9ORF72</i> ALS (-) and control (C) derived lymphoblastoid cell lines, as determined by FIRMA score. There was no significant difference between sample groups.</p

Plots of θ against the mean splicing rate with 95% confidence intervals.

<p>Exon inclusion events are shown in the left panel and exclusion inclusion events are shown in the right panel. θ is higher indicating reduced consistency of splicing in (A) <i>C9ORF72-ALS</i> (+) compared to non-<i>C9ORF72</i> ALS (-) and control (C) derived lymphoblastoid cell lines; and (B) in cell lines derived from patients with rapid (length <2 years, Fast) compared to slowly (length >4 years, Slow) progressive <i>C9ORF72-</i>ALS.</p

Clinical information relating to lymphoblastoid cell lines derived from ALS patients and controls, utilised in exon level microarray analysis.

<p>Age at symptom onset and disease duration is provided in years. Abbreviations: M = male, F = female.</p><p>Clinical information relating to lymphoblastoid cell lines derived from ALS patients and controls, utilised in exon level microarray analysis.</p