Genetic Polymorphisms at TIMP3 Are Associated with Survival of Adenocarcinoma of the Gastroesophageal Junction

The poor survival of adenocarcinomas of the gastroesophageal junction (GEJ) makes them clinically important. Discovery of host genetic factors that affect outcome may guide more individualized treatment. This study tests whether constitutional genetic variants in matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP) genes are associated with outcome of GEJ adenocarcinoma. Single nucleotide polymorphisms (SNPs) at four TIMP (TIMP1-4) and three MMP genes (MMP2, MMP7 and MMP9) were genotyped in DNA samples from a prospective cohort of patients with primary adenocarcinoma of the GEJ admitted to the British Columbia Cancer Agency. Cox proportional hazards regression, with adjustment for patient, disease and treatment variables, was used to estimate the association of SNPs with survival. Genotypes for 85 samples and 48 SNPs were analyzed. Four SNPs across TIMP3, (rs130274, rs715572, rs1962223 and rs5754312) were associated with survival. Interaction analyses revealed that the survival associations with rs715572 and rs5754312 are specific and significant for 5FU+cisplatin treated patients. Sanger sequencing of the TIMP3 coding and promoter regions revealed an additional SNP, rs9862, also associated with survival. TIMP3 genetic variants are associated with survival and may be potentially useful in optimizing treatment strategies for individual patients

Gel shift assay for TIMP3 SNPs rs9862 and rs11547635.

<p>A) Probe names and sequences. rs9862 and rs11547635 are indicated with arrows. The 12 bp palindromic sequence is highlighted in bold and core ETS1 consensus sites are underlined. Probes are named according to alleles at sites rs9862 and rs11547635, respectively. Only one strand of the double-stranded probes is shown. B) Results. Probe and competitor names correspond to the sequences in A. Lane 15 is a control, with no nuclear extract. Potential protein complexes bound to the probes are indicated with letters on the left side of the image. Complex I appears to be specific to probes with the rs9862 C allele, whereas complexes II and IV are specific to probes with the rs9862 T allele. Complex III binds irrespective of rs9862 allele, and is competed off by unlabelled ETS1.</p

Demographic and clinical features of the cohort by survival status.

<p>Demographic and clinical features of the cohort by survival status.</p

Hazard ratio (HR) and 95% Confidence intervals (CI) estimated for the association between <i>TIMP3</i> gene variations and survival of the study cohort.

*<p>Adjusted for patient age, disease stage, surgery, chemotherapy, radiation therapy, location of tumor.</p

Structure of the <i>TIMP3</i> gene.

<p>Coding regions of exons are shown as dark bars; 5′ and 3′ untranslated regions are shown as lighter bars; introns and flanking sequence are illustrated by a line. The diagram is not to scale. Thick lines below the gene structure indicate the regions sequenced. SNPs associated with survival are indicated by vertical lines. Variants detected by sequencing are shown as circles. An LD plot based on study data is below the gene. Numbers in the plot are r² values; boxes with darker shading illustrate higher LD; lighter shading represents weaker LD. Circled SNPs show significant association with survival.</p

Survival of the study cohort by <i>TIMP3</i> variations.

<p>Kaplan-Meier survival curves and log-rank test p-values are shown. <b>A</b>) rs130274, <b>B</b>) rs1962223, <b>C</b>) rs5754312, <b>D</b>) rs715572.</p