Identification and Validation of a Biomarker Signature in Patients With Resectable Pancreatic Cancer via Genome-Wide Screening for Functional Genetic Variants

Abstract

Importance: Surgery currently offers the only chance for a cure in pancreatic ductal adenocarcinoma (PDAC), but it carries a significant morbidity and mortality risk and results in varying oncologic outcomes. At present, to our knowledge, there are no tests available before surgical resection to identify tumors with an aggressive biological phenotype that could guide personalized treatment strategies.

Objective: Identification of noninvasive genetic biomarkers that could direct therapy in patients whose cases are amenable to pancreatic cancer resection.

Design, setting, and participants: This multicenter study combined a prospective European cohort of patients with PDAC who underwent pancreatic resection (from University Hospital of Zurich, Zurich, Switzerland; Cantonal Hospital of Winterthur, Winterthur, Switzerland; and University Clinic of Ulm, Ulm, Germany) with data from the Cancer Genome Atlas database in the United States, which includes prospectively registered patients with PDAC. A genome-wide screening for functional single-nucleotide polymorphisms (SNPs) that affect PDAC survival was conducted using the European cohort for identification and the Cancer Genome Atlas cohort for validation. We used Cox proportional hazards models to screen for high-frequency polymorphic variants that are associated with allelic differences in tumor-associated survival and either result in an altered protein structure and function or reside in known regulatory noncoding genomic regions. The false-discovery rate method was applied for multiple hypothesis-testing corrections. Data analysis occurred from November 2017 to May 2018.

Exposures: Pancreatic resection.

Main outcomes and measures: Tumor-associated survival.

Results: A total of 195 patients in the European cohort were included, as well as 136 patients in the Cancer Genome Atlas cohort (overall median [range] age, 66 [19-87] years; 156 [47.1%] were women, and 175 [52.9%] were men). Two SNPs in noncoding, functional regions of genes that regulate cancer progression, invasion, and metastasis were identified (CHI3L2 SNP rs684559 and CD44 SNP rs353630). These were associated with survival after PDAC resection; patients who carry the risk alleles at 1 of both SNP loci had a 2.63-fold increased risk for tumor-associated death compared with those with protective genotypes (hazard ratio for survival, 0.38 [95% CI, 0.27-0.53]; P = 1.0 × 10-8).

Conclusions and relevance: The identified polymorphisms may serve as a noninvasive biomarker signature of prospective survival after pancreatic resection that is readily available at the time of PDAC diagnosis. This signature can be used to identify a subset of high-risk patients with PDAC with very low survival probability who might be eligible for inclusion in clinical trials of new therapeutic strategies, including neoadjuvant chemotherapy protocols. In addition, the biological knowledge about these SNPs could help guide the development of individualized genomic strategies for PDAC therapies.

Conflict of interest statement

Conflict of Interest Disclosures: Dr Graf reported grants from Amelie Waring Stiftung during the conduct of the study. No other disclosures were reported.

Figures

Figure 1.. Survival Analysis of Individuals With CHI3L2 Single-Nucleotide Polymorphism rs684559

A genome-wide screen for polymorphic variants that affect pancreatic ductal adenocarcinoma (PDAC) survival identified a potentially functional single-nucleotide polymorphism (SNP) in an active regulatory genomic region of the CHI3L2 gene. The A/A genotype of the identified SNP (rs684559) correlates significantly with poorer tumor-specific survival after resection of PDAC. A, Results of the Cox analysis in 193 patients with PDAC from the European cohort who underwent a surgical resection of their primary pancreatic tumors (adjusted to the known independent prognostic factors tumor stage and resection status). Patients with an A/A genotype were associated with the shortest survival time compared with those with 1 or 2 G alleles. B, Results of the Cox analysis in 136 patients with PDAC from the publicly available Cancer Genome Atlas database who underwent a surgical resection of their tumors. Patients with an A/A genotype had the shortest survival time compared with those with a G allele. The results were significant after correction for multiple testing (Q = 0.027). C and D, The graphs display the survival curves of 329 patients in the merged data set in the Cox multivariate analysis and the Kaplan-Meier survival curves, respectively. The P values in the Kaplan-Meier analysis (D) were determined with the log-rank test. HR indicates hazard ratio; TCGA, the Cancer Genome Atlas.

Figure 2.. Survival Analysis of Individuals With CD44 Single-Nucleotide Polymorphism rs353630 and Biomarker Signature

Analysis of tumor-specific survival after resection of pancreatic ductal adenocarcinoma (PDAC). A, Results of the Cox analysis in 192 patients with PDAC from 3 European centers who underwent a surgical resection of their pancreatic tumors (adjusted to the known independent prognostic factors tumor stage and resection status). Patients with a single-nucleotide polymorphism (SNP) rs353630 T/T genotype were associated with the shortest survival time compared with those with 1 or 2 C alleles. B, Results of the Cox analysis in 136 patients with PDAC from the publicly available Cancer Genome Atlas database who underwent a surgical resection of their tumors. Patients with a SNP rs353630T/T genotype had the shortest survival time compared with those with a C allele. The results were significant after correction for multiple testing (Q = 0.0451). C, and D, The graphs displays the survival curves for SNP rs353630 of 328 patients in the merged data set in the Cox multivariate analysis (C) and the Kaplan-Meier survival curves (D). E, Cox analysis of tumor-associated survival with a 2-dimensional biomarker signature that combines both SNP loci (rs684559 and rs353630) in the merged data set that comprises of 331 PDAC patients (adjusted to the known independent prognostic factors tumor stage and resection status). The risk-indicating signature includes the genotypes of each individual SNP that has individually been shown to associate with an increased risk of death, precisely rs684559 A/A or rs353630 T/T. The protective signature consists of the remaining genotype combinations: at least 1 C allele of rs353630 and 1 G allele of rs684559. F, Biomarker signature: the graphs display the Kaplan-Meier survival curves in the merged data set. The P values in D and F were determined with the log-rank test. HR indicates hazard ratio; TCGA, the Cancer Genome Atlas.