Clinical study of genomic drivers in pancreatic ductal adenocarcinoma

Abstract

Background: Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer with complex genomes and dense fibrotic stroma. This study was designed to identify clinically relevant somatic aberrations in pancreatic cancer genomes of patients with primary and metastatic disease enrolled and treated in two clinical trials.

Methods: Tumour nuclei were flow sorted prior to whole genome copy number variant (CNV) analysis. Targeted or whole exome sequencing was performed on most samples. We profiled biopsies from 68 patients enrolled in two Stand Up to Cancer (SU2C)-sponsored clinical trials. These included 38 resected chemoradiation naïve tumours (SU2C 20206-003) and metastases from 30 patients who progressed on prior therapies (SU2C 20206-001). Patient outcomes including progression-free survival (PFS) and overall survival (OS) were observed.

Results: We defined: (a) CDKN2A homozygous deletions that included the adjacent MTAP gene, only its' 3' region, or excluded MTAP; (b) SMAD4 homozygous deletions that included ME2; (c) a pancreas-specific MYC super-enhancer region; (d) DNA repair-deficient genomes; and (e) copy number aberrations present in PDA patients with long-term (⩾ 40 months) and short-term (⩽ 12 months) survival after surgical resection.

Conclusions: We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments.

Figure 1

Summary of patients enrolled and samples profiled in SU2C clinical trials. (A) Copy number variant (CNV) analysis was performed on flow sorted primary pancreas cancer samples from 38 patients enrolled in SU2C 20206-003. Next generation sequencing (NGS) data were available from 25 of the 38 samples. (B) CNV analysis was obtained from 30 patients with metastatic pancreatic cancer. Targeted KRAS mutation analysis was done on 28 of these metastatic samples. *Sausen et al., Nat Commun 6: 7686.

Figure 2

Genome-wide view of recurring copy number aberrations in PDA genomes. (A) Deletions: The root mean square (RMS) of the log₂ratio genomic interval values with a sliding window of 0.5 Mb and a threshold of log₂ratio<−0.5 was initially applied to identify regions of recurrent loss. A window of 10 kb and a threshold of log₂ratio<−2.0 for ADM2 defined intervals with<−3.0 for individual probes was used to identify homozygous deletions. (B) Amplicons: The root mean square (RMS) of the log₂ratio genomic interval values with a sliding window of 0.5 Mb and a threshold of log₂ratio >0.6 was used to identify high level and recurring amplicons.

Figure 3

Chromosome 9p24.1 homozygous deletions. Homozygous deletions were detected and mapped that include (A) CDKN2A and MTAP in patient 20206-003 041, (B) CDKN2A in patient 20206-003 039, and (C) CDKN2A and the 3′ region of MTAP in patient 20206-001 015. Blue shade areas denote ADM2 defined genomic intervals. (D) Summary of homozygous 9p21.3 deletions in the SU2C trials.

Figure 4

Shortest region of overlap (SRO) of 8q24.1 MYC amplicon and superhancer loci. (A) Flow sort histogram of biopsy from patient 2026-001 046. (B) Whole genome CNV plot of sorted 2.6N PDA population. (C) Pancreas-specific superhancer loci and SRO of MYC amplicon mapped using genome browser and genome build HG19. Red shaded areas denote ADM2 defined amplicon in 20206-001 046.

Figure 5

GATA6 amplification and long-term 20206-003 survivors. Patients (A) 077 and (B) 036 from 20206-003 trial had ⩾40-month survival post surgery. Each had a GATA6 amplicon as the most significant copy number aberration in the genomes of their PDA. (C) In contrast patient the PDA genome of patient 061, 4-month survival after surgery, had additional AKT2 amplicon that exceeded the height of the co-occurring GATA6 amplicon.