Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis

Abstract

We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).

Trial registration: ClinicalTrials.gov NCT02155621.

Keywords: neoplasm of the breast; neoplasm of the pancreas; pancreatic adenocarcinoma.

© 2019 Thibodeau et al.; Published by Cold Spring Harbor Laboratory Press.

Figures

Figure 1.

Patient #1 compound heterozygous MUTYH germline variants. (A) Integrated Genomics Viewer (IGV) (Thorvaldsdóttir et al. 2013) capture of whole-genome sequencing of tumor and matched blood DNA with whole-transcriptome sequencing of tumor RNA data at the genomic region encompassing the two MUTYH variants (c.996G>A, p.Ser332Ser and c.815G>A, p.Gly272Glu; NM_001048171). Paired-end transcriptome reads showing the germline variants to be in trans with read pairs containing the p.Gly272Glu variant (exon 10) but not the p.Ser332Ser variant (exon 12) (red box). The splicing aberration caused by p.Ser332Ser variant was not visually apparent in IGV and required transcriptome TAP for detection and characterization. TAP was used to assemble reads into contigs. Contig 1 shows aberrant splicing and contig 2 shows normal splicing. (B) Schematic of TAP analysis results showing the synonymous germline variant (c.996G>A, p.Ser332Ser) creating a novel canonical AG acceptor splice site at Chr 1:45797480–45797481 and removing 42 bp (14 amino acids).

Figure 2.

Comparison of mutation signatures exposures of MUTYH germline or combined germline/somatic biallelic aberrations against 731 cancer genomes of mixed origins. The cohort distribution of mutation signature exposures for each signature is shown using signature composition reference matrices from COSMIC, SigProfiler, and SignatureAnalyzer. The mutation fraction exposures (proportion of all mutations contributed by each signature) of Patient #1, Patient #2, and Patient #3 are superimposed. Signatures previously associated with MUTYH-mediated BER deficiency are highlighted by a rectangle. Patient #1 (PDAC, pink diamond), Patient #2 (breast cancer, green diamond), and Patient #3 (breast cancer, blue diamond) demonstrated germline or combined germline/somatic biallelic MUTYH aberrations. Functional biallelic MUTYH loss of function was present in tumors of Patient #1, Patient #2, and Patient #3 and all three patients displayed elevated outlier (>1.5 interquartile range above third quartile) signatures previously associated with defective MUTYH (COSMIC Signature 18, SigProfiler SBS18 and SBS36, and SignatureAnalyzer SBS18 and SBS36).

Figure 3.

Mutation catalogs and COSMIC mutational signatures of MUTYH germline or combined germline/somatic biallelic aberrations. Complete catalogs of SNVs from WGS of tumors were classified based on variant and 3′/5′ contexts into 96 categories (left side) and mutation catalogs were used to calculate the contribution of each signature to mutational burden (right side). The proportion of mutations or mutation count in each of the 96 categories is shown here as a barplot (left side), whereas the signIT Markov Chain Monte Carlo simulation result for COSMIC mutational signatures is shown as a violin plot distribution (right side). COSMIC Signature 18 composition is shown at the top for reference. Patient #1 (germline MUTYH c.815G>A, p.Gly272Glu; c.996G>A, p.Ser332Ser; NM_001048171) and Patient #2 (germline MUTYH c.892-2A>G) tumors showed increased Signature 18 somatic mutation burden, as exemplified by the resemblance of their mutation catalogs to COSMIC reference Signature 18. Other mutational processes contributed most to the mutational burden of Patient #3's tumor.

Figure 4.

Germline MUTYH founder Asian splice site variant impact on splicing. The Asian founder mutation MUTYH disrupting the canonical acceptor splice site at exon 11 (c.892-2A>G) was found in six patients (Patient #2, Patient #6, Patient #9, Patient #10, Patient #11, and Patient #12). (A) Integrated Genomic Viewer (IGV) (Thorvaldsdóttir et al. 2013) capture of whole-genome sequencing of tumor and matched blood DNA with whole-transcriptome sequencing of tumor RNA data at the genomic region encompassing the MUTYH variant (c.892-2A>G; NM_001048171).Transcriptome data showing abnormal splicing removing 9 bp from exon 11 (19 reads with a black line) and marked intron 10 and intron 11 retention. (B) Schematic of abnormal splicing removing 9 bp from exon 11. (C) Schematic of abnormal splicing resulting in intron retention.