Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma.

Connor, AA, Denroche, RE, Jang, GH, Timms, L, Kalimuthu, SN, Selander, I, McPherson, T, Wilson, GW, Chan-Seng-Yue, MA, Borozan, I
et al (show 30 more authors) (2016) Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma. JAMA oncology, 3 (6). pp. 774-783.

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Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease.To classify PDAC according to distinct mutational processes, and explore their clinical significance.We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium. The discovery cohort comprised 160 PDAC cases from 154 patients (148 primary; 12 metastases) that underwent tumor enrichment prior to whole-genome and RNA sequencing. The replication cohort comprised 95 primary PDAC cases that underwent whole-genome sequencing and expression microarray on bulk biospecimens.Somatic mutations accumulate from sequence-specific processes creating signatures detectable by DNA sequencing. Using nonnegative matrix factorization, we measured the contribution of each signature to carcinogenesis, and used hierarchical clustering to subtype each cohort. We examined expression of antitumor immunity genes across subtypes to uncover biomarkers predictive of response to systemic therapies.The discovery cohort was 53% male (n = 79) and had a median age of 67 (interquartile range, 58-74) years. The replication cohort was 50% male (n = 48) and had a median age of 68 (interquartile range, 60-75) years. Five predominant mutational subtypes were identified that clustered PDAC into 4 major subtypes: age related, double-strand break repair, mismatch repair, and 1 with unknown etiology (signature 8). These were replicated and validated. Signatures were faithfully propagated from primaries to matched metastases, implying their stability during carcinogenesis. Twelve of 27 (45%) double-strand break repair cases lacked germline or somatic events in canonical homologous recombination genes-BRCA1, BRCA2, or PALB2. Double-strand break repair and mismatch repair subtypes were associated with increased expression of antitumor immunity, including activation of CD8-positive T lymphocytes (GZMA and PRF1) and overexpression of regulatory molecules (cytotoxic T-lymphocyte antigen 4, programmed cell death 1, and indolamine 2,3-dioxygenase 1), corresponding to higher frequency of somatic mutations and tumor-specific neoantigens.Signature-based subtyping may guide personalized therapy of PDAC in the context of biomarker-driven prospective trials.

Item Type: Article
Uncontrolled Keywords: CD8-Positive T-Lymphocytes, Humans, Carcinoma, Pancreatic Ductal, Pancreatic Neoplasms, Genetic Predisposition to Disease, Tumor Suppressor Proteins, Nuclear Proteins, Prognosis, Retrospective Studies, Mutation, Genes, BRCA1, Genes, BRCA2, Aged, Middle Aged, Female, Male, DNA Breaks, Double-Stranded, DNA Mismatch Repair, Genome-Wide Association Study, CTLA-4 Antigen, Programmed Cell Death 1 Receptor, Fanconi Anemia Complementation Group N Protein
Depositing User: Symplectic Admin
Date Deposited: 06 Apr 2017 15:37
Last Modified: 19 Jan 2023 07:26
DOI: 10.1001/jamaoncol.2016.3916
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