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Maurer C, Holmstrom SR, He J, Laise P, Su T, Ahmed A, Hibshoosh H, Chabot JA, Oberstein PE, Sepulveda AR, Genkinger JM, Zhang J, Iuga AC, Bansal M, Califano A, Olive KP. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut 2019; 68:1034-1043. [PMID: 30658994 PMCID: PMC6509007 DOI: 10.1136/gutjnl-2018-317706] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/08/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDA) has among the highest stromal fractions of any cancer and this has complicated attempts at expression-based molecular classification. The goal of this work is to profile purified samples of human PDA epithelium and stroma and examine their respective contributions to gene expression in bulk PDA samples. DESIGN We used laser capture microdissection (LCM) and RNA sequencing to profile the expression of 60 matched pairs of human PDA malignant epithelium and stroma samples. We then used these data to train a computational model that allowed us to infer tissue composition and generate virtual compartment-specific expression profiles from bulk gene expression cohorts. RESULTS Our analysis found significant variation in the tissue composition of pancreatic tumours from different public cohorts. Computational removal of stromal gene expression resulted in the reclassification of some tumours, reconciling functional differences between different cohorts. Furthermore, we established a novel classification signature from a total of 110 purified human PDA stroma samples, finding two groups that differ in the extracellular matrix-associated and immune-associated processes. Lastly, a systematic evaluation of cross-compartment subtypes spanning four patient cohorts indicated partial dependence between epithelial and stromal molecular subtypes. CONCLUSION Our findings add clarity to the nature and number of molecular subtypes in PDA, expand our understanding of global transcriptional programmes in the stroma and harmonise the results of molecular subtyping efforts across independent cohorts.
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Affiliation(s)
- C Maurer
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, Division of Digestiveand Liver Diseases, Columbia University Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - SR Holmstrom
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, Division of Digestiveand Liver Diseases, Columbia University Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - J He
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Biomedical Informatics, Columbia Unicersity Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - P Laise
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Biomedical Informatics, Columbia Unicersity Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - T Su
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - A Ahmed
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - H Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - JA Chabot
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Surgery, Division of GI/EndocrineSurgery, Columbia University Medical Center, New York, New York, USA
| | - PE Oberstein
- Department of Medicine, Division of Hematology and Oncology, New York University Langone Medical Center, New York, New York, USA
| | - AR Sepulveda
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - JM Genkinger
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, New York, New York, USA
| | - J Zhang
- Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - AC Iuga
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - M Bansal
- PsychoGenics Inc, Paramus, New Jersey, USA
| | - A Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Biomedical Informatics, Columbia Unicersity Medical Center, New York, New York, USA
- Department Systems Biology, Columbia University Medical Center, New York, New York, USA
- Correspondence should be addressed to: Kenneth P. Olive, Columbia University Medical Center, 1130 Saint Nicholas Avenue, ICRC 217A New York, NY 10032, phone: 212-851-4678, , Andrea Califano, Columbia University Medical Center 1130 Saint Nicholas Avenue, ICRC 912 New York, NY 10032, phone: 212-851-5183,
| | - KP Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, Division of Digestiveand Liver Diseases, Columbia University Medical Center, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
- Correspondence should be addressed to: Kenneth P. Olive, Columbia University Medical Center, 1130 Saint Nicholas Avenue, ICRC 217A New York, NY 10032, phone: 212-851-4678, , Andrea Califano, Columbia University Medical Center 1130 Saint Nicholas Avenue, ICRC 912 New York, NY 10032, phone: 212-851-5183,
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