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Gentles AJ, Bratman SV, Lee LJ, Harris JP, Feng W, Nair RV, Shultz DB, Nair VS, Hoang CD, West RB, Plevritis SK, Alizadeh AA, Diehn M. Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer. J Natl Cancer Inst 2015; 107:djv211. [PMID: 26286589 DOI: 10.1093/jnci/djv211] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 07/07/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Accurate survival stratification in early-stage non-small cell lung cancer (NSCLC) could inform the use of adjuvant therapy. We developed a clinically implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables. METHODS Gene expression profiles from 1106 nonsquamous NSCLCs were used for generation and internal validation of a nine-gene molecular prognostic index (MPI). A quantitative polymerase chain reaction (qPCR) assay was developed and validated on an independent cohort of formalin-fixed paraffin-embedded (FFPE) tissues (n = 98). A prognostic score using clinical variables was generated using Surveillance, Epidemiology, and End Results data and combined with the MPI. All statistical tests for survival were two-sided. RESULTS The MPI stratified stage I patients into prognostic categories in three microarray and one FFPE qPCR validation cohorts (HR = 2.99, 95% CI = 1.55 to 5.76, P < .001 in stage IA patients of the largest microarray validation cohort; HR = 3.95, 95% CI = 1.24 to 12.64, P = .01 in stage IA of the qPCR cohort). Prognostic genes were expressed in distinct tumor cell subpopulations, and genes implicated in proliferation and stem cells portended poor outcomes, while genes involved in normal lung differentiation and immune infiltration were associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR = 3.43, 95% CI = 2.18 to 5.39, P < .001 in stage I patients of the largest microarray cohort; HR = 3.99, 95% CI = 1.67 to 9.56, P < .001 in stage I patients of the qPCR cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK. CONCLUSION The MPI incorporates genes expressed in the tumor and its microenvironment and can be implemented clinically using qPCR assays on FFPE tissues. A composite model integrating the MPI with clinical variables provides the most accurate risk stratification.
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Affiliation(s)
- Andrew J Gentles
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Scott V Bratman
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Luke J Lee
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Jeremy P Harris
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Weiguo Feng
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Ramesh V Nair
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - David B Shultz
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Viswam S Nair
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Chuong D Hoang
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Robert B West
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA
| | - Sylvia K Plevritis
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA.
| | - Ash A Alizadeh
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA.
| | - Maximilian Diehn
- Department of Radiology (AJG, JPH, RVN, SKP), Department of Radiation Oncology (SVB, DBS, MD), Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine (LJL, WF, MD), Department of Medicine Division of Pulmonary and Critical Care Medicine (VSN), Department of Cardiothoracic Surgery Division of Thoracic Surgery (CDH), Department of Pathology (RBW), and Department of Medicine Division of Oncology (AAA), Stanford University, Stanford, CA.
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Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TAA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res 2012; 40:D984-91. [PMID: 22121217 PMCID: PMC3245064 DOI: 10.1093/nar/gkr1051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/13/2011] [Accepted: 10/25/2011] [Indexed: 11/24/2022] Open
Abstract
Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene and pathway signatures in cancers are inconsistent across experimental systems. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), we have developed the Stem Cell Discovery Engine (SCDE)-an online database of curated CSC experiments coupled to the Galaxy analytical framework. The SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. Our initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. The SCDE is available at http://discovery.hsci.harvard.edu.
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Affiliation(s)
- Shannan J. Ho Sui
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Kimberly Begley
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dorothy Reilly
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Brad Chapman
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ray McGovern
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philippe Rocca-Sera
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Eamonn Maguire
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Gabriel M. Altschuler
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Terah A. A. Hansen
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ramakrishna Sompallae
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Andrei Krivtsov
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ramesh A. Shivdasani
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Scott A. Armstrong
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Aedín C. Culhane
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Mick Correll
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Susanna-Assunta Sansone
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Oliver Hofmann
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Winston Hide
- Department of Biostatistics, HSPH Bioinformatics Core, Harvard School of Public Health, Boston, MA, Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, MA, USA, Oxford e-Research Centre, University of Oxford, UK, Department of Pediatric Oncology, Children's Hospital, Dana Farber Cancer Institute, and Harvard Medical School, Boston, Harvard Stem Cell Institute, Cambridge, Department of Biostatistics, Dana Farber Cancer Institute and Center for Cancer Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
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