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Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow JE, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman TJ, Coffey RJ, Aronow BJ. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol 2008; 8:R131. [PMID: 17615082 PMCID: PMC2323222 DOI: 10.1186/gb-2007-8-7-r131] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 02/12/2007] [Accepted: 07/05/2007] [Indexed: 12/27/2022] Open
Abstract
Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5. Background The expression of carcino-embryonic antigen by colorectal cancer is an example of oncogenic activation of embryonic gene expression. Hypothesizing that oncogenesis-recapitulating-ontogenesis may represent a broad programmatic commitment, we compared gene expression patterns of human colorectal cancers (CRCs) and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. Results We report here that 39 colon tumors from four independent mouse models and 100 human CRCs encompassing all clinical stages shared a striking recapitulation of embryonic colon gene expression. Compared to normal adult colon, all mouse and human tumors over-expressed a large cluster of genes highly enriched for functional association to the control of cell cycle progression, proliferation, and migration, including those encoding MYC, AKT2, PLK1 and SPARC. Mouse tumors positive for nuclear β-catenin shifted the shared embryonic pattern to that of early development. Human and mouse tumors differed from normal embryonic colon by their loss of expression modules enriched for tumor suppressors (EDNRB, HSPE, KIT and LSP1). Human CRC adenocarcinomas lost an additional suppressor module (IGFBP4, MAP4K1, PDGFRA, STAB1 and WNT4). Many human tumor samples also gained expression of a coordinately regulated module associated with advanced malignancy (ABCC1, FOXO3A, LIF, PIK3R1, PRNP, TNC, TIMP3 and VEGF). Conclusion Cross-species, developmental, and multi-model gene expression patterning comparisons provide an integrated and versatile framework for definition of transcriptional programs associated with oncogenesis. This approach also provides a general method for identifying pattern-specific biomarkers and therapeutic targets. This delineation and categorization of developmental and non-developmental activator and suppressor gene modules can thus facilitate the formulation of sophisticated hypotheses to evaluate potential synergistic effects of targeting within- and between-modules for next-generation combinatorial therapeutics and improved mouse models.
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Affiliation(s)
- Sergio Kaiser
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Young-Kyu Park
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Richard B Halberg
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - Ming Yu
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Walter J Jessen
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Johannes Freudenberg
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaodi Chen
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin Haigis
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Anil G Jegga
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sue Kong
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bhuvaneswari Sakthivel
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Huan Xu
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Timothy Reichling
- Division of Human Cancer Genetics, The Ohio State University College of Medicine, Columbus, Ohio 43210-2207, USA
| | - Mohammad Azhar
- Institute for Collaborative BioResearch, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Gregory P Boivin
- University of Cincinnati, Department of Pathology and Laboratory Medicine, Cincinnati, OH 45267, USA
| | - Reade B Roberts
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anika C Bissahoyo
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Fausto Gonzales
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Greg C Bloom
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Steven Eschrich
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Scott L Carter
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeremy E Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John Kleimeyer
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael Kleimeyer
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Vivek Ramaswamy
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Stephen H Settle
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Braden Boone
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Shawn Levy
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Jonathan M Graff
- University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Thomas Doetschman
- Institute for Collaborative BioResearch, University of Arizona, Tucson, AZ 85721-0036, USA
| | - Joanna Groden
- Division of Human Cancer Genetics, The Ohio State University College of Medicine, Columbus, Ohio 43210-2207, USA
| | - William F Dove
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | - David W Threadgill
- Department of Genetics and Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy J Yeatman
- H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert J Coffey
- Departments of Medicine, and Cell and Developmental Biology, Vanderbilt University and Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Bruce J Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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