1
|
Hsu TK, Asmussen J, Koire A, Choi BK, Gadhikar MA, Huh E, Lin CH, Konecki DM, Kim YW, Pickering CR, Kimmel M, Donehower LA, Frederick MJ, Myers JN, Katsonis P, Lichtarge O. A general calculus of fitness landscapes finds genes under selection in cancers. Genome Res 2022; 32:916-929. [PMID: 35301263 PMCID: PMC9104707 DOI: 10.1101/gr.275811.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Genetic variants drive the evolution of traits and diseases. We previously modeled these variants as small displacements in fitness landscapes and estimated their functional impact by differentiating the evolutionary relationship between genotype and phenotype. Conversely, here we integrate these derivatives to identify genes steering specific traits. Over cancer cohorts, integration identified 460 likely tumor-driving genes. Many have literature and experimental support but had eluded prior genomic searches for positive selection in tumors. Beyond providing cancer insights, these results introduce a general calculus of evolution to quantify the genotype-phenotype relationship and discover genes associated with complex traits and diseases.
Collapse
Affiliation(s)
- Teng-Kuei Hsu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer Asmussen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Byung-Kwon Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mayur A Gadhikar
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eunna Huh
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chih-Hsu Lin
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Daniel M Konecki
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Young Won Kim
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Marek Kimmel
- Departments of Statistics and Bioengineering, Rice University, Houston, Texas 77005, USA
- Department of Systems Engineering and Biology, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mitchell J Frederick
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Olivier Lichtarge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
2
|
Parvandeh S, Donehower LA, Katsonis P, Hsu TK, Asmussen J, Lee K, Lichtarge O. EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants. Nucleic Acids Res 2022; 50:e70. [PMID: 35412634 PMCID: PMC9262594 DOI: 10.1093/nar/gkac215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Discovering rare cancer driver genes is difficult because their mutational frequency is too low for statistical detection by computational methods. EPIMUTESTR is an integrative nearest-neighbor machine learning algorithm that identifies such marginal genes by modeling the fitness of their mutations with the phylogenetic Evolutionary Action (EA) score. Over cohorts of sequenced patients from The Cancer Genome Atlas representing 33 tumor types, EPIMUTESTR detected 214 previously inferred cancer driver genes and 137 new candidates never identified computationally before of which seven genes are supported in the COSMIC Cancer Gene Census. EPIMUTESTR achieved better robustness and specificity than existing methods in a number of benchmark methods and datasets.
Collapse
Affiliation(s)
- Saeid Parvandeh
- To whom correspondence should be addressed. Tel: +1 713 798 7677;
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Houston, TX 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Teng-Kuei Hsu
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jennifer K Asmussen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Correspondence may also be addressed to Olivier Lichtarge. Tel: +1 713 798 5646;
| |
Collapse
|
3
|
Nakahata K, Simons BW, Pozzo E, Shuck R, Kurenbekova L, Prudowsky Z, Dholakia K, Coarfa C, Patel TD, Donehower LA, Yustein JT. K-Ras and p53 mouse model with molecular characteristics of human rhabdomyosarcoma and translational applications. Dis Model Mech 2022; 15:274377. [PMID: 35174853 PMCID: PMC8844455 DOI: 10.1242/dmm.049004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, with overall long-term survival rates of ∼65-70%. Thus, additional molecular insights and representative models are critical for identifying and evaluating new treatment modalities. Using MyoD-Cre-mediated introduction of mutant K-RasG12D and perturbations in p53, we developed a novel genetically engineered mouse model (GEMM) for RMS. The anatomic sites of primary RMS development recapitulated human disease, including tumors in the head, neck, extremities and abdomen. We confirmed RMS histology and diagnosis through Hematoxylin and Eosin staining, and positive immunohistochemical staining for desmin, myogenin, and phosphotungstic acid-Hematoxylin. Cell lines from GEMM tumors were established with the ability to engraft in immunocompetent mice with comparable histological and staining features as the primary tumors. Tail vein injection of cell lines had high metastatic potential to the lungs. Transcriptomic analyses of p53R172H/K-RasG12D GEMM-derived tumors showed evidence of high molecular homology with human RMS. Finally, pre-clinical use of these murine RMS lines showed similar therapeutic responsiveness to chemotherapy and targeted therapies as human RMS cell lines.
Collapse
Affiliation(s)
- Kengo Nakahata
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian W Simons
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX 77030, USA, USA
| | - Enrico Pozzo
- Translational Cardiomyology Laboratory, Stem Cell Research Institute, Stem Cell Biology and Embryology Unit, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Ryan Shuck
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lyazat Kurenbekova
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zachary Prudowsky
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kshiti Dholakia
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA.,Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tajhal D Patel
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lawrence A Donehower
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason T Yustein
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX 77030, USA.,Cancer and Cell Biology Program, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
4
|
Zhang Y, Chen F, Donehower LA, Scheurer ME, Creighton CJ. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun 2021; 12:937. [PMID: 33568653 PMCID: PMC7876141 DOI: 10.1038/s41467-021-21081-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
The global impact of somatic structural variants (SSVs) on gene expression in pediatric brain tumors has not been thoroughly characterised. Here, using whole-genome and RNA sequencing from 854 tumors of more than 30 different types from the Children's Brain Tumor Tissue Consortium, we report the altered expression of hundreds of genes in association with the presence of nearby SSV breakpoints. SSV-mediated expression changes involve gene fusions, altered cis-regulation, or gene disruption. SSVs considerably extend the numbers of patients with tumors somatically altered for critical pathways, including receptor tyrosine kinases (KRAS, MET, EGFR, NF1), Rb pathway (CDK4), TERT, MYC family (MYC, MYCN, MYB), and HIPPO (NF2). Compared to initial tumors, progressive or recurrent tumors involve a distinct set of SSV-gene associations. High overall SSV burden associates with TP53 mutations, histone H3.3 gene H3F3C mutations, and the transcription of DNA damage response genes. Compared to adult cancers, pediatric brain tumors would involve a different set of genes with SSV-altered cis-regulation. Our comprehensive and pan-histology genomic analyses reveal SSVs to play a major role in shaping the transcriptome of pediatric brain tumors.
Collapse
Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
5
|
Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 2020; 28:1370-1384.e5. [PMID: 31365877 DOI: 10.1016/j.celrep.2019.07.001] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/09/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
The TP53 tumor suppressor gene is frequently mutated in human cancers. An analysis of five data platforms in 10,225 patient samples from 32 cancers reported by The Cancer Genome Atlas (TCGA) enables comprehensive assessment of p53 pathway involvement in these cancers. More than 91% of TP53-mutant cancers exhibit second allele loss by mutation, chromosomal deletion, or copy-neutral loss of heterozygosity. TP53 mutations are associated with enhanced chromosomal instability, including increased amplification of oncogenes and deep deletion of tumor suppressor genes. Tumors with TP53 mutations differ from their non-mutated counterparts in RNA, miRNA, and protein expression patterns, with mutant TP53 tumors displaying enhanced expression of cell cycle progression genes and proteins. A mutant TP53 RNA expression signature shows significant correlation with reduced survival in 11 cancer types. Thus, TP53 mutation has profound effects on tumor cell genomic structure, expression, and clinical outlook.
Collapse
Affiliation(s)
- Lawrence A Donehower
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Thierry Soussi
- Sorbonne Université, UPMC University Paris 06, 75005 Paris, France; Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska Institutet, Stockholm, Sweden; INSERM, U1138, Équipe 11, Centre de Recherche des Cordeliers, Paris, France
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Andre Schultz
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xubin Li
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Ozgun Babur
- Computational Biology Program, Oregon Health and Science University, Portland, OR 97239, USA
| | - Teng-Kuei Hsu
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, Division of Science, M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
6
|
Choi BK, Fujiwara K, Dayaram T, Darlington Y, Dickerson J, Goodell MA, Donehower LA. WIP1 dephosphorylation of p27 Kip1 Serine 140 destabilizes p27 Kip1 and reverses anti-proliferative effects of ATM phosphorylation. Cell Cycle 2020; 19:479-491. [PMID: 31959038 DOI: 10.1080/15384101.2020.1717025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The phosphoinositide-3-kinase like kinases (PIKK) such as ATM and ATR play a key role in initiating the cellular DNA damage response (DDR). One key ATM target is the cyclin-dependent kinase inhibitor p27Kip1 that promotes G1 arrest. ATM activates p27Kip1-induced arrest in part through phosphorylation of p27Kip1 at Serine 140. Here we show that this site is dephosphorylated by the type 2C serine/threonine phosphatase, WIP1 (Wildtype p53-Induced Phosphatase-1), encoded by the PPM1D gene. WIP1 has been shown to dephosphorylate numerous ATM target sites in DDR proteins, and its overexpression and/or mutation has often been associated with oncogenesis. We demonstrate that wildtype, but not phosphatase-dead WIP1, efficiently dephosphorylates p27Kip1 Ser140 both in vitro and in cells and that this dephosphorylation is sensitive to the WIP1-specific inhibitor GSK 2830371. Increased expression of wildtype WIP1 reduces stability of p27Kip1 while increased expression of similar amounts of phosphatase-dead WIP1 has no effect on p27Kip1 protein stability. Overexpression of wildtype p27Kip1 reduces cell proliferation and colony forming capability relative to the S140A (constitutively non-phosphorylated) form of p27. Thus, WIP1 plays a significant role in homeostatic modulation of p27Kip1 activity following activation by ATM.
Collapse
Affiliation(s)
- Byung-Kwon Choi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kenichiro Fujiwara
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Tajhal Dayaram
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Yolanda Darlington
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Dickerson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.,Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
7
|
Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 2019; 28:3010. [DOI: 10.1016/j.celrep.2019.08.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
8
|
Hsu JI, Dayaram T, Tovy A, De Braekeleer E, Jeong M, Wang F, Zhang J, Heffernan TP, Gera S, Kovacs JJ, Marszalek JR, Bristow C, Yan Y, Garcia-Manero G, Kantarjian H, Vassiliou G, Futreal PA, Donehower LA, Takahashi K, Goodell MA. PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy. Cell Stem Cell 2018; 23:700-713.e6. [PMID: 30388424 PMCID: PMC6224657 DOI: 10.1016/j.stem.2018.10.004] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/17/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Clonal hematopoiesis (CH), in which stem cell clones dominate blood production, becomes increasingly common with age and can presage malignancy development. The conditions that promote ascendancy of particular clones are unclear. We found that mutations in PPM1D (protein phosphatase Mn2+/Mg2+-dependent 1D), a DNA damage response regulator that is frequently mutated in CH, were present in one-fifth of patients with therapy-related acute myeloid leukemia or myelodysplastic syndrome and strongly correlated with cisplatin exposure. Cell lines with hyperactive PPM1D mutations expand to outcompete normal cells after exposure to cytotoxic DNA damaging agents including cisplatin, and this effect was predominantly mediated by increased resistance to apoptosis. Moreover, heterozygous mutant Ppm1d hematopoietic cells outcompeted their wild-type counterparts in vivo after exposure to cisplatin and doxorubicin, but not during recovery from bone marrow transplantation. These findings establish the clinical relevance of PPM1D mutations in CH and the importance of studying mutation-treatment interactions. VIDEO ABSTRACT.
Collapse
MESH Headings
- Aged
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Proliferation/drug effects
- Cisplatin/chemistry
- Cisplatin/pharmacology
- Clone Cells/drug effects
- Doxorubicin/chemistry
- Doxorubicin/pharmacology
- Drug Screening Assays, Antitumor
- Female
- HEK293 Cells
- Hematopoiesis/drug effects
- Hematopoiesis/genetics
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Middle Aged
- Mutation
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Protein Phosphatase 2C/genetics
- Protein Phosphatase 2C/metabolism
Collapse
Affiliation(s)
- Joanne I Hsu
- Translational Biology and Molecular Medicine Graduate Program and Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tajhal Dayaram
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayala Tovy
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Wellcome-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
| | - Mira Jeong
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy P Heffernan
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonal Gera
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J Kovacs
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph R Marszalek
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher Bristow
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanqing Yan
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George Vassiliou
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Wellcome-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Koichi Takahashi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Margaret A Goodell
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
9
|
Fuja DG, Rainusso NC, Shuck RL, Kurenbekova L, Donehower LA, Yustein JT. Transglutaminase-2 promotes metastatic and stem-like phenotypes in osteosarcoma. Am J Cancer Res 2018; 8:1752-1763. [PMID: 30323968 PMCID: PMC6176192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023] Open
Abstract
Osteosarcoma (OS) is a highly aggressive mesenchymal malignancy and the most common primary bone tumor in the pediatric population. OS frequently presents with or develops distal metastases. Patients with metastatic disease have extremely poor survival rates, thus necessitating improved molecular insights into OS metastatic biology. Utilizing our previously characterized genetically engineered mouse model (GEMM) of metastatic OS, we identified enhanced differential expression of Transglutaminase-2 (TGM2) in metastatic OS. However, the role of TGM2 in sarcoma development and metastatic progression remains largely undefined. To further investigate the role of TGM2 in OS metastasis, we performed both gain- and loss-of-function studies for TGM2 in human and mouse OS cell lines. Our data provide evidence that enhanced expression of TGM2 in metastatic OS contributes to migratory and invasive phenotypes. Besides the effects on metastatic phenotypes, we also observed that TGM2 contributes to OS stem-like properties. In addition, treatment with transglutaminase inhibitors had analogous effects on proliferation and migration to TGM2 knockdown. Finally, in vivo xenograft studies demonstrated that TGM2 functionally alters metastatic potential and survival outcome. Together, these data highlight TGM2 as a pro-metastatic factor in OS and a potential avenue for future therapeutic intervention to inhibit metastatic disease.
Collapse
Affiliation(s)
- Daniel G Fuja
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
- Integrative Molecular and Biological Sciences Program, Baylor College of MedicineHouston 77030, Texas, USA
| | - Nino C Rainusso
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
| | - Ryan L Shuck
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
| | - Lyazat Kurenbekova
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
| | - Lawrence A Donehower
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
- Integrative Molecular and Biological Sciences Program, Baylor College of MedicineHouston 77030, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of MedicineHouston 77030, Texas, USA
- Department of Molecular Virology & Microbiology, Baylor College of MedicineHouston 77030, Texas, USA
- Dan L. Duncan Cancer Center, Baylor College of MedicineHouston 77030, Texas, USA
| | - Jason T Yustein
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of MedicineHouston 77030, Texas, USA
- Integrative Molecular and Biological Sciences Program, Baylor College of MedicineHouston 77030, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of MedicineHouston 77030, Texas, USA
- Dan L. Duncan Cancer Center, Baylor College of MedicineHouston 77030, Texas, USA
| |
Collapse
|
10
|
Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 2018; 23:239-254.e6. [PMID: 29617664 PMCID: PMC5961503 DOI: 10.1016/j.celrep.2018.03.076] [Citation(s) in RCA: 652] [Impact Index Per Article: 108.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.
Collapse
Affiliation(s)
| | - Linghua Wang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA; Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Feng
- TESARO Inc., Waltham, MA 02451, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase Miller
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Haoran Chen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Denise Wolf
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer, Houston, TX 77030, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Raymond J Monnat
- Departments of Pathology & Genome Sciences, University of Washington, Seattle, WA 98195-7705, USA.
| | | | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA; Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
| |
Collapse
|
11
|
Parikh N, Shuck RL, Gagea M, Shen L, Donehower LA. Enhanced inflammation and attenuated tumor suppressor pathways are associated with oncogene-induced lung tumors in aged mice. Aging Cell 2018; 17. [PMID: 29047229 PMCID: PMC5771401 DOI: 10.1111/acel.12691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 01/09/2023] Open
Abstract
Aging is often accompanied by a dramatic increase in cancer susceptibility. To gain insights into how aging affects tumor susceptibility, we generated a conditional mouse model in which oncogenic KrasG12D was activated specifically in lungs of young (3–5 months) and old (19–24 months) mice. Activation of KrasG12D in old mice resulted in shorter survival and development of higher‐grade lung tumors. Six weeks after KrasG12D activation, old lung tissues contained higher numbers of adenomas than their young tissue counterparts. Lung tumors in old mice displayed higher proliferation rates, as well as attenuated DNA damage and p53 tumor suppressor responses. Gene expression comparison of lung tumors from young and old mice revealed upregulation of extracellular matrix‐related genes in young tumors, indicative of a robust cancer‐associated fibroblast response. In old tumors, numerous inflammation‐related genes such as Ccl7,IL‐1β, Cxcr6, and IL‐15ra were consistently upregulated. Increased numbers of immune cells were localized around the periphery of lung adenomas from old mice. Our experiments indicate that more aggressive lung tumor formation in older KrasG12D mice may be in part the result of subdued tumor suppressor and DNA damage responses, an enhanced inflammatory milieu, and a more accommodating tissue microenvironment.
Collapse
Affiliation(s)
- Neha Parikh
- Department of Molecular Virology and Microbiology; Baylor College of Medicine; Houston TX 77030 USA
| | - Ryan L. Shuck
- Department of Molecular Virology and Microbiology; Baylor College of Medicine; Houston TX 77030 USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery; UT MD Anderson Cancer Center; Houston TX 77030 USA
| | - Lanlan Shen
- Children's Nutrition Research Center; Houston TX 77030 USA
| | - Lawrence A. Donehower
- Department of Molecular Virology and Microbiology; Baylor College of Medicine; Houston TX 77030 USA
| |
Collapse
|
12
|
Leroy B, Ballinger ML, Baran-Marszak F, Bond GL, Braithwaite A, Concin N, Donehower LA, El-Deiry WS, Fenaux P, Gaidano G, Langerød A, Hellstrom-Lindberg E, Iggo R, Lehmann-Che J, Mai PL, Malkin D, Moll UM, Myers JN, Nichols KE, Pospisilova S, Ashton-Prolla P, Rossi D, Savage SA, Strong LC, Tonin PN, Zeillinger R, Zenz T, Fraumeni JF, Taschner PEM, Hainaut P, Soussi T. Recommended Guidelines for Validation, Quality Control, and Reporting of TP53 Variants in Clinical Practice. Cancer Res 2017; 77:1250-1260. [PMID: 28254861 DOI: 10.1158/0008-5472.can-16-2179] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/12/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Accurate assessment of TP53 gene status in sporadic tumors and in the germline of individuals at high risk of cancer due to Li-Fraumeni Syndrome (LFS) has important clinical implications for diagnosis, surveillance, and therapy. Genomic data from more than 20,000 cancer genomes provide a wealth of information on cancer gene alterations and have confirmed TP53 as the most commonly mutated gene in human cancer. Analysis of a database of 70,000 TP53 variants reveals that the two newly discovered exons of the gene, exons 9β and 9γ, generated by alternative splicing, are the targets of inactivating mutation events in breast, liver, and head and neck tumors. Furthermore, germline rearrange-ments in intron 1 of TP53 are associated with LFS and are frequently observed in sporadic osteosarcoma. In this context of constantly growing genomic data, we discuss how screening strategies must be improved when assessing TP53 status in clinical samples. Finally, we discuss how TP53 alterations should be described by using accurate nomenclature to avoid confusion in scientific and clinical reports. Cancer Res; 77(6); 1250-60. ©2017 AACR.
Collapse
Affiliation(s)
- Bernard Leroy
- Sorbonne Université, UPMC Univ Paris 06, Paris, France
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Fanny Baran-Marszak
- Hôpital Avicenne, Assistance Publique-Hôpitaux De Paris, Bobigny, Service D'H ematologie Biologique, France
| | - Gareth L Bond
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Oxford, United Kingdom
| | - Antony Braithwaite
- Dept of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Children's Medical Research Institute, University of Sydney, Westmead NSW, Australia
| | - Nicole Concin
- Department of Gynecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria
| | | | - Wafik S El-Deiry
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pierre Fenaux
- Service d'hématologie séniors, Hôpital St Louis/Université Paris 7, 1 avenue Claude Vellefaux, Paris, France
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Eva Hellstrom-Lindberg
- Karolinska Institute, Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Iggo
- Bergonié Cancer Institute University of Bordeaux 229 cours de l'Argonne 33076 Bordeaux, France
| | | | - Phuong L Mai
- Cancer Genetics Program, Magee Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Ute M Moll
- Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Jeffrey N Myers
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sarka Pospisilova
- Masaryk University, CEITEC - Molecular Medicine and University Hospital Brno, Department of Internal Medicine - Hematology and Oncology, Brno, Czech Republic
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul (UFRGS) e Serviço deGenética Médica-HCPA, Rua Ramiro Barcelos, Porto Alegre, Brasil
| | - Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Louise C Strong
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University and Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Thorsten Zenz
- University of Heidelberg, Department of Medicine V, Heidelberg, Germany; Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Peter E M Taschner
- Generade Centre of Expertise Genomics and University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Pierre Hainaut
- Institut Albert Bonniot, Inserm 823, Université Grenoble Alpes, Rond Point de la Chantourne, La Tronche, France
| | - Thierry Soussi
- Sorbonne Université, UPMC Univ Paris 06, Paris, France. .,Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden.,INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France
| |
Collapse
|
13
|
Satterfield L, Shuck R, Kurenbekova L, Allen-Rhoades W, Edwards D, Huang S, Rajapakshe K, Coarfa C, Donehower LA, Yustein JT. miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. Int J Cancer 2017; 141:2062-2075. [PMID: 28748534 DOI: 10.1002/ijc.30909] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Ewing Sarcoma (ES) is a highly aggressive bone tumor with peak incidence in the adolescent population. It has a high propensity to metastasize, which is associated with dismal survival rates of approximately 25%. To further understand mechanisms of metastasis we investigated microRNA regulatory networks in ES. Our studies focused on miR-130b due to our analysis that enhanced expression of this microRNA has clinical relevance in multiple sarcomas, including ES. Our studies provide insights into a novel positive feedback network involving the direct regulation of miR-130b and activation of downstream signaling events contributing toward sarcoma metastasis. Specifically, we demonstrated miR-130b induces proliferation, invasion, and migration in vitro and increased metastatic potential in vivo. Using microarray analysis of ES cells with differential miR-130b expression we identified alterations in downstream signaling cascades including activation of the CDC42 pathway. We identified ARHGAP1, which is a negative regulator of CDC42, as a novel, direct target of miR-130b. In turn, downstream activation of PAK1 activated the JNK and AP-1 cascades and downstream transcriptional targets including IL-8, MMP1 and CCND1. Furthermore, chromatin immunoprecipitation of endogenous AP-1 in ES cells demonstrated direct binding to an upstream consensus binding site within the miR-130b promoter. Finally, small molecule inhibition of PAK1 blocked miR-130b activation of JNK and downstream AP-1 target genes, including primary miR-130b transcripts, and miR-130b oncogenic properties, thus identifying PAK1 as a novel therapeutic target for ES. Taken together, our findings identify and characterize a novel, targetable miR-130b regulatory network that promotes ES metastasis.
Collapse
Affiliation(s)
- Laura Satterfield
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX
| | - Ryan Shuck
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Lyazat Kurenbekova
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Wendy Allen-Rhoades
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX
| | - Dean Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Lawrence A Donehower
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Jason T Yustein
- Texas Children's Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Baylor College of Medicine, Houston, TX.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| |
Collapse
|
14
|
Wamsley JJ, Issaeva N, An H, Lu X, Donehower LA, Yarbrough WG. LZAP is a novel Wip1 binding partner and positive regulator of its phosphatase activity in vitro. Cell Cycle 2016; 16:213-223. [PMID: 28027003 DOI: 10.1080/15384101.2016.1261767] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The phosphatase Wip1 attenuates the DNA damage response (DDR) by removing phosphorylation marks from a number of DDR proteins (p53, MDM2, Chk1/2, p38). Wip1 also dephosphorylates and inactivates RelA. Notably, LZAP, a putative tumor suppressor, has been linked to dephosphorylation of several of these substrates, including RelA, p38, Chk1, and Chk2. LZAP has no known catalytic activity or functional motifs, suggesting that it exerts its effects through interaction with other proteins. Here we show that LZAP binds Wip1 and stimulates its phosphatase activity. LZAP had been previously shown to bind many Wip1 substrates (RelA, p38, Chk1/2), and our results show that LZAP also binds the previously identified Wip1 substrate, MDM2. This work identifies 2 novel Wip1 substrates, ERK1 and HuR, and demonstrates that HuR is a binding partner of LZAP. Pleasingly, LZAP potentiated Wip1 catalytic activity toward each substrate tested, regardless of whether full-length substrates or phosphopeptides were utilized. Since this effect was observed on ERK1, which does not bind LZAP, as well as for each of 7 peptides tested, we hypothesize that LZAP binding to the substrate is not required for this effect and that LZAP directly binds Wip1 to augment its phosphatase activity.
Collapse
Affiliation(s)
- J Jacob Wamsley
- a Department of Surgery, Division of Otolaryngology , Yale University , New Haven , CT , USA
| | - Natalia Issaeva
- a Department of Surgery, Division of Otolaryngology , Yale University , New Haven , CT , USA.,b Yale Cancer Center, Yale University , New Haven , CT , USA
| | - Hanbing An
- c Department of Surgery , Vanderbilt University , Nashville , TN , USA
| | - Xinyuan Lu
- d Department of Medicine , University of California San Francisco , San Francisco , CA , USA
| | - Lawrence A Donehower
- e Department of Molecular Virology and Microbiology , Baylor College of Medicine , Houston , TX , USA
| | - Wendell G Yarbrough
- a Department of Surgery, Division of Otolaryngology , Yale University , New Haven , CT , USA.,b Yale Cancer Center, Yale University , New Haven , CT , USA.,f Department of Pathology , Yale University , New Haven , CT , USA
| |
Collapse
|
15
|
Techavichit P, Gao Y, Kurenbekova L, Shuck R, Donehower LA, Yustein JT. Secreted Frizzled-Related Protein 2 (sFRP2) promotes osteosarcoma invasion and metastatic potential. BMC Cancer 2016; 16:869. [PMID: 27821163 PMCID: PMC5100268 DOI: 10.1186/s12885-016-2909-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background Osteosarcoma (OS), which has a high potential for developing metastatic disease, is the most frequent malignant bone tumor in children and adolescents. Molecular analysis of a metastatic genetically engineered mouse model of osteosarcoma identified enhanced expression of Secreted Frizzled-Related Protein 2 (sFRP2), a putative regulator of Wnt signaling within metastatic tumors. Subsequent analysis correlated increased expression in the human disease, and within highly metastatic OS cells. However, the role of sFRP2 in osteosarcoma development and progression has not been well elucidated. Methods Studies using stable gain or loss-of-function alterations of sFRP2 within human and mouse OS cells were performed to assess changes in cell proliferation, migration, and invasive ability in vitro, via both transwell and 3D matrigel assays. In additional, xenograft studies using overexpression of sFRP2 were used to assess effects on in vivo metastatic potential. Results Functional studies revealed stable overexpression of sFRP2 within localized human and mouse OS cells significantly increased cell migration and invasive ability in vitro and enhanced metastatic potential in vivo. Additional studies exploiting knockdown of sFRP2 within metastatic human and mouse OS cells demonstrated decreased cell migration and invasion ability in vitro, thus corroborating a critical biological phenotype carried out by sFRP2. Interestingly, alterations in sFRP2 expression did not alter OS proliferation rates or primary tumor development. Conclusions While future studies further investigating the molecular mechanisms contributing towards this sFRP2-dependent phenotype are needed, our studies clearly provide evidence that aberrant expression of sFRP2 can contribute to the invasive and metastatic potential for osteosarcoma. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2909-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Piti Techavichit
- Department of Pediatrics, Hematology-Oncology, Bumrungrad Hospital, Bangkok, Thailand
| | - Yang Gao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lyazat Kurenbekova
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ryan Shuck
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lawrence A Donehower
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason T Yustein
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Integrative Molecular and Biological Sciences Program, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
16
|
Gingras MC, Covington KR, Chang DK, Donehower LA, Gill AJ, Ittmann MM, Creighton CJ, Johns AL, Shinbrot E, Dewal N, Fisher WE, Pilarsky C, Grützmann R, Overman MJ, Jamieson NB, Van Buren G, Drummond J, Walker K, Hampton OA, Xi L, Muzny DM, Doddapaneni H, Lee SL, Bellair M, Hu J, Han Y, Dinh HH, Dahdouli M, Samra JS, Bailey P, Waddell N, Pearson JV, Harliwong I, Wang H, Aust D, Oien KA, Hruban RH, Hodges SE, McElhany A, Saengboonmee C, Duthie FR, Grimmond SM, Biankin AV, Wheeler DA, Gibbs RA. Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation. Cell Rep 2016; 14:907-919. [PMID: 26804919 PMCID: PMC4982376 DOI: 10.1016/j.celrep.2015.12.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 10/30/2015] [Accepted: 11/19/2015] [Indexed: 02/08/2023] Open
Abstract
The ampulla of Vater is a complex cellular environment from which adenocarcinomas arise to form a group of histopathologically heterogenous tumors. To evaluate the molecular features of these tumors, 98 ampullary adenocarcinomas were evaluated and compared to 44 distal bile duct and 18 duodenal adenocarcinomas. Genomic analyses revealed mutations in the WNT signaling pathway among half of the patients and in all three adenocarcinomas irrespective of their origin and histological morphology. These tumors were characterized by a high frequency of inactivating mutations of ELF3, a high rate of microsatellite instability, and common focal deletions and amplifications, suggesting common attributes in the molecular pathogenesis are at play in these tumors. The high frequency of WNT pathway activating mutation, coupled with small-molecule inhibitors of β-catenin in clinical trials, suggests future treatment decisions for these patients may be guided by genomic analysis.
Collapse
Affiliation(s)
- Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kyle R Covington
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Lawrence A Donehower
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anthony J Gill
- The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, Sydney, NSW 2065, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael M Ittmann
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX 77030, USA
| | - Chad J Creighton
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amber L Johns
- The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Eve Shinbrot
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ninad Dewal
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - William E Fisher
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; Academic Unit of Surgery, Institute of Cancer Sciences, Glasgow Royal Infirmary, Level 2, New Lister Building, University of Glasgow, Glasgow G31 2ER, UK
| | - George Van Buren
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Drummond
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kimberly Walker
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oliver A Hampton
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liu Xi
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Lee
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michelle Bellair
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mike Dahdouli
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaswinder S Samra
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, NSW 2065, Australia
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - John V Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Huamin Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Aust
- Department of Pathology, TU Dresden, 01307 Dresden, Germany
| | - Karin A Oien
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Department of Pathology, Southern General Hospital, Greater Glasgow and Clyde NHS, Glasgow G51 4TF, UK
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, the Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Sally E Hodges
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy McElhany
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; The Elkins Pancreas Center at Baylor College of Medicine, Houston, TX 77030, USA
| | - Charupong Saengboonmee
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Fraser R Duthie
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Department of Pathology, Southern General Hospital, Greater Glasgow and Clyde NHS, Glasgow G51 4TF, UK
| | - Sean M Grimmond
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK; The Kinghorn Cancer Centre and the Cancer Research Program Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
17
|
Wang L, Ni X, Covington KR, Yang BY, Shiu J, Zhang X, Xi L, Meng Q, Langridge T, Drummond J, Donehower LA, Doddapaneni H, Muzny DM, Gibbs RA, Wheeler DA, Duvic M. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat Genet 2015; 47:1426-34. [PMID: 26551670 PMCID: PMC4829974 DOI: 10.1038/ng.3444] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 10/16/2015] [Indexed: 12/16/2022]
Abstract
Sézary syndrome is a rare leukemic form of cutaneous T cell lymphoma characterized by generalized redness, scaling, itching and increased numbers of circulating atypical T lymphocytes. It is rarely curable, with poor prognosis. Here we present a multiplatform genomic analysis of 37 patients with Sézary syndrome that implicates dysregulation of cell cycle checkpoint and T cell signaling. Frequent somatic alterations were identified in TP53, CARD11, CCR4, PLCG1, CDKN2A, ARID1A, RPS6KA1 and ZEB1. Activating CCR4 and CARD11 mutations were detected in nearly one-third of patients. ZEB1, encoding a transcription repressor essential for T cell differentiation, was deleted in over one-half of patients. IL32 and IL2RG were overexpressed in nearly all cases. Our results demonstrate profound disruption of key signaling pathways in Sézary syndrome and suggest potential targets for new therapies.
Collapse
Affiliation(s)
- Linghua Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao Ni
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kyle R. Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Betty Y. Yang
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jessica Shiu
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiang Zhang
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Liu Xi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Langridge
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jennifer Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lawrence A. Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Madeleine Duvic
- Department of Dermatology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
18
|
Rao PH, Zhao S, Zhao YJ, Yu A, Rainusso N, Trucco M, Allen-Rhoades W, Satterfield L, Fuja D, Borra VJ, Man TK, Donehower LA, Yustein JT. Coamplification ofMyc/Pvt1and homozygous deletion ofNlrp1locus are frequent genetics changes in mouse osteosarcoma. Genes Chromosomes Cancer 2015; 54:796-808. [DOI: 10.1002/gcc.22291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/19/2015] [Accepted: 07/29/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Pulivarthi H. Rao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Shuying Zhao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Yi-Jue Zhao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Alexander Yu
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Nino Rainusso
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Matteo Trucco
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Wendy Allen-Rhoades
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Laura Satterfield
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Daniel Fuja
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Vishnupriya J. Borra
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Tsz-Kwong Man
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Lawrence A. Donehower
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
- Department of Molecular & Cellular Biology; Baylor College of Medicine; Houston TX 77030
- Department of Molecular Virology & Microbiology; Baylor College of Medicine; Houston TX 77030
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Jason T. Yustein
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
- Department of Molecular & Cellular Biology; Baylor College of Medicine; Houston TX 77030
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| |
Collapse
|
19
|
Garcia JM, Chen JA, Guillory B, Donehower LA, Smith RG, Lamb DJ. Ghrelin Prevents Cisplatin-Induced Testicular Damage by Facilitating Repair of DNA Double Strand Breaks Through Activation of p53 in Mice. Biol Reprod 2015; 93:24. [PMID: 26019260 DOI: 10.1095/biolreprod.115.129759] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/22/2015] [Indexed: 12/20/2022] Open
Abstract
Cisplatin administration induces DNA damage resulting in germ cell apoptosis and subsequent testicular atrophy. Although 50 percent of male cancer patients receiving cisplatin-based chemotherapy develop long-term secondary infertility, medical treatment to prevent spermatogenic failure after chemotherapy is not available. Under normal conditions, testicular p53 promotes cell cycle arrest, which allows time for DNA repair and reshuffling during meiosis. However, its role in the setting of cisplatin-induced infertility has not been studied. Ghrelin administration ameliorates the spermatogenic failure that follows cisplatin administration in mice, but the mechanisms mediating these effects have not been well established. The aim of the current study was to characterize the mechanisms of ghrelin and p53 action in the testis after cisplatin-induced testicular damage. Here we show that cisplatin induces germ cell damage through inhibition of p53-dependent DNA repair mechanisms involving gamma-H2AX and ataxia telangiectasia mutated protein kinase. As a result, testicular weight and sperm count and motility were decreased with an associated increase in sperm DNA damage. Ghrelin administration prevented these sequelae by restoring the normal expression of gamma-H2AX, ataxia telangiectasia mutated, and p53, which in turn allows repair of DNA double stranded breaks. In conclusion, these findings indicate that ghrelin has the potential to prevent or diminish infertility caused by cisplatin and other chemotherapeutic agents by restoring p53-dependent DNA repair mechanisms.
Collapse
Affiliation(s)
- Jose M Garcia
- Division of Endocrinology, Diabetes and Metabolism, MCL, Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center, Department of Medicine, Baylor College of Medicine, Houston, Texas Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Ji-an Chen
- Division of Endocrinology, Diabetes and Metabolism, MCL, Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center, Department of Medicine, Baylor College of Medicine, Houston, Texas Department of Health Education, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Bobby Guillory
- Division of Endocrinology, Diabetes and Metabolism, MCL, Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center, Department of Medicine, Baylor College of Medicine, Houston, Texas Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Roy G Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Huffington Center on Aging, Baylor College of Medicine, Houston, Texas Department of Metabolism and Aging, The Scripps Research Institute Florida, Jupiter, Florida
| | - Dolores J Lamb
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, Texas Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas Scott Department of Urology, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
20
|
Allen-Rhoades W, Kurenbekova L, Satterfield L, Parikh N, Fuja D, Shuck RL, Rainusso N, Trucco M, Barkauskas DA, Jo E, Ahern C, Hilsenbeck S, Donehower LA, Yustein JT. Cross-species identification of a plasma microRNA signature for detection, therapeutic monitoring, and prognosis in osteosarcoma. Cancer Med 2015; 4:977-88. [PMID: 25784290 PMCID: PMC4529336 DOI: 10.1002/cam4.438] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/23/2015] [Accepted: 02/02/2015] [Indexed: 12/25/2022] Open
Abstract
Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, noninvasive biologic markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. MicroRNAs (miRNAs) are evolutionarily conserved, stable, small noncoding RNA molecules that are key posttranscriptional regulators and are ideal candidates for circulating biomarker development due to their stability in plasma, ease of isolation, and the unique expressions associated with specific disease states. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from a genetically engineered mouse model of OS to identify a profile of four plasma miRNAs. Subsequent analysis of 40 human patient samples corroborated these results. We also identified disease-specific endogenous reference plasma miRNAs for mouse and human studies. Specifically, we observed plasma miR-205-5p was decreased 2.68-fold in mice with OS compared to control mice, whereas, miR-214, and miR-335-5p were increased 2.37- and 2.69-fold, respectively. In human samples, the same profile was seen with miR-205-5p decreased 1.75-fold in patients with OS, whereas miR-574-3p, miR-214, and miR-335-5p were increased 3.16-, 8.31- and 2.52-fold, respectively, compared to healthy controls. Furthermore, low plasma levels of miR-214 in metastatic patients at time of diagnosis conveyed a significantly better overall survival. This is the first study to identify plasma miRNAs that could be used to prospectively identify disease, potentially monitor therapeutic efficacy and have prognostic implications for OS patients.
Collapse
Affiliation(s)
| | | | - Laura Satterfield
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Neha Parikh
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Daniel Fuja
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ryan L Shuck
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Nino Rainusso
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Matteo Trucco
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Donald A Barkauskas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Eunji Jo
- Biostatistics and Informatics Shared Resource, The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Charlotte Ahern
- Biostatistics and Informatics Shared Resource, The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Susan Hilsenbeck
- Biostatistics and Informatics Shared Resource, The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Lawrence A Donehower
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Jason T Yustein
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
21
|
Richter M, Dayaram T, Gilmartin AG, Ganji G, Pemmasani SK, Van Der Key H, Shohet JM, Donehower LA, Kumar R. WIP1 phosphatase as a potential therapeutic target in neuroblastoma. PLoS One 2015; 10:e0115635. [PMID: 25658463 PMCID: PMC4319922 DOI: 10.1371/journal.pone.0115635] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/25/2014] [Indexed: 12/15/2022] Open
Abstract
The wild-type p53-induced phosphatase 1 (WIP1) is a serine/threonine phosphatase that negatively regulates multiple proteins involved in DNA damage response including p53, CHK2, Histone H2AX, and ATM, and it has been shown to be overexpressed or amplified in human cancers including breast and ovarian cancers. We examined WIP1 mRNA levels across multiple tumor types and found the highest levels in breast cancer, leukemia, medulloblastoma and neuroblastoma. Neuroblastoma is an exclusively TP53 wild type tumor at diagnosis and inhibition of p53 is required for tumorigenesis. Neuroblastomas in particular have previously been shown to have 17q amplification, harboring the WIP1 (PPM1D) gene and associated with poor clinical outcome. We therefore sought to determine whether inhibiting WIP1 with a selective antagonist, GSK2830371, can attenuate neuroblastoma cell growth through reactivation of p53 mediated tumor suppression. Neuroblastoma cell lines with wild-type TP53 alleles were highly sensitive to GSK2830371 treatment, while cell lines with mutant TP53 were resistant to GSK2830371. The majority of tested neuroblastoma cell lines with copy number gains of the PPM1D locus were also TP53 wild-type and sensitive to GSK2830371A; in contrast cell lines with no copy gain of PPM1D were mixed in their sensitivity to WIP1 inhibition, with the primary determinant being TP53 mutational status. Since WIP1 is involved in the cellular response to DNA damage and drugs used in neuroblastoma treatment induce apoptosis through DNA damage, we sought to determine whether GSK2830371 could act synergistically with standard of care chemotherapeutics. Treatment of wild-type TP53 neuroblastoma cell lines with both GSK2830371 and either doxorubicin or carboplatin resulted in enhanced cell death, mediated through caspase 3/7 induction, as compared to either agent alone. Our data suggests that WIP1 inhibition represents a novel therapeutic approach to neuroblastoma that could be integrated with current chemotherapeutic approaches.
Collapse
Affiliation(s)
- Mark Richter
- Oncology R&D, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, United States of America
| | - Tajhal Dayaram
- Department of Molecular Virology and Microbiology and Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aidan G. Gilmartin
- Oncology R&D, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, United States of America
| | - Gopinath Ganji
- Oncology R&D, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, United States of America
| | | | - Harjeet Van Der Key
- Platform Technology & Science, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, United States of America
| | - Jason M. Shohet
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lawrence A. Donehower
- Department of Molecular Virology and Microbiology and Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (LAD); (RK)
| | - Rakesh Kumar
- Oncology R&D, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, United States of America
- * E-mail: (LAD); (RK)
| |
Collapse
|
22
|
Xia Z, Donehower LA, Cooper TA, Neilson JR, Wheeler DA, Wagner EJ, Li W. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun 2014; 5:5274. [PMID: 25409906 DOI: 10.1038/ncomms6274] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/15/2014] [Indexed: 12/26/2022] Open
Abstract
Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumour/normal pairs across seven tumour types, DaPars reveals 1,346 genes with recurrent and tumour-specific APAs. Most APA genes (91%) have shorter 3'-untranslated regions (3' UTRs) in tumours that can avoid microRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumour proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3'-UTR shortening across multiple tumour types.
Collapse
Affiliation(s)
- Zheng Xia
- 1] Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lawrence A Donehower
- 1] Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- 1] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA [3] Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David A Wheeler
- 1] Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Wei Li
- 1] Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
23
|
Lu X, Nguyen TA, Appella E, Donehower LA. Homeostatic Regulation of Base Excision Repair by a p53-Induced Phosphatase: Linking Stress Response Pathways with DNA Repair Proteins. Cell Cycle 2014; 3:1363-6. [PMID: 15539943 DOI: 10.4161/cc.3.11.1241] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The p53 protein plays a central role in the integration of cellular stress responses. If the cell incurs DNA damage, p53-induced cell cycle arrest is accompanied by p53-facilitated DNA repair. In particular, p53 has been demonstrated to promote both nucleotide excision repair (NER) and base excision repair (BER). Once these repair processes are completed, p53 activity declines and the cell can reenter the cell cycle. A critical mediator of this p53 negative regulatory feedback loop is Mdm2, a p53 transcriptional target whose protein mediates p53 proteolytic degradation. Another such p53 transcriptional target that may function in a p53 negative regulation is the PPM1D phosphatase. PPM1D may inhibit p53 activity through inactivating dephosphorylation of the p38 MAP kinase. We have recently shown that PPM1D suppresses BER in part through dephosphorylation of a key BER effector, the nuclear isoform of uracil DNA glycosylase, or UNG2. This finding further links p53 signaling to DNA repair pathways and illustrates a mechanism by which activated DNA repair systems are returned to a deactivated, homeostatic state.
Collapse
Affiliation(s)
- Xiongbin Lu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | |
Collapse
|
24
|
Covington KR, Donehower LA, Creighton C, Slagle BL, Goss JA, Cotton RT, Gingras MC, Shinbrot E, Guiteau JJ, Nguyen TN, Harring TR, Muzny DM, Walker K, Doddapaneni H, Gibbs RA, Aburatani H, Shibata T, Wheeler DA. Abstract 2211: Viral subtypes in hepatocellular carcinoma are associated with different mechanisms of WNT/CTNNB1 alteration. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent human cancers, especially in Asia, and regions of endemic hepatitis infection. The primary risk factors for HCC are chronic hepatitis infection by hepatitis C (HCV) or hepatitis B (HBV). We performed whole exome sequencing on 549 matched tumor and normal samples from three centers (BCM HGSC, RCAST, NCC) to identify somatic changes in protein coding regions and changes in copy number. Here we describe variants associated with specific viral etiologies in HCC.
We found TP53, CTNNB1, ARID1A, ARID2, and AXIN1 to be among the most frequently mutated genes in the entire dataset, implicating DNA damage, WNT signaling, and chromatin remodeling as recurrently altered pathways in HCC. Our validation rate for mutations in significantly mutated genes was over 95%. We identified 18 genes which differed significantly (p < 0.05) in mutation frequency between viral subtypes. Of these, AXIN1 was mutated in over 15% of HBV-associated HCC but less than 5% of HCV and non-viral-associated HCC. Additionally, we performed GISTIC analysis based on read depth from our whole exome sequencing data. We found that WNT3A and MYC were significantly amplified and AXIN1 and TP53 were significantly deleted in HCV-associated HCC but not HBV or non-virus-associated HCC.
Our findings indicate that WNT/beta-catenin signaling is a frequently altered pathway in HCC. While aberrations in this pathway were present in all viral etiologies, HBV-associated HCC tended to mutate AXIN1 while HCV-associated HCC tended to have AXIN1 deletion. These differences may result from virus-specific oncogenic processes.
Citation Format: Kyle R. Covington, Lawrence A. Donehower, Chad Creighton, Betty L. Slagle, John A. Goss, Ronald T. Cotton, Marie-Claude Gingras, Eve Shinbrot, Jacfranz J. Guiteau, Thao N. Nguyen, Theresa R. Harring, Donna M. Muzny, Kimberly Walker, HarshaVardhan Doddapaneni, Richard A. Gibbs, Hiroyuki Aburatani, Tatsuhiro Shibata, David A. Wheeler, Japan ICGC HCC Project. Viral subtypes in hepatocellular carcinoma are associated with different mechanisms of WNT/CTNNB1 alteration. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2211. doi:10.1158/1538-7445.AM2014-2211
Collapse
|
25
|
Tao J, Jiang MM, Jiang L, Salvo JS, Zeng HC, Dawson B, Bertin TK, Rao PH, Chen R, Donehower LA, Gannon F, Lee BH. Notch activation as a driver of osteogenic sarcoma. Cancer Cell 2014; 26:390-401. [PMID: 25203324 PMCID: PMC4159617 DOI: 10.1016/j.ccr.2014.07.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/21/2014] [Accepted: 07/26/2014] [Indexed: 12/22/2022]
Abstract
Osteogenic sarcoma (OS) is a deadly skeletal malignancy whose cause is unknown. We report here a mouse model of OS based on conditional expression of the intracellular domain of Notch1 (NICD). Expression of the NICD in immature osteoblasts was sufficient to drive the formation of bone tumors, including OS, with complete penetrance. These tumors display features of human OS; namely, histopathology, cytogenetic complexity, and metastatic potential. We show that Notch activation combined with loss of p53 synergistically accelerates OS development in mice, although p53-driven OS is not Rbpj dependent, which demonstrates a dual dominance of the Notch oncogene and p53 mutation in the development of OS. Using this model, we also reveal the osteoblasts as the potential sources of OS.
Collapse
Affiliation(s)
- Jianning Tao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Ming-Ming Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Lichun Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Jason S Salvo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Huan-Chang Zeng
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Brian Dawson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Terry K Bertin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Pulivarthi H Rao
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Lawrence A Donehower
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Francis Gannon
- Department of Pathology, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, R815, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA.
| |
Collapse
|
26
|
Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 2014; 26:319-330. [PMID: 25155756 PMCID: PMC4160352 DOI: 10.1016/j.ccr.2014.07.014] [Citation(s) in RCA: 568] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/29/2014] [Accepted: 07/17/2014] [Indexed: 11/27/2022]
Abstract
We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations.
Collapse
Affiliation(s)
- Caleb F Davis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, CRC Room 1W-5940, Bethesda, MD 20892, USA
| | - Min Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lixing Yang
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Hui Shen
- USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyojin Kang
- National Institute of Supercomputing and Networking, Korea Institute of Science and Technology Information, Daejeon, Korea
| | - Sang Cheol Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Catherine C Fahey
- Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kathryn E Hacker
- Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gyan Bhanot
- Department of Molecular Biology and Biochemistry, Rutgers University, Busch Campus, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Dmitry A Gordenin
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Andy Chu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver BC V5Z 4S6, Canada
| | - Preethi H Gunaratne
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biology & Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204, USA
| | - Michael Biehl
- Johann Bernoulli Institute for Mathematics and Computer Science, Intelligent Systems Group, University of Groningen, P.O. Box 407, 9700 AK Groningen, the Netherlands
| | - Sahil Seth
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benny A Kaipparettu
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher A Bristow
- Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lawrence A Donehower
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric M Wallen
- Department of Urology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Angela B Smith
- Department of Urology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Satish K Tickoo
- Department of Pathology, Memorial Sloan-Kettering Cancer, 1275 York Avenue, New York, NY 10065, USA
| | - Pheroze Tamboli
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Victor Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer, 1275 York Avenue, New York, NY 10065, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, CRC Room 1W-5940, Bethesda, MD 20892, USA; Leidos Biomedical Research, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - James J Hsieh
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10021, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - A Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | | | - Lynda Chin
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Genomic Medicine, Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver BC V5Z 4S6, Canada
| | - Peter W Laird
- USC Epigenome Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Elizabeth P Henske
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - David J Kwiatkowski
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Peter J Park
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Margaret Morgan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Shuch
- Department of Urology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, CRC Room 1W-5940, Bethesda, MD 20892, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Department of Urology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Hematology and Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Chad J Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
27
|
Donehower LA. Insights into Wild-Type and Mutant p53 Functions Provided by Genetically Engineered Mice. Hum Mutat 2014; 35:715-27. [DOI: 10.1002/humu.22507] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/02/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Lawrence A. Donehower
- Departments of Molecular Virology and Microbiology, Molecular and Cellular Biology, and Pediatrics; Baylor College of Medicine; Houston Texas 77030
| |
Collapse
|
28
|
Parikh N, Hilsenbeck S, Creighton CJ, Dayaram T, Shuck R, Shinbrot E, Xi L, Gibbs RA, Wheeler DA, Donehower LA. Effects of TP53 mutational status on gene expression patterns across 10 human cancer types. J Pathol 2014; 232:522-33. [PMID: 24374933 DOI: 10.1002/path.4321] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 01/13/2023]
Abstract
Mutations in the TP53 tumour suppressor gene occur in half of all human cancers, indicating its critical importance in inhibiting cancer development. Despite extensive studies, the mechanisms by which mutant p53 enhances tumour progression remain only partially understood. Here, using data from the Cancer Genome Atlas (TCGA), genomic and transcriptomic analyses were performed on 2256 tumours from 10 human cancer types. We show that tumours with TP53 mutations have altered gene expression profiles compared to tumours retaining two wild-type TP53 alleles. Among 113 known p53-up-regulated target genes identified from cell culture assays, 10 were consistently up-regulated in at least eight of 10 cancer types that retain both copies of wild-type TP53. RPS27L, CDKN1A (p21(CIP1)) and ZMAT3 were significantly up-regulated in all 10 cancer types retaining wild-type TP53. Using this p53-based expression analysis as a discovery tool, we used cell-based assays to identify five novel p53 target genes from genes consistently up-regulated in wild-type p53 cancers. Global gene expression analyses revealed that cell cycle regulatory genes and transcription factors E2F1, MYBL2 and FOXM1 were disproportionately up-regulated in many TP53 mutant cancer types. Finally, > 93% of tumours with a TP53 mutation exhibited greatly reduced wild-type p53 messenger expression, due to loss of heterozygosity or copy neutral loss of heterozygosity, supporting the concept of p53 as a recessive tumour suppressor. The data indicate that tumours with wild-type TP53 retain some aspects of p53-mediated growth inhibitory signalling through activation of p53 target genes and suppression of cell cycle regulatory genes.
Collapse
Affiliation(s)
- Neha Parikh
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
MOTIVATION Combinatorial therapies play increasingly important roles in combating complex diseases. Owing to the huge cost associated with experimental methods in identifying optimal drug combinations, computational approaches can provide a guide to limit the search space and reduce cost. However, few computational approaches have been developed for this purpose, and thus there is a great need of new algorithms for drug combination prediction. RESULTS Here we proposed to formulate the optimal combinatorial therapy problem into two complementary mathematical algorithms, Balanced Target Set Cover (BTSC) and Minimum Off-Target Set Cover (MOTSC). Given a disease gene set, BTSC seeks a balanced solution that maximizes the coverage on the disease genes and minimizes the off-target hits at the same time. MOTSC seeks a full coverage on the disease gene set while minimizing the off-target set. Through simulation, both BTSC and MOTSC demonstrated a much faster running time over exhaustive search with the same accuracy. When applied to real disease gene sets, our algorithms not only identified known drug combinations, but also predicted novel drug combinations that are worth further testing. In addition, we developed a web-based tool to allow users to iteratively search for optimal drug combinations given a user-defined gene set. AVAILABILITY Our tool is freely available for noncommercial use at http://www.drug.liuzlab.org/. CONTACT zhandong.liu@bcm.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Kaifang Pang
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Department of Pediatrics-Neurology, Department of Obstetrics and Gynaecology, Department of Molecular Virology and Microbiology, Baylor College of Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
Zhao S, Kurenbekova L, Donehower LA, Yustein JT. Abstract 3867: Novel mouse models to investigate the molecular pathogenesis of metastatic osteosarcoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Osteosarcoma (OS) is the primary bone tumor in the pediatric population with the main determinant for patient prognosis being the presence of metastatic disease. Approximately 25-30% of patients will present with metastatic osteosarcoma. Patients with metastatic disease have long-term survival rates often <20%.
Objectives: We hypothesize that the molecular pathogenesis of metastatic osteosarcoma is different from localized disease. We intend this work to provide a relevant, endogenous model of metastatic OS that can be utilized to advance our understanding of the molecular pathogenesis of the disease, insights into novel therapeutic targets and as a pre-clinical model for investigating the efficacy of novel therapies.
Design: We have developed a tissue-specific alteration of the p53 status by using osteoblast specific Cre-recombinase expressing mice to generate progeny that spontaneously form endogenous osteosarcomas. Through the use of a mutated, gain of function form of p53, shown previously to be associated with metastatic disease, we have developed a novel immunocompetent model that significantly enhances the endogenous development of metastatic OS.
Results: Tumor analysis has revealed genetic insights in the metastatic progression of osteosarcoma. These include the significant downregulation of Wnt-signaling inhibitors, such as NKD2, APCDD1 and Wnt5a in the metastatic tumors. Functional studies have determined that overexpression of NKD2, also downregulated in several human OS metastatic cell lines, in metastatic mouse OS cell lines leads to a significant decrease in metastatic lung lesions upon transplantation into immunodeficient mice. Possible NKD2-dependent functions include regulation of not only the Wnt signaling pathway, but also blood vessel formation, regulation of cell migration and cell adhesion.
We have also noted the dysregulation of several critical microRNAs in metastatic OS, including the upregulation of mir-130b in the metastatic lesions. This particular microRNA has recently been shown to have clinical correlation in Ewing's sarcoma, with higher levels of tumor mir-130b having a significantly poorer outcome. We are actively pursuing the role of this (and other) microRNA(s) in the molecular pathogenesis of metastatic osteosarcoma.
Conclusion: This novel model has enabled valuable molecular insights into the development and progression of metastatic OS that can lead to the identification of novel therapeutic targets.
Citation Format: Shuying Zhao, Lyazat Kurenbekova, Lawrence A. Donehower, Jason T. Yustein. Novel mouse models to investigate the molecular pathogenesis of metastatic osteosarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3867. doi:10.1158/1538-7445.AM2013-3867
Collapse
|
31
|
Shinbrot E, Weinhold N, Schultz N, Donehower LA, Drummond J, Chang K, Gibbs R, Sander C, Wheeler DA. Abstract 1114: Polymerase epsilon (POLE) mutations and mutator phenotypes in colorectal and endometrial tumors. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal rectal and endometrial cancers are divided into microsatellite instable (MSI) and microsatellite stable (MSS) types. MSS tumors have chromosome instability with mutation rates of 1-10/Mb. MSI patients have a better prognosis than MSS patients and are treated less aggressively. These tumors exhibit microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP), an increased mutation rate (10-100/Mb, hypermutated). Here we demonstrate a novel class of tumor in these two diseases exhibiting an ultramutator phenotype with mutation rates exceeding 100/ Mb, MSS and chromosome stable. The ultra-high mutation rates appear to be caused by recurrent mutations in the exonuclease domain of DNA polymerase epsilon (POLE).
Matched tumor and normal whole exomes for 512 colorectal and 248 endometrial cancers (TCGA data control center) were evaluated for mutation frequency and MSI status. Among the colorectal tumors, 70/512(14%) were hyper mutated, endometroid tumors had 65/248(26%) hypermutated tumors. Within the hypermutated tumors, we identified tumors with extremely high mutation rates (100 mutations/Mb) termed “ultramutated”. 14 (3%) colorectal and 17 (7%) endometrial were ultramutated. 100% of the colorectal and endometrial ultramutated contain an exonuclease domain mutation in POLE with three recurrently mutated positions: P286R/H/S and V411L and S459F, these mutations are found exclusively in ultramutated samples. The functional relevance of these mutations has been demonstrated by previous mutational analysis of the exonuclease domain in bacteria phage (T4) yeast,and mice. Disruption of residues in the active site leads to high error rates, a mutator phenotype and tumor formation. The defined exonuclease active site aligns closely with the recurrent mutation found in the ultramutated tumors.
The ultramuted tumors have a distinct mutation spectrum, occur in context and exhibit strand biases. POLE exonuclease domain mutation tumors have high rates of C to A and T to G mutations with low rates of C to G and T to A. Changes of C to A occur predominately in context of 3’ and 5’ flanking T bases. This mutation spectrum and context of flanking bases suggests replicative strand bias. We found that mutations on the leading strand, exhibited a preference for C to A over G to T (60:40). Suggesting transcription-coupled repair (TCR) plays a role in ultramutation.
Our results demonstrate that ultra mutated tumors are driven by recurrent mutations in the exonuclease domain of DNA polymerase epsilon. The distinct mutation spectrum, strand bias and mutation context all suggest TCR is involved in ultramutated tumors. We describe a previously unknown role of POLE in colorectal tumors as well as identification of a previously undescribed hot spot for cancer mutations.
Citation Format: Eve Shinbrot, Nils Weinhold, Nikolaus Schultz, Lawrence A. Donehower, Jennifer Drummond, Kyle Chang, Richard Gibbs, Chris Sander, David A. Wheeler. Polymerase epsilon (POLE) mutations and mutator phenotypes in colorectal and endometrial tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1114. doi:10.1158/1538-7445.AM2013-1114
Collapse
Affiliation(s)
| | - Nils Weinhold
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Kyle Chang
- 1Baylor College of Medicine, Houston, TX
| | | | - Chris Sander
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | |
Collapse
|
32
|
Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne PH, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. J Pathol 2013; 229:99-110. [PMID: 22899370 DOI: 10.1002/path.4087] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 07/31/2012] [Accepted: 08/04/2012] [Indexed: 12/28/2022]
Abstract
Approximately 15% of colorectal carcinomas (CRCs) exhibit a hypermutated genotype accompanied by high levels of microsatellite instability (MSI-H) and defects in DNA mismatch repair. These tumours, unlike the majority of colorectal carcinomas, are often diploid, exhibit frequent epigenetic silencing of the MLH1 DNA mismatch repair gene, and have a better clinical prognosis. As an adjunct study to The Cancer Genome Atlas consortium that recently analysed 224 colorectal cancers by whole exome sequencing, we compared the 35 CRCs (15.6%) with a hypermutated genotype to those with a non-hypermutated genotype. We found that 22 (63%) of the hypermutated CRCs exhibited transcriptional silencing of the MLH1 gene, a high frequency of BRAF V600E gene mutations, and infrequent APC and KRAS mutations, a mutational pattern significantly different from their non-hypermutated counterparts. However, the remaining 13 (37%) hypermutated CRCs lacked MLH1 silencing, contained tumours with the highest mutation rates ('ultramutated' CRCs), and exhibited higher incidences of APC and KRAS mutations, but infrequent BRAF mutations. These patterns were confirmed in an independent validation set of 250 exome-sequenced CRCs. Analysis of mRNA and microRNA expression signatures revealed that hypermutated CRCs with MLH1 silencing had greatly reduced levels of WNT signalling and increased BRAF signalling relative to non-hypermutated CRCs. Our findings suggest that hypermutated CRCs include one subgroup with fundamentally different pathways to malignancy than the majority of CRCs. Examination of MLH1 expression status and frequencies of APC, KRAS, and BRAF mutation in CRC may provide a useful diagnostic tool that could supplement the standard microsatellite instability assays and influence therapeutic decisions.
Collapse
Affiliation(s)
- Lawrence A Donehower
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Dayaram T, Lemoine FJ, Donehower LA, Marriott SJ. Activation of WIP1 phosphatase by HTLV-1 Tax mitigates the cellular response to DNA damage. PLoS One 2013; 8:e55989. [PMID: 23405243 PMCID: PMC3566092 DOI: 10.1371/journal.pone.0055989] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 01/08/2013] [Indexed: 12/21/2022] Open
Abstract
Genomic instability stemming from dysregulation of cell cycle checkpoints and DNA damage response (DDR) is a common feature of many cancers. The cancer adult T cell leukemia (ATL) can occur in individuals infected with human T cell leukemia virus type 1 (HTLV-1), and ATL cells contain extensive chromosomal abnormalities, suggesting that they have defects in the recognition or repair of DNA damage. Since Tax is the transforming protein encoded by HTLV-1, we asked whether Tax can affect cell cycle checkpoints and the DDR. Using a combination of flow cytometry and DNA repair assays we showed that Tax-expressing cells exit G1 phase and initiate DNA replication prematurely following damage. Reduced phosphorylation of H2AX (γH2AX) and RPA2, phosphoproteins that are essential to properly initiate the DDR, was also observed in Tax-expressing cells. To determine the cause of decreased DDR protein phosphorylation in Tax-expressing cells, we examined the cellular phosphatase, WIP1, which is known to dephosphorylate γH2AX. We found that Tax can interact with Wip1 in vivo and in vitro, and that Tax-expressing cells display elevated levels of Wip1 mRNA. In vitro phosphatase assays showed that Tax can enhance Wip1 activity on a γH2AX peptide target by 2-fold. Thus, loss of γH2AX in vivo could be due, in part, to increased expression and activity of WIP1 in the presence of Tax. siRNA knockdown of WIP1 in Tax-expressing cells rescued γH2AX in response to damage, confirming the role of WIP1 in the DDR. These studies demonstrate that Tax can disengage the G1/S checkpoint by enhancing WIP1 activity, resulting in reduced DDR. Premature G1 exit of Tax-expressing cells in the presence of DNA lesions creates an environment that tolerates incorporation of random mutations into the host genome.
Collapse
Affiliation(s)
- Tajhal Dayaram
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Francene J. Lemoine
- Department of Biological Sciences, Northwestern State University of Louisiana, Natchitoches, Louisiana, United States of America
| | - Lawrence A. Donehower
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Susan J. Marriott
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
34
|
Zhao S, Kurenbekova L, Donehower LA, Yustein JT. Abstract A85: Novel mouse models to investigate the molecular pathogenesis of metastatic osteosarcoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.tim2013-a85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Osteosarcoma (OS) is the primary bone tumor in the pediatric population with the main determinant for patient prognosis being the presence of metastatic disease. Approximately 25-30% of patients will present with metastatic osteosarcoma. Patients with metastatic disease have long-term survival rates often <20%.
Objectives: We hypothesize that the molecular pathogenesis of metastatic osteosarcoma is different from localized disease. We intend this work to provide a relevant, endogenous model of metastatic OS that can be utilized to advance our understanding of the molecular pathogenesis of the disease, insights into novel therapeutic targets and as a pre-clinical model for investigating the efficacy of novel therapies.
Design: We have developed a tissue-specific alteration of the p53 status by using osteoblast specific Cre-recombinase expressing mice to generate progeny that spontaneously form endogenous osteosarcomas. Through the use of a mutated, gain of function form of p53, shown previously to be associated with metastatic disease, we have developed a novel immunocompetent model that significantly enhances the endogenous development of metastatic OS.
Results: Tumor analysis has revealed genetic insights in the metastatic progression of osteosarcoma. These include the significant downregulation of Wnt-signaling inhibitors, such as NKD2, APCDD1 and Wnt5a in the metastatic tumors. Functional studies have determined that overexpression of NKD2, also downregulated in several human OS metastatic cell lines, in metastatic mouse OS cell lines leads to a significant decrease in metastatic lung lesions upon transplantation into immunodeficient mice. Possible NKD2-dependent functions include regulation of not only the Wnt signaling pathway, but also blood vessel formation, regulation of cell migration and cell adhesion.
We have also noted the dysregulation of several critical microRNAs in metastatic OS, including the upregulation of mir-130b in the metastatic lesions. This particular microRNA has recently been shown to have clinical correlation in Ewing's sarcoma, with higher levels of tumor mir-130b having a significantly poorer outcome. We are actively pursuing the role of this (and other) microRNA(s) in the molecular pathogenesis of metastatic osteosarcoma.
Conclusion: This novel model has enabled valuable molecular insights into the development and progression of metastatic OS that can lead to the identification of novel therapeutic targets.
Citation Format: Shuying Zhao, Lyazat Kurenbekova, Lawrence A. Donehower, Jason T. Yustein. Novel mouse models to investigate the molecular pathogenesis of metastatic osteosarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr A85.
Collapse
|
35
|
Donehower LA. Rapamycin as longevity enhancer and cancer preventative agent in the context of p53 deficiency. Aging (Albany NY) 2012; 4:660-1. [PMID: 23128359 PMCID: PMC3517935 DOI: 10.18632/aging.100494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 11/25/2022]
Abstract
Comment on: 1. Komarova et al. Rapamycin extends lifespan and delays tumorigenesis in heterozygous p53+/- mice. Aging. 2012; 4:10 2. Comas et al. New nanoformulation of rapamycin Rapatar extends lifespan in homozygous p53-/- mice by delaying carcinogenesis. Aging.2012; 4;10.
Collapse
|
36
|
Parikh N, Shuck RL, Nguyen TA, Herron A, Donehower LA. Mouse tissues that undergo neoplastic progression after K-Ras activation are distinguished by nuclear translocation of phospho-Erk1/2 and robust tumor suppressor responses. Mol Cancer Res 2012; 10:845-55. [PMID: 22532587 DOI: 10.1158/1541-7786.mcr-12-0089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mutation of K-Ras is a frequent oncogenic event in human cancers, particularly cancers of lungs, pancreas, and colon. It remains unclear why some tissues are more susceptible to Ras-induced transformation than others. Here, we globally activated a mutant oncogenic K-Ras allele (K-Ras(G12D)) in mice and examined the tissue-specific effects of this activation on cancer pathobiology, Ras signaling, tumor suppressor, DNA damage, and inflammatory responses. Within 5 to 6 weeks of oncogenic Ras activation, mice develop oral and gastric papillomas, lung adenomas, and hematopoietic hyperproliferation and turn moribund. The oral, gastric, and lung premalignant lesions display activated extracellular signal-regulated kinases (Erk)1/2 and NF-κB signaling as well as activated tumor suppressor and DNA damage responses. Other organs such as pancreas, liver, and small intestine do not exhibit neoplastic progression within 6 weeks following K-Ras(G12D) activation and do not show a potent tumor suppressor response. Even though robust Erk1/2 signaling is activated in all the tissues examined, the pErk1/2 distribution remains largely cytoplasmic in K-Ras(G12D)-refractory tissues (pancreas, liver, and intestines) as opposed to a predominantly nuclear localization in K-Ras(G12D)-induced neoplasms of lung, oral, and gastric mucosa. The downstream targets of Ras signaling, pElk-1 and c-Myc, are elevated in K-Ras(G12D)-induced neoplastic lesions but not in K-Ras(G12D)-refractory tissues. We propose that oncogenic K-Ras-refractory tissues delay oncogenic progression by spatially limiting the efficacy of Ras/Raf/Erk1/2 signaling, whereas K-Ras-responsive tissues exhibit activated Ras/Raf/Erk1/2 signaling, rapidly form premalignant tumors, and activate potent antitumor responses that effectively prevent further malignant progression.
Collapse
Affiliation(s)
- Neha Parikh
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | | | | | | | | |
Collapse
|
37
|
Abstract
Wild-type p53-induced phosphatase 1 (WIP1) is a serine/threonine phosphatase that dephosphorylates proteins in the ataxia telangiectasia mutated (ATM)-initiated DNA damage response pathway. WIP1 may have a homeostatic role in ATM signaling by returning the cell to a normal pre-stress state following completion of DNA repair. To better understand the effects of WIP1 on ATM signaling, we crossed Atm-deficient mice to Wip1-deficient mice and characterized phenotypes of the double knockout progeny. We hypothesized that the absence of Wip1 might rescue Atm deficiency phenotypes. Atm null mice, like ATM-deficient humans with the inherited syndrome ataxia telangiectasia, exhibit radiation sensitivity, fertility defects, and are T-cell lymphoma prone. Most double knockout mice were largely protected from lymphoma development and had a greatly extended lifespan compared with Atm null mice. Double knockout mice had increased p53 and H2AX phosphorylation and p21 expression compared with their Atm null counterparts, indicating enhanced p53 and DNA damage responses. Additionally, double knockout splenocytes displayed reduced chromosomal instability compared with Atm null mice. Finally, doubly null mice were partially rescued from gametogenesis defects observed in Atm null mice. These results indicate that inhibition of WIP1 may represent a useful strategy for cancer treatment in general and A-T patients in particular.
Collapse
Affiliation(s)
- Y Darlington
- Interdepartmental Graduate Program in Cell and Molecular Biology, Houston, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Terzian T, Dumble M, Arbab F, Thaller C, Donehower LA, Lozano G, Justice MJ, Roop DR, Box NF. Rpl27a mutation in the sooty foot ataxia mouse phenocopies high p53 mouse models. J Pathol 2011; 224:540-52. [PMID: 21674502 DOI: 10.1002/path.2891] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/28/2011] [Accepted: 03/04/2011] [Indexed: 01/06/2023]
Abstract
Ribosomal stress is an important, yet poorly understood, mechanism that results in activation of the p53 tumour suppressor. We present a mutation in the ribosomal protein Rpl27a gene (sooty foot ataxia mice), isolated through a sensitized N-ethyl-N-nitrosourea (ENU) mutagenesis screen for p53 pathway defects, that shares striking phenotypic similarities with high p53 mouse models, including cerebellar ataxia, pancytopenia and epidermal hyperpigmentation. This phenocopy is rescued in a haploinsufficient p53 background. A detailed examination of the bone marrow in these mice identified reduced numbers of haematopoietic stem cells and a p53-dependent c-Kit down-regulation. These studies suggest that reduced Rpl27a increases p53 activity in vivo, further evident with a delay in tumorigenesis in mutant mice. Taken together, these data demonstrate that Rpl27a plays a crucial role in multiple tissues and that disruption of this ribosomal protein affects both development and transformation.
Collapse
|
39
|
Gannon HS, Donehower LA, Lyle S, Jones SN. Mdm2-p53 signaling regulates epidermal stem cell senescence and premature aging phenotypes in mouse skin. Dev Biol 2011; 353:1-9. [PMID: 21334322 DOI: 10.1016/j.ydbio.2011.02.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 01/20/2011] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
Abstract
The p53 transcription factor is activated by various types of cell stress or DNA damage and induces the expression of genes that control cell growth and inhibit tumor formation. Analysis of mice that express mutant forms of p53 suggest that inappropriate p53 activation can alter tissue homeostasis and life span, connecting p53 tumor suppressor functions with accelerated aging. However, other mouse models that display increased levels of wildtype p53 in various tissues fail to corroborate a link between p53 and aging phenotypes, possibly due to the retention of signaling pathways that negatively regulate p53 activity in these models. In this present study, we have generated mice lacking Mdm2 in the epidermis. Deletion of Mdm2, the chief negative regulator of p53, induced an aging phenotype in the skin of mice, including thinning of the epidermis, reduced wound healing, and a progressive loss of fur. These phenotypes arise due to an induction of p53-mediated senescence in epidermal stem cells and a gradual loss of epidermal stem cell function. These results reveal that activation of endogenous p53 by ablation of Mdm2 can induce accelerated aging phenotypes in mice.
Collapse
Affiliation(s)
- Hugh S Gannon
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | | | | |
Collapse
|
40
|
Fuchs-Young R, Shirley SH, Lambertz I, Colby JKL, Tian J, Johnston D, Gimenez-Conti IB, Donehower LA, Conti CJ, Hursting SD. P53 genotype as a determinant of ER expression and tamoxifen response in the MMTV-Wnt-1 model of mammary carcinogenesis. Breast Cancer Res Treat 2010; 130:399-408. [PMID: 21191649 DOI: 10.1007/s10549-010-1308-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 12/10/2010] [Indexed: 10/18/2022]
Abstract
Clinical studies show that estrogen receptor-α (ER) expressing tumors tend to have better prognosis, respond to antiestrogen therapy and have wild-type p53. Conversely, tumors with inactivating mutations in p53 tend to have worse outcomes and to be ER-negative and unresponsive to antihormone treatment. Previous studies from our laboratory have shown that p53 regulates ER expression transcriptionally, by binding the ER promoter and forming a complex with CARM1, CBP, c-Jun, RNA polymerase II and Sp1. In this study, the MMTV-Wnt-1 transgenic mouse model was used to demonstrate that p53 regulation of ER expression and function is not solely an in vitro phenomenon, but it is also operational in mammary tumorigenesis in vivo. The expression of ER and the ability to respond to tamoxifen were determined in mammary tumors arising in p53 wild type (WT) or p53 heterozygous (HT) animals carrying the Wnt-1 transgene. In p53 WT mice, development of ER-positive tumors was delayed by tamoxifen treatment, while tumors arising in p53 HT mice had significantly reduced levels of ER and were not affected by tamoxifen. P53 null tumors were also found in the p53 HT mice and these tumors were ER-negative. ER expression was upregulated in mouse mammary tumor cell lines following transfection with WT p53 or treatment with doxorubicin. These data demonstrate that p53 regulates ER expression in vivo, and affects response to tamoxifen. Results also provide an explanation for the concordant relationship between these prognostic proteins in human breast tumors.
Collapse
Affiliation(s)
- Robin Fuchs-Young
- Department of Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Research Center at The University of Texas MD Anderson Cancer Center, Science Park Research Division, 1808 Park Road 1C, Smithville, TX 78957, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Shang X, Vasudevan SA, Yu Y, Ge N, Ludwig AD, Wesson CL, Wang K, Burlingame SM, Zhao YJ, Rao PH, Lu X, Russell HV, Okcu MF, Hicks MJ, Shohet JM, Donehower LA, Nuchtern JG, Yang J. Dual-specificity phosphatase 26 is a novel p53 phosphatase and inhibits p53 tumor suppressor functions in human neuroblastoma. Oncogene 2010; 29:4938-46. [PMID: 20562916 DOI: 10.1038/onc.2010.244] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemoresistance is a major cause of treatment failure and poor outcome in neuroblastoma. In this study, we investigated the expression and function of dual-specificity phosphatase 26 (DUSP26), also known as mitogen-activated protein kinase phophatase-8, in human neuroblastoma. We found that DUSP26 was expressed in a majority of neuroblastoma cell lines and tissue specimens. Importantly, we found that DUSP26 promotes the resistance of human neuroblastoma to doxorubicin-induced apoptosis by acting as a p53 phosphatase to downregulate p53 tumor suppressor function in neuroblastoma cells. Inhibiting DUSP26 expression in the IMR-32 neuroblastoma cell line enhanced doxorubicin-induced p53 phosphorylation at Ser20 and Ser37, p21, Puma, Bax expression as well as apoptosis. In contrast, DUSP26 overexpression in the SK-N-SH cell line inhibited doxorubicin-induced p53 phosphorylation at Ser20 and Ser37, p21, Puma, Bax expression and apoptosis. Using in vitro and in vivo assays, we found that DUSP26 binds to p53 and dephosphorylates p53 at Ser20 and Ser37. In this report, we show that DUSP26 functions as a p53 phosphatase, which suppresses downstream p53 activity in response to genotoxic stress. This suggests that inhibition of this phosphatase may increase neuroblastoma chemosensitivity and DUSP26 is a novel therapeutic target for this aggressive pediatric malignancy.
Collapse
Affiliation(s)
- X Shang
- Texas Children's Cancer Center, Department of Pediatrics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Lee S, Donehower LA, Herron AJ, Moore DD, Fu L. Disrupting circadian homeostasis of sympathetic signaling promotes tumor development in mice. PLoS One 2010; 5:e10995. [PMID: 20539819 PMCID: PMC2881876 DOI: 10.1371/journal.pone.0010995] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 05/11/2010] [Indexed: 01/17/2023] Open
Abstract
Background Cell proliferation in all rapidly renewing mammalian tissues follows a circadian rhythm that is often disrupted in advanced-stage tumors. Epidemiologic studies have revealed a clear link between disruption of circadian rhythms and cancer development in humans. Mice lacking the circadian genes Period1 and 2 (Per) or Cryptochrome1 and 2 (Cry) are deficient in cell cycle regulation and Per2 mutant mice are cancer-prone. However, it remains unclear how circadian rhythm in cell proliferation is generated in vivo and why disruption of circadian rhythm may lead to tumorigenesis. Methodology/Principal Findings Mice lacking Per1 and 2, Cry1 and 2, or one copy of Bmal1, all show increased spontaneous and radiation-induced tumor development. The neoplastic growth of Per-mutant somatic cells is not controlled cell-autonomously but is dependent upon extracellular mitogenic signals. Among the circadian output pathways, the rhythmic sympathetic signaling plays a key role in the central-peripheral timing mechanism that simultaneously activates the cell cycle clock via AP1-controlled Myc induction and p53 via peripheral clock-controlled ATM activation. Jet-lag promptly desynchronizes the central clock-SNS-peripheral clock axis, abolishes the peripheral clock-dependent ATM activation, and activates myc oncogenic potential, leading to tumor development in the same organ systems in wild-type and circadian gene-mutant mice. Conclusions/Significance Tumor suppression in vivo is a clock-controlled physiological function. The central circadian clock paces extracellular mitogenic signals that drive peripheral clock-controlled expression of key cell cycle and tumor suppressor genes to generate a circadian rhythm in cell proliferation. Frequent disruption of circadian rhythm is an important tumor promoting factor.
Collapse
Affiliation(s)
- Susie Lee
- Department of Pediatrics/U.S. Department of Agriculture/Agricultural Research Service/Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas, United States of America
| | | | | | | | | |
Collapse
|
43
|
Moon SH, Nguyen TA, Darlington Y, Lu X, Donehower LA. Dephosphorylation of γ-H2AX by WIP1: an important homeostatic regulatory event in DNA repair and cell cycle control. Cell Cycle 2010; 9:2092-6. [PMID: 20495376 DOI: 10.4161/cc.9.11.11810] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA double strand breaks are a particularly toxic form of DNA damage and the mammalian cell has evolved an intricate set of responses to repair this type of DNA lesion. A key early event in the DNA damage response (DDR) is ATM phosphorylation of the histone variant H2AX at serine 139 at the site of the DNA break. Phosphorylated S139 H2AX, or γ-H2AX, forms a docking site for binding of MDC1, leading to sustained recruitment of other DNA repair factors that mediate the repair of the DNA double strand break. Moreover, recruitment of MDC1 to the break site activates cell cycle checkpoints, protecting the cell from replication of damaged DNA templates. While the molecular events leading to DNA double strand break repair have been well described, the deactivating or homeostatic mechanisms following completion of repair remain largely unexplored. Recent publications by our laboratories and the Medema laboratory shed new light on this issue. Both publications showed that the Wild-type p53-Induced Phosphatase 1 (WIP1) directly dephosphorylates γ-H2AX. WIP1 migrates to the sites of irradiation-induced foci (IRIF), though at a delayed rate relative to MDC1 and mediates γ-H2AX dephosphorylation, presumably after DNA repair is complete. This prevents recruitment of other repair factors such as MDC1 and 53BP1 to the DNA damage sites and promotes the dissolution of IRIF. In addition, overexpression of WIP1 has a suppressive effect on DNA double strand break repair. Taken together, these reports further implicate WIP1 as a critical homeostatic regulator of the DDR.
Collapse
Affiliation(s)
- Sung-Hwan Moon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | |
Collapse
|
44
|
Liu H, Herrmann CH, Chiang K, Sung TL, Moon SH, Donehower LA, Rice AP. 55K isoform of CDK9 associates with Ku70 and is involved in DNA repair. Biochem Biophys Res Commun 2010; 397:245-50. [PMID: 20493174 DOI: 10.1016/j.bbrc.2010.05.092] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 05/16/2010] [Indexed: 10/19/2022]
Abstract
Positive elongation factor b (P-TEFb) is a cellular protein kinase that is required for RNA polymerase II (RNAP II) transcriptional elongation of protein coding genes. P-TEFb is a set of different molecular complexes, each containing CDK9 as the catalytic subunit. There are two isoforms of the CDK9 protein - the major 42KDa CDK9 isoform and the minor 55KDa isoform that is translated from an in-frame mRNA that arises from an upstream transcriptional start site. We found that shRNA depletion of the 55K CDK9 protein in HeLa cells induces apoptosis and double-strand DNA breaks (DSBs). The levels of apoptosis and DSBs induced by the depletion were reduced by expression of a 55K CDK9 protein variant resistant to the shRNA, indicating that these phenotypes are the consequence of depletion of the 55K protein and not off-target effects. We also found that the 55K CDK9 protein, but not the 42K CDK9 protein, specifically associates with Ku70, a protein involved in DSB repair. Our findings suggest that the 55K CDK9 protein may function in repair of DNA through an association with Ku70.
Collapse
Affiliation(s)
- Hongbing Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | |
Collapse
|
45
|
Blagosklonny MV, Campisi J, Sinclair DA, Bartke A, Blasco MA, Bonner WM, Bohr VA, Brosh RM, Brunet A, Depinho RA, Donehower LA, Finch CE, Finkel T, Gorospe M, Gudkov AV, Hall MN, Hekimi S, Helfand SL, Karlseder J, Kenyon C, Kroemer G, Longo V, Nussenzweig A, Osiewacz HD, Peeper DS, Rando TA, Rudolph KL, Sassone-Corsi P, Serrano M, Sharpless NE, Skulachev VP, Tilly JL, Tower J, Verdin E, Vijg J. Impact papers on aging in 2009. Aging (Albany NY) 2010; 2:111-21. [PMID: 20351400 PMCID: PMC2871240 DOI: 10.18632/aging.100132] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 03/22/2010] [Indexed: 01/09/2023]
Abstract
The editorial board of Aging reviews research papers published in 2009, which they
believe have or will have a significant impact on aging research. Among many
others, the topics include genes that accelerate aging or in contrast promote
longevity in model organisms, DNA damage responses and telomeres, molecular
mechanisms of life span extension by calorie restriction and pharmacologic
interventions into aging. The emerging message in 2009 is that aging is not
random but determined by a genetically-regulated longevity network and can be
decelerated both genetically and pharmacologically.
Collapse
|
46
|
Moon SH, Lin L, Zhang X, Nguyen TA, Darlington Y, Waldman AS, Lu X, Donehower LA. Wild-type p53-induced phosphatase 1 dephosphorylates histone variant gamma-H2AX and suppresses DNA double strand break repair. J Biol Chem 2010; 285:12935-47. [PMID: 20118229 DOI: 10.1074/jbc.m109.071696] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In response to DNA double strand breaks, the histone variant H2AX at the break site is phosphorylated at serine 139 by DNA damage sensor kinases such as ataxia telangiectasia-mutated, forming gamma-H2AX. This phosphorylation event is critical for sustained recruitment of other proteins to repair the break. After repair, restoration of the cell to a prestress state is associated with gamma-H2AX dephosphorylation and dissolution of gamma-H2AX-associated damage foci. The phosphatases PP2A and PP4 have previously been shown to dephosphorylate gamma-H2AX. Here, we demonstrate that the wild-type p53-induced phosphatase 1 (WIP1) also dephosphorylates gamma-H2AX at serine 139 in vitro and in vivo. Overexpression of WIP1 reduces formation of gamma-H2AX foci in response to ionizing and ultraviolet radiation and blocks recruitment of MDC1 (mediator of DNA damage checkpoint 1) and 53BP1 (p53 binding protein 1) to DNA damage foci. Finally, these inhibitory effects of WIP1 on gamma-H2AX are accompanied by WIP1 suppression of DNA double strand break repair. Thus, WIP1 has a homeostatic role in reversing the effects of ataxia telangiectasia-mutated phosphorylation of H2AX.
Collapse
Affiliation(s)
- Sung-Hwan Moon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Maegawa S, Hinkal G, Kim HS, Shen L, Zhang L, Zhang J, Zhang N, Liang S, Donehower LA, Issa JPJ. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res 2010; 20:332-40. [PMID: 20107151 DOI: 10.1101/gr.096826.109] [Citation(s) in RCA: 379] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer. It is not known whether this age-related DNA methylation phenomenon is specific to human tissues. We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis. By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation. We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methylation changes for all 12 genomic regions examined. We then examined 11 changed genomic loci for age-related methylation in other tissues. Of these, three of 11 showed similar changes in lung, seven of 11 changed in liver, and six of 11 changed in spleen, though to a lower degree than the changes seen in colon. There was partial conservation between age-related hypermethylation in human and mouse intestines, and Polycomb targets in embryonic stem cells were enriched among the hypermethylated genes. Our findings demonstrate a surprisingly high rate of hyper- and hypomethylation as a function of age in normal mouse small intestine tissues and a strong tissue-specificity to the process. We conclude that epigenetic deregulation is a common feature of aging in mammals.
Collapse
Affiliation(s)
- Shinji Maegawa
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Colbert LH, Westerlind KC, Perkins SN, Haines DC, Berrigan D, Donehower LA, Fuchs-Young R, Hursting SD. Exercise effects on tumorigenesis in a p53-deficient mouse model of breast cancer. Med Sci Sports Exerc 2009; 41:1597-605. [PMID: 19568200 DOI: 10.1249/mss.0b013e31819f1f05] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PURPOSE Physically active women have a reduced risk of breast cancer, but the dose of activity necessary and the role of energy balance and other potential mechanisms have not been fully explored in animal models. We examined treadmill and wheel running effects on mammary tumorigenesis and biomarkers in p53-deficient (p53(+/-)):MMTV-Wnt-1 transgenic mice. METHODS Female mice (9 wk old) were randomly assigned to the following groups in experiment 1: treadmill exercise 5 d x wk(-1), 45 min x d(-1), 5% grade at 20 m x min(-1), approximately 0.90 km x d(-1) (TREX1, n = 20) or at 24 m x min(-1), approximately 1.08 km x d(-1) (TREX2, n = 21); or a nonexercise control (CON-TREX, n = 22). In experiment 2, mice were randomly assigned to voluntary wheel running (WHL, n = 21, 2.46 +/- 1.11 km x d(-1) (mean +/- SD)) or to a nonexercise control (CON-WHL, n = 22). Body composition was measured at approximately 9 wk and serum insulin-like growth factor 1 (IGF-1) at two to three monthly time points beginning at approximately 9 wk on study. Mice were sacrificed when tumors reached 1.5 cm, mice became moribund, or there was only one mouse per treatment group remaining. RESULTS TREX1 (24 wk) and TREX2 (21 wk) had shorter median survival times than CON-TREX (34 wk; P < 0.01), whereas those of WHL and CON-WHL were similar (23 vs 24 wk; P = 0.32). TREX2 had increased multiplicity of mammary gland carcinomas compared with CON-TREX; WHL had a higher tumor incidence than CON-WHL. All exercising animals were lighter than their respective controls, and WHL had lower body fat than CON-WHL (P < 0.01). There was no difference in IGF-1 between groups (P > 0.05). CONCLUSIONS Despite beneficial or no effects on body weight, body fat, or IGF-1, exercise had detrimental effects on tumorigenesis in this p53-deficient mouse model of spontaneous mammary cancer.
Collapse
|
49
|
Abstract
The p53 tumor suppressor is a multifaceted transcription factor that responds to a diverse array of stresses that include DNA damage and aberrant oncogene signaling. On activation, p53 prevents the emergence of cancer cells by initiating cell cycle arrest, senescence (terminal cell cycle arrest), or apoptosis. Although its role in assuring longevity by suppressing cancer is well established, recent studies obtained largely from genetically engineered mouse models suggest that p53 may regulate longevity and aging. In some contexts, it appears that altered p53 activity may enhance longevity, and in others, it appears to suppress longevity and accelerate aging phenotypes. Here, we discuss how genetically engineered mouse models have been used to explore antiproliferative functions of p53 in cancer suppression and how mouse models with altered aging phenotypes have shed light on how p53 might influence the aging process.
Collapse
Affiliation(s)
- Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA.
| |
Collapse
|
50
|
Abstract
Cell and molecular biological studies of p53 functions over the past 30 years have been complemented in the past 20 years by studies that use genetically engineered mice. As expected, mice that have mutant Trp53 alleles usually develop cancers of various types more rapidly than their counterparts that have wild-type Trp53 genes. These mouse studies have been instrumental in providing important new insights into p53 tumour suppressor function. Such studies have been facilitated by the development of increasingly sophisticated genetic engineering approaches, which allow the more precise manipulation of p53 structure and function in a mammalian model.
Collapse
Affiliation(s)
- Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA.
| | | |
Collapse
|