1
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Kinnaman MD, Zaccaria S, Makohon-Moore A, Arnold B, Levine MF, Gundem G, Arango Ossa JE, Glodzik D, Rodríguez-Sánchez MI, Bouvier N, Li S, Stockfisch E, Dunigan M, Cobbs C, Bhanot UK, You D, Mullen K, Melchor JP, Ortiz MV, O'Donohue TJ, Slotkin EK, Wexler LH, Dela Cruz FS, Hameed MR, Glade Bender JL, Tap WD, Meyers PA, Papaemmanuil E, Kung AL, Iacobuzio-Donahue CA. Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma. Cancer Res 2023; 83:3796-3812. [PMID: 37812025 PMCID: PMC10646480 DOI: 10.1158/0008-5472.can-23-0385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. We conducted longitudinal whole-genome sequencing of 37 tumor samples from 8 patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. Subclonal copy-number alterations were identified in all patients except one. In 5 patients, subclones from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clones in 6 of 7 patients with multiple clones. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy-number clones. A chromosomal duplication timing analysis revealed that complex genomic rearrangements typically occurred prior to diagnosis, supporting a macroevolutionary model of evolution, where a large number of genomic aberrations are acquired over a short period of time followed by clonal selection, as opposed to ongoing evolution. A mutational signature analysis of recurrent tumors revealed that homologous repair deficiency (HRD)-related SBS3 increases at each time point in patients with recurrent disease, suggesting that HRD continues to be an active mutagenic process after diagnosis. Overall, by examining the clonal relationships between temporally and spatially separated samples from patients with relapsed/refractory osteosarcoma, this study sheds light on the intratumor heterogeneity and potential drivers of treatment resistance in this disease. SIGNIFICANCE The chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.
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Affiliation(s)
- Michael D. Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, United Kingdom
| | - Alvin Makohon-Moore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian Arnold
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey
| | - Max F. Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Juan E. Arango Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dominik Glodzik
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shanita Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marisa Dunigan
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cassidy Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh K. Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katelyn Mullen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York
| | - Jerry P. Melchor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tara J. O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily K. Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard H. Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera R. Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julia L. Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D. Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A. Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A. Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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2
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Urlić I, Jovičić MŠ, Ostojić K, Ivković A. Cellular and Genetic Background of Osteosarcoma. Curr Issues Mol Biol 2023; 45:4344-4358. [PMID: 37232745 DOI: 10.3390/cimb45050276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
Osteosarcoma describes a tumor of mesenchymal origin with an annual incidence rate of four to five people per million. Even though chemotherapy treatment has shown success in non-metastatic osteosarcoma, metastatic disease still has a low survival rate of 20%. A targeted therapy approach is limited due to high heterogeneity of tumors, and different underlying mutations. In this review, we will summarize new advances obtained by new technologies, such as next generation sequencing and single-cell sequencing. These new techniques have enabled better assessment of cell populations within osteosarcoma, as well as an understanding of the molecular pathogenesis. We also discuss the presence and properties of osteosarcoma stem cells-the cell population within the tumor that is responsible for metastasis, recurrence, and drug resistance.
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Affiliation(s)
- Inga Urlić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Marijana Šimić Jovičić
- Department of Paediatric Orthopaedics, Children's Hospital Zagreb, 10000 Zagreb, Croatia
| | - Karla Ostojić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Alan Ivković
- Department of Orthopaedics and Traumatology, University Hospital Sveti Duh, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Professional Study in Physiotherapy, University of Applied Health Sciences, 10000 Zagreb, Croatia
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3
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Kinnaman MD, Zaccaria S, Makohon-Moore A, Arnold B, Levine M, Gundem G, Ossa JEA, Glodzik D, Rodríguez-Sánchez MI, Bouvier N, Li S, Stockfisch E, Dunigan M, Cobbs C, Bhanot U, You D, Mullen K, Melchor J, Ortiz MV, O'Donohue T, Slotkin E, Wexler LH, Dela Cruz FS, Hameed M, Glade Bender JL, Tap WD, Meyers PA, Papaemmanuil E, Kung AL, Iacobuzio-Donahue CA. Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522765. [PMID: 36711976 PMCID: PMC9881990 DOI: 10.1101/2023.01.05.522765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Multiple large-scale tumor genomic profiling efforts have been undertaken in osteosarcoma, however, little is known about the spatial and temporal intratumor heterogeneity and how it may drive treatment resistance. We performed whole-genome sequencing of 37 tumor samples from eight patients with relapsed or refractory osteosarcoma. Each patient had at least one sample from a primary site and a metastatic or relapse site. We identified subclonal copy number alterations in all but one patient. We observed that in five patients, a subclonal copy number clone from the primary tumor emerged and dominated at subsequent relapses. MYC gain/amplification was enriched in the treatment-resistant clone in 6 out of 7 patients with more than one clone. Amplifications in other potential driver genes, such as CCNE1, RAD21, VEGFA, and IGF1R, were also observed in the resistant copy number clones. Our study sheds light on intratumor heterogeneity and the potential drivers of treatment resistance in osteosarcoma.
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Affiliation(s)
- Michael D Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Alvin Makohon-Moore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA (current affiliation)
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA (current affiliation)
| | - Brian Arnold
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Max Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Isabl, New York, NY, USA (current affiliation)
| | - Gunes Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan E Arango Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dominik Glodzik
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA (current affiliation)
| | - M Irene Rodríguez-Sánchez
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Wunderman Thompson Health, New York, NY, USA (current affiliation)
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- IT and Digital Initiatives, Memorial Sloan Kettering Cancer Center, New York, NY, USA (current affiliation)
| | - Shanita Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marisa Dunigan
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cassidy Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umesh Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katelyn Mullen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Jerry Melchor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tara O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julia L Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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4
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Ning B, Liu Y, Xu T, Li Y, Wei D, Huang T, Wei Y. Construction and validation of a prognostic model for osteosarcoma patients based on autophagy-related genes. Discov Oncol 2022; 13:146. [PMID: 36586072 PMCID: PMC9805482 DOI: 10.1007/s12672-022-00608-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Osteosarcoma is the most frequent primary bone malignancy with a poor prognosis because of pulmonary metastasis. Autophagy is strongly associated with tumor metastasis, and it is valuable to construct an autophagy-related gene risk model for predicting the prognosis of osteosarcoma. METHODS We obtained ARGs from the Human Autophagy Database and RNA-sequencing data of osteosarcoma patients from the Gene Expression Omnibus (GEO) database. Subsequently, univariate and multivariate cox regression analyses were performed to construct a three-gene prognostic model and its accuracy was further confirmed in the Therapeutic Applications Research to Generate Effective Treatments (TARGET) database. Afterward, we detected the expression levels and effects on osteosarcoma cells metastasis of MYC and MBTPS2, which were involved in the model. RESULTS In both training and verification cohorts, patients with lower risk scores had longer OS, and the model was identified as an independent prognostic factor in osteosarcoma. Besides, the ROC curve demonstrated the reliability of the model. Furthermore, RT-qPCR, Western Blotting and IHC results indicated that MYC and MBTPS2 were differently expressed in osteosarcoma tissues and cell lines. MYC knockdown or MBTPS2 overexpression prevented the capacity of migration and invasion in osteosarcoma cell lines through inhibiting cellular autophagy. CONCLUSION The risk model based on three ARGs had a strong ability to predict the prognosis of osteosarcoma patients. Our findings also suggested that MYC and MBTPS2 were two major factors regulating autophagy in osteosarcoma, and could serve as potential therapeutic targets for osteosarcoma.
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Affiliation(s)
- Biao Ning
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China
| | - Yixin Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China
| | - Tianzi Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China
| | - Yi Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China
| | - Dongyi Wei
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China
| | - Tianhe Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China.
| | - Yongchang Wei
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No. 169 Donghu Road, Wuchang District, Wuhan, 430072, Hubei Province, People's Republic of China.
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5
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Taylor AM, Sun JM, Yu A, Voicu H, Shen J, Barkauskas DA, Triche TJ, Gastier-Foster JM, Man TK, Lau CC. Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma. Int J Mol Sci 2022; 23:ijms23148036. [PMID: 35887382 PMCID: PMC9319262 DOI: 10.3390/ijms23148036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma is a primary malignant bone tumor arising from bone-forming mesenchymal cells in children and adolescents. Despite efforts to understand the biology of the disease and identify novel therapeutics, the survival of osteosarcoma patients remains dismal. We have concurrently profiled the copy number and gene expression of 226 osteosarcoma samples as part of the Strategic Partnering to Evaluate Cancer Signatures (SPECS) initiative. Our results demonstrate the heterogeneous landscape of osteosarcoma in younger populations by showing the presence of genome-wide copy number abnormalities occurring both recurrently among samples and in a high frequency. Insulin growth factor receptor 1 (IGF1R) is a receptor tyrosine kinase which binds IGF1 and IGF2 to activate downstream pathways involved in cell apoptosis and proliferation. We identify prevalent amplification of IGF1R corresponding with increased gene expression in patients with poor survival outcomes. Our results substantiate previously tenuously associated copy number abnormalities identified in smaller datasets (13q34+, 20p13+, 4q35-, 20q13.33-), and indicate the significance of high fibroblast growth factor receptor 2 (FGFR2) expression in distinguishing patients with poor prognosis. FGFR2 is involved in cellular proliferation processes such as division, growth and angiogenesis. In summary, our findings demonstrate the prognostic significance of several genes associated with osteosarcoma pathogenesis.
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Affiliation(s)
- Aaron M. Taylor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi M. Sun
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Yu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
| | - Horatiu Voicu
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Jianhe Shen
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Timothy J. Triche
- Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | | | - Tsz-Kwong Man
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ching C. Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
- Cancer and Hematology Center, Texas Children’s Hospital, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-207-288-6000
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6
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Mills LJ, Scott MC, Shah P, Cunanan AR, Deshpande A, Auch B, Curtin B, Beckman KB, Spector LG, Sarver AL, Subramanian S, Richmond TA, Modiano JF. Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma. Bone 2022; 158:115716. [PMID: 33127576 PMCID: PMC8076342 DOI: 10.1016/j.bone.2020.115716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/24/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023]
Abstract
Osteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor protein p53 (TP53) is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples. SIGNIFICANCE: Genome wide comparison of DNA methylation patterns in osteosarcoma across two species lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of varied mutational landscapes.
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Affiliation(s)
- Lauren J Mills
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Milcah C Scott
- Department of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pankti Shah
- Roche Sequencing Solution, Pleasanton, CA, USA
| | | | | | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Bridget Curtin
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Logan G Spector
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subbaya Subramanian
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Jaime F Modiano
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, UDS Institute for Engineering in Medicine, Minneapolis, MN 55455, USA
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7
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Fu Y, He G, Liu Z, Wang J, Zhang Z, Bao Q, Wen J, Jin Z, Zhang W. Exploration and Validation of a Novel Inflammatory Response-Associated Gene Signature to Predict Osteosarcoma Prognosis and Immune Infiltration. J Inflamm Res 2021; 14:6719-6734. [PMID: 34916821 PMCID: PMC8668229 DOI: 10.2147/jir.s340477] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023] Open
Abstract
Background Inflammatory response took part in the progression of tumor and was regarded as the hallmark of cancer. However, the prognostic relationship between osteosarcoma and inflammatory response-associated genes (IRGs) was unclear. This research aimed to explore the correlations between osteosarcoma prognosis and IRG signature. Methods The inflammatory response-associated differentially expressed messenger RNAs (DEmRNAs) were screened out through Gene Expression Omnibus (GEO) and Molecular Signature Database (MSigDB) databases. Univariate and multivariate cox regression analyses were utilized to construct the IRG signature. The prognostic value of signature was investigated through Kaplan–Meier (KM) survival curve and nomogram. DEmRNAs among high and low inflammatory response-associated risks were identified and functional enrichment analyses were conducted. ESTIMATE, CIBERSORT and single-sample gene set enrichment analyses (ssGSEA) were implied to reveal the alterations in immune infiltration. All the above results were validated in Target database. The expression of IRGs was also validated in different cell lines by quantitative real-time PCR (qRT-PCR) and osteosarcoma patient samples by immunohistochemistry. Results The IRG signature that consisted of two genes (MYC, CLEC5A) was established. In training and validation datasets, patients with lower risk scores survived longer and the IRG signature was confirmed as the independent prognostic factor in osteosarcoma. The nomogram was constructed and the calibration curves demonstrated the reliability of this model. Functional analysis of risk score-associated DEmRNAs indicated that immune-related pathways and functions were significantly enriched. ssGSEA revealed that 14 immune cells and 11 immune functions were significantly dysregulated. The qRT-PCR results indicated IRGs were significantly differently expressed in osteosarcoma and osteoblast cell lines. The immunohistochemistry analyses of patients’ samples revealed the same result. Conclusion The novel osteosarcoma inflammatory response-associated prognostic signature was established and validated in this study. This model could serve as the biomarker and therapeutic target for osteosarcoma in the future.
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Affiliation(s)
- Yucheng Fu
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Guoyu He
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhuochao Liu
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Jun Wang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhusheng Zhang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Qiyuan Bao
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Junxiang Wen
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Zhijian Jin
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Weibin Zhang
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
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8
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Gong Y, Wei ZR. Identification of PSMD14 as a potential novel prognosis biomarker and therapeutic target for osteosarcoma. Cancer Rep (Hoboken) 2021; 5:e1522. [PMID: 34383385 PMCID: PMC9327663 DOI: 10.1002/cnr2.1522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/08/2021] [Accepted: 06/14/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Osteosarcoma is the most common primary bone tumor. The survival rate of osteosarcoma patients has not significantly increased in the past decades. Uncovering the mechanisms of malignancy, progression, and metastasis will shed light on the development of new therapeutic targets and treatment for osteosarcoma. AIM The aim of this study is to identify potential osteosarcoma biomarker and/or therapeutic targets by using integrated bioinformatics analysis. METHODS AND RESULTS We utilized existing gene expression datasets to identify differential expressed genes (DEGs) that could serve as osteosarcoma biomarkers or even as therapeutic targets. We found 48 DEGs were overlapped in three datasets. Among these 48 DEGs, PSMD14 was on the top of the up-regulated gene list. We further found that higher PSMD14 expression was correlated with higher risk group (younger age group, ≤20.83 years of age), metastasis within 5 years and higher grade of tumor. Higher PSMD14 expression in osteosarcoma had positive correlation with higher infiltration of CD8+ T cells, neutrophils and myeloid dendritic cells. Kaplan-Myer survival data further revealed that higher expression of PSMD14 predicted significantly worse prognosis (p = .013). Gene set enrichment analysis was further performed for the DEGs related to PSMD14 in osteosarcoma. We found that lower PSMD14 expression group had more immune responses such as interferon γ, α responses, inflammation response etc. However, the higher PSMD14 expression group had more cell proliferation-related biological processes, such as G2M checkpoints and Myc targets. Through establishing protein-protein interaction networks using PSMD14 related DEGs, we identified 10 hub genes that were all ribosomal proteins. These hub genes may play roles in osteosarcoma tumorigenesis, progression and/or metastasis. CONCLUSION We identified PSMD14 gene as a possible osteosarcoma biomarker, and/or a possible therapeutic target.
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Affiliation(s)
- Yubao Gong
- Department of Orthopedics, Jilin University First Hospital, Jilin, China
| | - Zheng-Ren Wei
- Department of Pharmocology, Jilin University Bethune College of Medicine, Jilin, China
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9
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Czarnecka AM, Synoradzki K, Firlej W, Bartnik E, Sobczuk P, Fiedorowicz M, Grieb P, Rutkowski P. Molecular Biology of Osteosarcoma. Cancers (Basel) 2020; 12:E2130. [PMID: 32751922 PMCID: PMC7463657 DOI: 10.3390/cancers12082130] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Osteosarcoma (OS) is the most frequent primary bone cancer in children and adolescents and the third most frequent in adults. Many inherited germline mutations are responsible for syndromes that predispose to osteosarcomas including Li Fraumeni syndrome, retinoblastoma syndrome, Werner syndrome, Bloom syndrome or Diamond-Blackfan anemia. TP53 is the most frequently altered gene in osteosarcoma. Among other genes mutated in more than 10% of OS cases, c-Myc plays a role in OS development and promotes cell invasion by activating MEK-ERK pathways. Several genomic studies showed frequent alterations in the RB gene in pediatric OS patients. Osteosarcoma driver mutations have been reported in NOTCH1, FOS, NF2, WIF1, BRCA2, APC, PTCH1 and PRKAR1A genes. Some miRNAs such as miR-21, -34a, -143, -148a, -195a, -199a-3p and -382 regulate the pathogenic activity of MAPK and PI3K/Akt-signaling pathways in osteosarcoma. CD133+ osteosarcoma cells have been shown to exhibit stem-like gene expression and can be tumor-initiating cells and play a role in metastasis and development of drug resistance. Although currently osteosarcoma treatment is based on adriamycin chemoregimens and surgery, there are several potential targeted therapies in development. First of all, activity and safety of cabozantinib in osteosarcoma were studied, as well as sorafenib and pazopanib. Finally, novel bifunctional molecules, of potential imaging and osteosarcoma targeting applications may be used in the future.
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Affiliation(s)
- Anna M Czarnecka
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute-Oncology Centre, 02-781 Warsaw, Poland
| | - Kamil Synoradzki
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Wiktoria Firlej
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute-Oncology Centre, 02-781 Warsaw, Poland
- Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Pawel Sobczuk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute-Oncology Centre, 02-781 Warsaw, Poland
- Department of Experimental and Clinical Physiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Michal Fiedorowicz
- Small Animal Magnetic Resonance Imaging Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Interinstitute Laboratory of New Diagnostic Applications of MRI, Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, 02-109 Warsaw, Poland
| | - Pawel Grieb
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute-Oncology Centre, 02-781 Warsaw, Poland
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Thoenen E, Curl A, Iwakuma T. TP53 in bone and soft tissue sarcomas. Pharmacol Ther 2019; 202:149-164. [PMID: 31276706 DOI: 10.1016/j.pharmthera.2019.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022]
Abstract
Genomic and functional study of existing and emerging sarcoma targets, such as fusion proteins, chromosomal aberrations, reduced tumor suppressor activity, and oncogenic drivers, is broadening our understanding of sarcomagenesis. Among these mechanisms, the tumor suppressor p53 (TP53) plays significant roles in the suppression of bone and soft tissue sarcoma progression. Although mutations in TP53 were thought to be relatively low in sarcomas, modern techniques including whole-genome sequencing have recently illuminated unappreciated alterations in TP53 in osteosarcoma. In addition, oncogenic gain-of-function activities of missense mutant p53 (mutp53) have been reported in sarcomas. Moreover, new targeting strategies for TP53 have been discovered: restoration of wild-type p53 (wtp53) activity through inhibition of TP53 negative regulators, reactivation of the wtp53 activity from mutp53, depletion of mutp53, and targeting of vulnerabilities in cells with TP53 deletions or mutations. These discoveries enable development of novel therapeutic strategies for therapy-resistant sarcomas. We have outlined nine bone and soft tissue sarcomas for which TP53 plays a crucial tumor suppressive role. These include osteosarcoma, Ewing sarcoma, chondrosarcoma, rhabdomyosarcoma (RMS), leiomyosarcoma (LMS), synovial sarcoma, liposarcoma (LPS), angiosarcoma, and undifferentiated pleomorphic sarcoma (UPS).
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Affiliation(s)
- Elizabeth Thoenen
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66010, USA
| | - Amanda Curl
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66010, USA
| | - Tomoo Iwakuma
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66010, USA; Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66010, USA; Translational Laboratory Oncology Research, Children's Mercy Research Institute, Kansas City, MO 64108, USA.
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11
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MicroRNA-155 targets MAP3K10 and regulates osteosarcoma cell growth. Pathol Res Pract 2017; 213:389-393. [DOI: 10.1016/j.prp.2016.12.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/26/2016] [Accepted: 12/18/2016] [Indexed: 02/07/2023]
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12
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Osteosarcoma: Cells-of-Origin, Cancer Stem Cells, and Targeted Therapies. Stem Cells Int 2016; 2016:3631764. [PMID: 27366153 PMCID: PMC4913005 DOI: 10.1155/2016/3631764] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/10/2016] [Indexed: 12/25/2022] Open
Abstract
Osteosarcoma (OS) is the most common type of primary solid tumor that develops in bone. Although standard chemotherapy has significantly improved long-term survival over the past few decades, the outcome for those patients with metastatic or recurrent OS remains dismally poor and, therefore, novel agents and treatment regimens are urgently required. A hypothesis to explain the resistance of OS to chemotherapy is the existence of drug resistant CSCs with progenitor properties that are responsible of tumor relapses and metastasis. These subpopulations of CSCs commonly emerge during tumor evolution from the cell-of-origin, which are the normal cells that acquire the first cancer-promoting mutations to initiate tumor formation. In OS, several cell types along the osteogenic lineage have been proposed as cell-of-origin. Both the cell-of-origin and their derived CSC subpopulations are highly influenced by environmental and epigenetic factors and, therefore, targeting the OS-CSC environment and niche is the rationale for many recently postulated therapies. Likewise, some strategies for targeting CSC-associated signaling pathways have already been tested in both preclinical and clinical settings. This review recapitulates current OS cell-of-origin models, the properties of the OS-CSC and its niche, and potential new therapies able to target OS-CSCs.
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BET inhibitors induce apoptosis through a MYC independent mechanism and synergise with CDK inhibitors to kill osteosarcoma cells. Sci Rep 2015; 5:10120. [PMID: 25944566 PMCID: PMC4421868 DOI: 10.1038/srep10120] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/27/2015] [Indexed: 12/11/2022] Open
Abstract
Osteosarcoma (OS) survival rates have plateaued in part due to a lack of new therapeutic options. Here we demonstrate that bromodomain inhibitors (BETi), JQ1, I-BET151, I-BET762, exert potent anti-tumour activity against primary and established OS cell lines, mediated by inhibition of BRD4. Strikingly, unlike previous observations in long-term established human OS cell lines, the antiproliferative activity of JQ1 in primary OS cells was driven by the induction of apoptosis, not cell cycle arrest. In further contrast, JQ1 activity in OS was mediated independently of MYC downregulation. We identified that JQ1 suppresses the transcription factor FOSL1 by displacement of BRD4 from its locus. Loss of FOSL1 phenocopied the antiproliferative effects of JQ1, identifying FOSL1 suppression as a potential novel therapeutic approach for OS. As a monotherapy JQ1 demonstrated significant anti-tumour activity in vivo in an OS graft model. Further, combinatorial treatment approaches showed that JQ1 increased the sensitivity of OS cells to doxorubicin and induced potent synergistic activity when rationally combined with CDK inhibitors. The greater level of activity achieved with the combination of BETi with CDK inhibitors demonstrates the efficacy of this combination therapy. Taken together, our studies show that BET inhibitors are a promising new therapeutic for OS.
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Ng AJM, Walia MK, Smeets MF, Mutsaers AJ, Sims NA, Purton LE, Walsh NC, Martin TJ, Walkley CR. The DNA helicase recql4 is required for normal osteoblast expansion and osteosarcoma formation. PLoS Genet 2015; 11:e1005160. [PMID: 25859855 PMCID: PMC4393104 DOI: 10.1371/journal.pgen.1005160] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/19/2015] [Indexed: 12/04/2022] Open
Abstract
RECQL4 mutations are associated with Rothmund Thomson Syndrome (RTS), RAPADILINO Syndrome and Baller-Gerold Syndrome. These patients display a range of benign skeletal abnormalities such as low bone mass. In addition, RTS patients have a highly increased incidence of osteosarcoma (OS). The role of RECQL4 in normal adult bone development and homeostasis is largely uncharacterized and how mutation of RECQL4 contributes to OS susceptibility is not known. We hypothesised that Recql4 was required for normal skeletal development and both benign and malignant osteoblast function, which we have tested in the mouse. Recql4 deletion in vivo at the osteoblastic progenitor stage of differentiation resulted in mice with shorter bones and reduced bone volume, assessed at 9 weeks of age. This was associated with an osteoblast intrinsic decrease in mineral apposition rate and bone formation rate in the Recql4-deficient cohorts. Deletion of Recql4 in mature osteoblasts/osteocytes in vivo, however, did not cause a detectable phenotype. Acute deletion of Recql4 in primary osteoblasts or shRNA knockdown in an osteoblastic cell line caused failed proliferation, accompanied by cell cycle arrest, induction of apoptosis and impaired differentiation. When cohorts of animals were aged long term, the loss of Recql4 alone was not sufficient to initiate OS. We then crossed the Recql4fl/fl allele to a fully penetrant OS model (Osx-Cre p53fl/fl). Unexpectedly, the Osx-Cre p53fl/flRecql4fl/fl (dKO) animals had a significantly increased OS-free survival compared to Osx-Cre p53fl/fl or Osx-Cre p53fl/flRecql4fl/+ (het) animals. The extended survival was explained when the Recql4 status in the tumors that arose was assessed, and in no case was there complete deletion of Recql4 in the dKO OS. These data provide a mechanism for the benign skeletal phenotypes of RECQL4 mutation syndromes. We propose that tumor suppression and osteosarcoma susceptibility are most likely a function of mutant, not null, alleles of RECQL4. Rothmund Thomson Syndrome (RTS), RAPADILINO Syndrome and Baller-Gerold Syndrome are very rare human syndromes associated with mutations in RECQL4. RECQL4 is important for controlling how cells divide and for preventing genome damage. Patients with RECQL4 mutations have problems with bone formation and a low bone mass, similar to osteoporosis. RTS patients have a highly increased risk of developing bone cancer (osteosarcoma). The role of RECQL4 in normal bone development and osteosarcoma formation is largely unknown. We have used mouse models to understand the specific role of Recql4 in bone development. Mice with Recql4 removed specifically from their bone cells have shortened bones and a reduced rate of bone formation. Therefore, RECQL4 is essential for normal bone development. Interestingly, the animals with no Recql4 in bone cells did not develop osteosarcoma. Using mouse models of osteosarcoma, we observed delayed cancer formation when Recql4 was also deleted. Further analysis demonstrated that bone cancer could not arise from Recql4 null cells even with concurrent p53 deletion. These studies clarify the role of RECQL4 in both normal and malignant bone biology and suggest that RECQL4 mutations that cause osteosarcoma most likely result in proteins with reduced, but not absent, function.
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Affiliation(s)
- Alvin J. M. Ng
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Mannu K. Walia
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Monique F. Smeets
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Natalie A. Sims
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Louise E. Purton
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Nicole C. Walsh
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
| | - T. John Martin
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
| | - Carl R. Walkley
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Fitzroy, Victoria, Australia
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- * E-mail:
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15
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Lamoureux F, Baud’huin M, Rodriguez Calleja L, Jacques C, Berreur M, Rédini F, Lecanda F, Bradner JE, Heymann D, Ory B. Selective inhibition of BET bromodomain epigenetic signalling interferes with the bone-associated tumour vicious cycle. Nat Commun 2014; 5:3511. [DOI: 10.1038/ncomms4511] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/25/2014] [Indexed: 12/22/2022] Open
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16
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How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PLoS Comput Biol 2013; 9:e1003210. [PMID: 24009496 PMCID: PMC3757060 DOI: 10.1371/journal.pcbi.1003210] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/19/2013] [Indexed: 12/25/2022] Open
Abstract
Osteosarcomas (OS) are complex bone tumors with various genomic alterations. These alterations affect the expression and function of several genes due to drastic changes in the underlying gene regulatory network. However, we know little about critical gene regulators and their functional consequences on the pathogenesis of OS. Therefore, we aimed to determine microRNA and transcription factor (TF) co-regulatory networks in OS cell proliferation. Cell proliferation is an essential part in the pathogenesis of OS and deeper understanding of its regulation might help to identify potential therapeutic targets. Based on expression data of OS cell lines divided according to their proliferative activity, we obtained 12 proliferation-related microRNAs and corresponding target genes. Therewith, microRNA and TF co-regulatory networks were generated and analyzed regarding their structure and functional influence. We identified key co-regulators comprising the microRNAs miR-9-5p, miR-138, and miR-214 and the TFs SP1 and MYC in the derived networks. These regulators are implicated in NFKB- and RB1-signaling and focal adhesion processes based on their common or interacting target genes (e.g., CDK6, CTNNB1, E2F4, HES1, ITGA6, NFKB1, NOTCH1, and SIN3A). Thus, we proposed a model of OS cell proliferation which is primarily co-regulated through the interactions of the mentioned microRNA and TF combinations. This study illustrates the benefit of systems biological approaches in the analysis of complex diseases. We integrated experimental data with publicly available information to unravel the coordinated (post)-transcriptional control of microRNAs and TFs to identify potential therapeutic targets in OS. The resulting microRNA and TF co-regulatory networks are publicly available for further exploration to generate or evaluate own hypotheses of the pathogenesis of OS (http://www.complex-systems.uni-muenster.de/co_networks.html).
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Ng AJ, Mutsaers AJ, Baker EK, Walkley CR. Genetically engineered mouse models and human osteosarcoma. Clin Sarcoma Res 2012; 2:19. [PMID: 23036272 PMCID: PMC3523007 DOI: 10.1186/2045-3329-2-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/30/2011] [Indexed: 12/19/2022] Open
Abstract
Osteosarcoma is the most common form of bone cancer. Pivotal insight into the genes involved in human osteosarcoma has been provided by the study of rare familial cancer predisposition syndromes. Three kindreds stand out as predisposing to the development of osteosarcoma: Li-Fraumeni syndrome, familial retinoblastoma and RecQ helicase disorders, which include Rothmund-Thomson Syndrome in particular. These disorders have highlighted the important roles of P53 and RB respectively, in the development of osteosarcoma. The association of OS with RECQL4 mutations is apparent but the relevance of this to OS is uncertain as mutations in RECQL4 are not found in sporadic OS. Application of the knowledge or mutations of P53 and RB in familial and sporadic OS has enabled the development of tractable, highly penetrant murine models of OS. These models share many of the cardinal features associated with human osteosarcoma including, importantly, a high incidence of spontaneous metastasis. The recent development of these models has been a significant advance for efforts to improve our understanding of the genetics of human OS and, more critically, to provide a high-throughput genetically modifiable platform for preclinical evaluation of new therapeutics.
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Affiliation(s)
- Alvin Jm Ng
- St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, VIC, 3065, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Fitzroy, VIC, 3065, Australia
| | - Anthony J Mutsaers
- St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, VIC, 3065, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Fitzroy, VIC, 3065, Australia.,Ontario Veterinary College, University of Guelph, 50 Stone Road, Guelph, ON, N1G 2W1, Canada
| | - Emma K Baker
- St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, VIC, 3065, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Fitzroy, VIC, 3065, Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, VIC, 3065, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Fitzroy, VIC, 3065, Australia
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Abstract
Soft tissue sarcomas are an uncommon and diverse group of more than 50 mesenchymal malignancies. The pathogenesis of many of these is poorly understood, but others have begun to reveal the secrets of their underlying mechanisms. With considerable effort over recent years, soft tissue sarcomas have increasingly been classified on the basis of underlying molecular alterations. In turn, this has allowed the development and application of targeted agents in several specific, molecularly defined, sarcoma subtypes. This review will focus on the rationale for targeted therapy in sarcoma, with emphasis on the relevance of specific molecular factors and pathways in both translocation-associated sarcomas and in genetically complex tumors. In addition, we will address some of the early successes in sarcoma-targeted therapy as well as a few challenges and disappointments in this field. Finally, we will discuss several possible opportunities represented by poorly understood, but potentially promising new therapeutic targets, as well as several novel biological agents currently in preclinical and early phase I/II trials. This will provide the reader with the context for understanding the current state of this field and a sense of where it may be headed in the coming years.
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Affiliation(s)
- Elizabeth G Demicco
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, 77030-4009, USA
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Thayanithy V, Sarver AL, Kartha RV, Lihua L, Angstadt AY, Breen M, Steer CJ, Modiano JF, Subramanian S. Perturbation of 14q32 miRNAs-cMYC gene network in osteosarcoma. Bone 2012; 50:171-81. [PMID: 22037351 PMCID: PMC3755949 DOI: 10.1016/j.bone.2011.10.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/04/2011] [Accepted: 10/10/2011] [Indexed: 01/07/2023]
Abstract
Osteosarcoma (OS) is the common histological form of primary bone cancer and one of the leading aggressive cancers in children under age fifteen. Although several genetic predisposing conditions have been associated with OS the understanding of its molecular etiology is limited. Here, we show that microRNAs (miRNAs) at the chr.14q32 locus are significantly downregulated in osteosarcoma compared to normal bone tissues. Bioinformatic predictions identified that a subset of 14q32 miRNAs (miR-382, miR-369-3p, miR-544 and miR-134) could potentially target cMYC transcript. The physical interaction between these 14q32 miRNAs and cMYC was validated using reporter assays. Further, restoring expression of these four 14q32 miRNAs decreased cMYC levels and induced apoptosis in Saos2 cells. We also show that exogenous expression of 14q32 miRNAs in Saos2 cells significantly downregulated miR-17-92, a transcriptional target of cMYC. The pro-apoptotic effect of 14q32 miRNAs in Saos2 cells was rescued either by overexpression of cMYC cDNA without the 3'UTR or with miR-17-92 cluster. Further, array comparative genomic hybridization studies showed no DNA copy number changes at 14q32 locus in OS patient samples suggesting that downregulation of 14q32 miRNAs are not due to deletion at this locus. Together, our data support a model where the deregulation of a network involving 14q32 miRNAs, cMYC and miR-17-92 miRNAs could contribute to osteosarcoma pathogenesis.
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Affiliation(s)
- Venugopal Thayanithy
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota, MN 55455 USA
| | - Aaron L. Sarver
- Masonic Cancer Center, University of Minnesota, MN 55455 USA
| | - Reena V. Kartha
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, MN 55455 USA
| | - Li Lihua
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota, MN 55455 USA
| | - Andrea Y. Angstadt
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, NC-27606, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, NC-27606, USA
| | - Clifford J. Steer
- Masonic Cancer Center, University of Minnesota, MN 55455 USA
- Department of Medicine, University of Minnesota, MN 55455 USA
- Department of Genetics Cell Biology & Development, University of Minnesota, MN 55455 USA
| | - Jaime F. Modiano
- Masonic Cancer Center, University of Minnesota, MN 55455 USA
- Department of Veterinary Clinical Sciences, University of Minnesota, MN 55455 USA
| | - Subbaya Subramanian
- Division of Basic and Translational Research, Department of Surgery, University of Minnesota, MN 55455 USA
- Masonic Cancer Center, University of Minnesota, MN 55455 USA
- Manuscript correspondence to: Subbaya Subramanian, PhD, 11-212 Moos Tower, 515 Delaware Street S.E, Minneapolis, MN 55455, , Tel: 612-626-4330; Fax: 612-626-7031
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Ruggieri P, Calabrò T, Montalti M, Mercuri M. The role of surgery and adjuvants to survival in Pagetic osteosarcoma. Clin Orthop Relat Res 2010; 468:2962-8. [PMID: 20652460 PMCID: PMC2947701 DOI: 10.1007/s11999-010-1473-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Osteosarcoma is a rare complication of Paget's disease with a very poor prognosis. Treatment is controversial: the older age of the patients affected by Paget's disease may limit the use of chemotherapy and axial involvement may limit the practicality of surgery. QUESTIONS/PURPOSES The purposes of this study are (1) to report the survival in patients treated for osteosarcoma in Paget's disease; (2) to identify correlations between type of treatment and survival comparing our data with those in the literature; (3) to determine if the extent of Paget's disease and risk of malignant transformation are associated; (4) to assess if prognosis is related with site; and (5) to identify the variations of histologic subtypes of these osteosarcomas. METHODS We retrospectively reviewed the medical records of 26 patients treated between 1961 and 2006 who had bone sarcoma arising from a site of Paget's disease. Twenty two of the 26 patients had surgery. In six surgery only was performed; three had surgery, adjuvant chemotherapy, and radiotherapy; one surgery and radiotherapy; 12 underwent surgery and chemotherapy, adjuvant in 10 patients and neoadjuvant in two; two had only radiotherapy and two had only chemotherapy. We performed survival analyses between various combinations of treatment. RESULTS At last followup four patients had no evidence of disease (NED) at a minimum followup of 42.6 months (mean, 139 months; range, 42.6-257.4 months) and 22 died with disease (DWD) at a minimum time of 1 month (mean, 20.2 months; range, 1-84 months). One of the six patients (11%) treated with surgery only had NED at 10 years; the other five died from disease at a mean of 30 months. Three of 12 patients (25%) treated with surgery and chemotherapy are NED at a mean followup of 12 years; nine died of disease at a mean of 24 months. All patients treated without surgery died at a mean of 7.5 months (range, 1-13.7 months). CONCLUSIONS Despite improvements in surgery and medical treatments the prognosis remains poor in patients with Paget's sarcoma.
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Affiliation(s)
- Pietro Ruggieri
- Department of Orthopedics, Istituto Ortopedico Rizzoli and University of Bologna, Via Pupilli 1, Bologna, Emilia Romagna, 40136, Italy.
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Ladanyi M, Gorlick R. Molecular Pathology and Molecular Pharmacology of Osteosarcoma. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/15513810009168647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Sandberg AA, Bridge JA. Updates on the cytogenetics and molecular genetics of bone and soft tissue tumors: osteosarcoma and related tumors. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0165-4608(03)00105-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Baruffi MR, Engel EE, Squire JA, Tone LG, Rogatto SR. Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization. Genet Mol Biol 2003. [DOI: 10.1590/s1415-47572003000200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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