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Chen H, Garbutt CC, Spentzos D, Choy E, Hornicek FJ, Duan Z. Expression and Therapeutic Potential of SOX9 in Chordoma. Clin Cancer Res 2017; 23:5176-5186. [PMID: 28606919 DOI: 10.1158/1078-0432.ccr-17-0177] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/21/2017] [Accepted: 06/05/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Conventional chemotherapeutic agents are ineffective in the treatment of chordoma. We investigated the functional roles and therapeutic relevance of the sex-determining region Y (SRY)-box 9 (SOX9) in chordoma.Experimental Design: SOX9 expression was examined by immunohistochemistry (IHC) using 50 chordoma tissue samples. SOX9 expression in chordoma cell lines was examined by Western blot and immunofluorescent assays. We used synthetic human SOX9 siRNA to inhibit the expression of SOX9. Cell proliferation ability and cytotoxicity of inhibiting SOX9 were assessed by 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide (MTT) and clonogenic assays. The effect of SOX9 knockdown on chordoma cell motility was evaluated by a wound-healing assay and a Transwell invasion chamber assay. Knockdown of SOX9 induced apoptosis, cell-cycle arrest, as well as decreased expression of cancer stem cell markers were determined by Western blot and flow cytometric assays. The effect of the combination of SOX9 siRNA and the chemotherapeutic drug doxorubicin/cisplatin on chordoma cells was assessed by an MTT assay.Results: Tissue microarray and IHC analysis showed that SOX9 is broadly expressed in chordomas and that higher expression levels of SOX9 correlated with a poor prognosis. RNA interference (RNAi)-mediated knockdown of SOX9 inhibited chordoma cell growth, decreased cell motility, and induced apoptosis as well as cell-cycle arrest. Moreover, the combination of SOX9 inhibition and chemotherapeutic drugs had an enhanced anti-cancer effect on chordoma cells.Conclusions: Our results demonstrate that SOX9 plays a crucial role in chordoma. Targeting SOX9 provides a new rationale for treatment of chordoma. Clin Cancer Res; 23(17); 5176-86. ©2017 AACR.
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Affiliation(s)
- Hua Chen
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Emergency Surgery, ShenZhen People's Hospital, 2nd Clinical Medical College of Jinan University, Shenzhen, Guangdong Province, China
| | - Cassandra C Garbutt
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dimitrios Spentzos
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin Choy
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Francis J Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, Duan Z, Quackenbush J, Haibe-Kains B, Spentzos D. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. J Hematol Oncol 2017; 10:107. [PMID: 28506242 PMCID: PMC5433149 DOI: 10.1186/s13045-017-0465-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 11/29/2016] [Accepted: 04/18/2017] [Indexed: 12/25/2022] Open
Abstract
Background A microRNA (miRNA) collection on the imprinted 14q32 MEG3 region has been associated with outcome in osteosarcoma. We assessed the clinical utility of this miRNA set and their association with methylation status. Methods We integrated coding and non-coding RNA data from three independent annotated clinical osteosarcoma cohorts (n = 65, n = 27, and n = 25) and miRNA and methylation data from one in vitro (19 cell lines) and one clinical (NCI Therapeutically Applicable Research to Generate Effective Treatments (TARGET) osteosarcoma dataset, n = 80) dataset. We used time-dependent receiver operating characteristic (tdROC) analysis to evaluate the clinical value of candidate miRNA profiles and machine learning approaches to compare the coding and non-coding transcriptional programs of high- and low-risk osteosarcoma tumors and high- versus low-aggressiveness cell lines. In the cell line and TARGET datasets, we also studied the methylation patterns of the MEG3 imprinting control region on 14q32 and their association with miRNA expression and tumor aggressiveness. Results In the tdROC analysis, miRNA sets on 14q32 showed strong discriminatory power for recurrence and survival in the three clinical datasets. High- or low-risk tumor classification was robust to using different microRNA sets or classification methods. Machine learning approaches showed that genome-wide miRNA profiles and miRNA regulatory networks were quite different between the two outcome groups and mRNA profiles categorized the samples in a manner concordant with the miRNAs, suggesting potential molecular subtypes. Further, miRNA expression patterns were reproducible in comparing high-aggressiveness versus low-aggressiveness cell lines. Methylation patterns in the MEG3 differentially methylated region (DMR) also distinguished high-aggressiveness from low-aggressiveness cell lines and were associated with expression of several 14q32 miRNAs in both the cell lines and the large TARGET clinical dataset. Within the limits of available CpG array coverage, we observed a potential methylation-sensitive regulation of the non-coding RNA cluster by CTCF, a known enhancer-blocking factor. Conclusions Loss of imprinting/methylation changes in the 14q32 non-coding region defines reproducible previously unrecognized osteosarcoma subtypes with distinct transcriptional programs and biologic and clinical behavior. Future studies will define the precise relationship between 14q32 imprinting, non-coding RNA expression, genomic enhancer binding, and tumor aggressiveness, with possible therapeutic implications for both early- and advanced-stage patients. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0465-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine E Hill
- Hematology-Oncology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Marieke L Kuijjer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William Barry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ahmed Rattani
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA, USA
| | - Cassandra C Garbutt
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Haydn Kissick
- Department of Urology, Medical School, Emory University, Atlanta, GA, USA
| | - Katherine Janeway
- Department of Pediatric Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Perez-Atayde
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Goldsmith
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark C Gebhardt
- Orthopedics, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mohamed S Arredouani
- Surgery, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Greg Cote
- Cancer Center, Division of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Francis Hornicek
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin Choy
- Cancer Center, Division of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhenfeng Duan
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Ontario Institute of Cancer Research, Toronto, Canada
| | - Dimitrios Spentzos
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Hematology-Oncology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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Garbutt CC, Bangalore PV, Kannar P, Mukhtar MS. Getting to the edge: protein dynamical networks as a new frontier in plant-microbe interactions. Front Plant Sci 2014; 5:312. [PMID: 25071795 PMCID: PMC4074768 DOI: 10.3389/fpls.2014.00312] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/11/2014] [Indexed: 05/18/2023]
Abstract
A systems perspective on diverse phenotypes, mechanisms of infection, and responses to environmental stresses can lead to considerable advances in agriculture and medicine. A significant promise of systems biology within plants is the development of disease-resistant crop varieties, which would maximize yield output for food, clothing, building materials, and biofuel production. A systems or "-omics" perspective frames the next frontier in the search for enhanced knowledge of plant network biology. The functional understanding of network structure and dynamics is vital to expanding our knowledge of how the intercellular communication processes are executed. This review article will systematically discuss various levels of organization of systems biology beginning with the building blocks termed "-omes" and ending with complex transcriptional and protein-protein interaction networks. We will also highlight the prevailing computational modeling approaches of biological regulatory network dynamics. The latest developments in the "-omics" approach will be reviewed and discussed to underline and highlight novel technologies and research directions in plant network biology.
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Affiliation(s)
- Cassandra C. Garbutt
- Department of Biology, The University of Alabama at BirminghamBirmingham, AL, USA
| | - Purushotham V. Bangalore
- Department of Computer and Information Sciences, The University of Alabama at BirminghamBirmingham, AL, USA
| | - Pegah Kannar
- Department of Biology, The University of Alabama at BirminghamBirmingham, AL, USA
| | - M. S. Mukhtar
- Department of Biology, The University of Alabama at BirminghamBirmingham, AL, USA
- Nutrition Obesity Research Center, The University of Alabama at BirminghamBirmingham, AL, USA
- *Correspondence: M. S. Mukhtar, Department of Biology, The University of Alabama at Birmingham, Campbell Hall 369, 1300 University Boulevard, Birmingham, AL 35294-1170, USA e-mail:
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