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Ghosh PK, Ghosh A. Dysregulation of noncoding RNA in chordoma; implications in identifying potential targets for novel therapeutic approaches. Mol Biol Rep 2024; 51:125. [PMID: 38236360 DOI: 10.1007/s11033-023-09017-9] [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: 08/19/2023] [Accepted: 10/23/2023] [Indexed: 01/19/2024]
Abstract
Chordoma is a rare form of bone cancer develops in the spinal cord and skull. Instead of conventional (radio/chemotherapies) and targeted therapies, the disease is associated with high rate of recurrence and poor patient survival. Thus, for better disease management, the molecular pathogenesis of chordoma should be studied in detail to identify dysregulated biomolecules that can be targeted by novel therapeutics. Recent research showed frequent dysregulation of long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA) in association with aggressive tumor phenotypes like cell proliferation, migration, invasion, and metastasis in a variety of cancers, including chordoma. Apart from diagnostic and prognostic importance, noncoding RNAs may serve as promising targets for novel therapeutics in cancer. In this review, we summarized a list of miRNAs, lncRNAs, and circRNA found to be dysregulated in chordoma from available data published in relevant databases (PubMed), as such an approach seems to be rare to date. The dysregulated noncoding RNAs were also associated with adverse tumor phenotypes to assess the impact on disease pathogenesis and, associated downstream molecular pathways were focused. Synthetic compounds and natural products that were reported to target the noncoding RNAs in other malignancies were also listed from published literature and proposed as potential therapeutic agents in chordoma. This review will provide information for further research on chordoma focusing on detailed characterization of dysregulated lncRNAs, miRNAs, and circRNA to understand the disease pathogenesis and, exploration of suitable natural and synthetic products targeting dysregulated non-coding RNAs to develop effective therapeutic measures.
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Affiliation(s)
- Pramit Kumar Ghosh
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
- Genetics of Non-communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India.
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Rubino F, Alvarez-Breckenridge C, Akdemir K, Conley AP, Bishop AJ, Wang WL, Lazar AJ, Rhines LD, DeMonte F, Raza SM. Prognostic molecular biomarkers in chordomas: A systematic review and identification of clinically usable biomarker panels. Front Oncol 2022; 12:997506. [PMID: 36248987 PMCID: PMC9557284 DOI: 10.3389/fonc.2022.997506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction and objectiveDespite the improvements in management and treatment of chordomas over time, the risk of disease recurrence remains high. Consequently, there is a push to develop effective systemic therapeutics for newly diagnosed and recurrent disease. In order to tailor treatment for individual chordoma patients and develop effective surveillance strategies, suitable clinical biomarkers need to be identified. The objective of this study was to systematically review all prognostic biomarkers for chordomas reported to date in order to classify them according to localization, study design and statistical analysis.MethodsUsing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we systematically reviewed published studies reporting biomarkers that correlated with clinical outcomes. We included time-to-event studies that evaluated biomarkers in skull base or spine chordomas. To be included in our review, the study must have analyzed the outcomes with univariate and/or multivariate methods (log-rank test or a Cox-regression model).ResultsWe included 68 studies, of which only 5 were prospective studies. Overall, 103 biomarkers were analyzed in 3183 patients. According to FDA classification, 85 were molecular biomarkers (82.5%) mainly located in nucleus and cytoplasm (48% and 27%, respectively). Thirty-four studies analyzed biomarkers with Cox-regression model. Within these studies, 32 biomarkers (31%) and 22 biomarkers (21%) were independent prognostic factors for PFS and OS, respectively.ConclusionOur analysis identified a list of 13 biomarkers correlating with tumor control rates and survival. The future point will be gathering all these results to guide the clinical validation for a chordoma biomarker panel. Our identified biomarkers have strengths and weaknesses according to FDA’s guidelines, some are affordable, have a low-invasive collection method and can be easily measured in any health care setting (RDW and D-dimer), but others molecular biomarkers need specialized assay techniques (microRNAs, PD-1 pathway markers, CDKs and somatic chromosome deletions were more chordoma-specific). A focused list of biomarkers that correlate with local recurrence, metastatic spread and survival might be a cornerstone to determine the need of adjuvant therapies.
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Affiliation(s)
- Franco Rubino
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Christopher Alvarez-Breckenridge
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Kadir Akdemir
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Anthony P. Conley
- Department of Sarcoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Andrew J. Bishop
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Wei-Lien Wang
- Department of Pathology, Division of Pathology-Lab Medicine Division, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Alexander J. Lazar
- Department of Pathology, Division of Pathology-Lab Medicine Division, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Laurence D. Rhines
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Franco DeMonte
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Shaan M. Raza
- Department of Neurosurgery, Division of surgery, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, United States
- *Correspondence: Shaan M. Raza,
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Wang Y, Tang Z, Guo W. XIST sponges miR-320d to promote chordoma progression by regulating ARF6. J Bone Oncol 2022; 35:100447. [PMID: 35899235 PMCID: PMC9309415 DOI: 10.1016/j.jbo.2022.100447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
XIST was highly expressed in chordoma tissues. XIST knockdown inhibited chordoma progression by downregulating ARF6. MiR-320d inhibited the malignant behaviors of chordoma cells. XIST positively upregulated ARF6 expression via sponging miR-320d in chordoma cells.
Background Long non-coding RNAs (lncRNAs) have been demonstrated to play important roles in various tumors, including chordoma. The purpose of this study was to investigate the role and mechanism of lncRNA X-inactive specific transcript (XIST) in chordoma. Methods RNA levels and protein levels were measured by real-time quantitative polymerase chain reaction (RT‑qPCR) and western blot assay, respectively. Cell proliferation was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 5-ethynyl-2′-deoxyuridine (EdU) assay and colony formation assay. Tanswell assay was used to examine cell migration and invasion. Cellular glycolysis was examined via the measurement of extracellular acidification rate (ECAR) and lactate production. The interaction between microRNA-320d (miR-320d) and XIST or ADP-ribosylation factor 6 (ARF6) was predicted by bioinformatics analysis and verified by a dual-luciferase reporter and RNA-pull down assays. The xenograft tumor model was used to explore the biological function of XIST in vivo. Results XIST was overexpressed in chordoma tissues. XIST knockdown suppressed chordoma cell proliferation, migration, invasion, and glycolysis. XIST acted as a sponge of miR-320d. Moreover, miR-320d overexpression inhibited the proliferation, migration, invasion, and glycolysis of chordoma cells. ARF6 was a direct target of miR-320d, and XIST upregulated ARF6 expression via sponging miR-320d. Furthermore, overexpression of ARF6 reversed the inhibitory effects of XIST knockdown on chordoma cell proliferation, migration, invasion, and glycolysis. Importantly, XIST silencing blocked xenograft tumor growth in vivo. Conclusion XIST knockdown inhibited chordoma progression via regulating the miR-320d/ARF6 axis, providing a novel insight into chordoma pathogenesis.
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Affiliation(s)
- Yonggang Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Zhouzhou Tang
- Department of Orthopedics, Jingzhou Central Hospital, Jingzhou 434020, Hubei Province, China
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
- Corresponding author at: Department of Orthopedics, Renmin Hospital of Wuhan University, No. 238, Jiefang Road, Wuchang District, Wuhan City, Hubei Province, China.
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Tu K, Lee S, Roy S, Sawant A, Shukla H. Dysregulated Epigenetics of Chordoma: Prognostic Markers and Therapeutic Targets. Curr Cancer Drug Targets 2022; 22:678-690. [PMID: 35440334 DOI: 10.2174/1568009622666220419122716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022]
Abstract
Chordoma is a rare, slow-growing sarcoma that is locally aggressive, and typically resistant to conventional chemo- and radiotherapies. Despite its low incidence, chordoma remains a clinical challenge because therapeutic options for chordoma are limited, and little is known about the molecular mechanisms involved in resistance to therapies. Furthermore, there are currently no established predictive or prognostic biomarkers to follow disease progression or treatment. Whole-genome sequencing of chordoma tissues has demonstrated a low-frequency mutation rate compared to other cancers. This has generated interest in the role of epigenetic events in chordoma pathogenesis. In this review, we discuss the current understanding of the epigenetic drivers of chordoma and their potential applications in prognosis and the development of new therapies.
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Affiliation(s)
- Kevin Tu
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Sang Lee
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Sanjit Roy
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
| | - Amit Sawant
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
| | - Hem Shukla
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
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