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Khan S, Zuccato JA, Ignatchenko V, Singh O, Govindarajan M, Waas M, Mejia-Guerrero S, Gao A, Zadeh G, Kislinger T. Organelle resolved proteomics uncovers PLA2R1 as a novel cell surface marker required for chordoma growth. Acta Neuropathol Commun 2024; 12:39. [PMID: 38454495 PMCID: PMC10921702 DOI: 10.1186/s40478-024-01751-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024] Open
Abstract
Chordomas are clinically aggressive tumors with a high rate of disease progression despite maximal therapy. Given the limited therapeutic options available, there remains an urgent need for the development of novel therapies to improve clinical outcomes. Cell surface proteins are attractive therapeutic targets yet are challenging to profile with common methods. Four chordoma cell lines were analyzed by quantitative proteomics using a differential ultracentrifugation organellar fractionation approach. A subtractive proteomics strategy was applied to select proteins that are plasma membrane enriched. Systematic data integration prioritized PLA2R1 (secretory phospholipase A2 receptor-PLA2R1) as a chordoma-enriched surface protein. The expression profile of PLA2R1 was validated across chordoma cell lines, patient surgical tissue samples, and normal tissue lysates via immunoblotting. PLA2R1 expression was further validated by immunohistochemical analysis in a richly annotated cohort of 25-patient tissues. Immunohistochemistry analysis revealed that elevated expression of PLA2R1 is correlated with poor prognosis. Using siRNA- and CRISPR/Cas9-mediated knockdown of PLA2R1, we demonstrated significant inhibition of 2D, 3D and in vivo chordoma growth. PLA2R1 depletion resulted in cell cycle defects and metabolic rewiring via the MAPK signaling pathway, suggesting that PLA2R1 plays an essential role in chordoma biology. We have characterized the proteome of four chordoma cell lines and uncovered PLA2R1 as a novel cell-surface protein required for chordoma cell survival and association with patient outcome.
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Affiliation(s)
- Shahbaz Khan
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Jeffrey A Zuccato
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Canada
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Olivia Singh
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Meinusha Govindarajan
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Matthew Waas
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Salvador Mejia-Guerrero
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
| | - Andrew Gao
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Princess Margaret Cancer Research Tower, University Health Network, 101 College Street, Room 9-807, Toronto, ON, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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2
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Hoch CC, Knoedler L, Knoedler S, Bashiri Dezfouli A, Schmidl B, Trill A, Douglas JE, Adappa ND, Stögbauer F, Wollenberg B. Integrated Molecular and Histological Insights for Targeted Therapies in Mesenchymal Sinonasal Tract Tumors. Curr Oncol Rep 2024; 26:272-291. [PMID: 38376625 PMCID: PMC10920452 DOI: 10.1007/s11912-024-01506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
PURPOSE OF REVIEW This review aims to provide a comprehensive overview of mesenchymal sinonasal tract tumors (STTs), a distinct subset of STTs. Despite their rarity, mesenchymal STTs represent a unique clinical challenge, characterized by their rarity, often slow progression, and frequently subtle or overlooked symptoms. The complex anatomy of the sinonasal area, which includes critical structures such as the orbit, brain, and cranial nerves, further complicates surgical treatment options. This underscores an urgent need for more advanced and specialized therapeutic approaches. RECENT FINDINGS Advancements in molecular diagnostics, particularly in next-generation sequencing, have significantly enhanced our understanding of STTs. Consequently, the World Health Organization has updated its tumor classification to better reflect the distinct histological and molecular profiles of these tumors, as well as to categorize mesenchymal STTs with greater accuracy. The growing understanding of the molecular characteristics of mesenchymal STTs opens new possibilities for targeted therapeutic interventions, marking a significant shift in treatment paradigms. This review article concentrates on mesenchymal STTs, specifically addressing sinonasal tract angiofibroma, sinonasal glomangiopericytoma, biphenotypic sinonasal sarcoma, and skull base chordoma. These entities are marked by unique histopathological and molecular features, which challenge conventional treatment approaches and simultaneously open avenues for novel targeted therapies. Our discussion is geared towards delineating the molecular underpinnings of mesenchymal STTs, with the objective of enhancing therapeutic strategies and addressing the existing shortcomings in the management of these intricate tumors.
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Affiliation(s)
- Cosima C Hoch
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich (TUM), Ismaningerstrasse 22, 81675, Munich, Germany
| | - Leonard Knoedler
- Department of Surgery, Division of Plastic Surgery, Yale School of Medicine, New Haven, CT, USA
- Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel Knoedler
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum Munich, Munich, Germany
| | - Ali Bashiri Dezfouli
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich (TUM), Ismaningerstrasse 22, 81675, Munich, Germany
- Central Institute for Translational Cancer Research, Technical University of Munich (TranslaTUM), Department of Radiation Oncology, Klinikum rechts der Isar, Munich, Germany
| | - Benedikt Schmidl
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich (TUM), Ismaningerstrasse 22, 81675, Munich, Germany
| | - Anskar Trill
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich (TUM), Ismaningerstrasse 22, 81675, Munich, Germany
- Central Institute for Translational Cancer Research, Technical University of Munich (TranslaTUM), Department of Radiation Oncology, Klinikum rechts der Isar, Munich, Germany
| | - Jennifer E Douglas
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Nithin D Adappa
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Barbara Wollenberg
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich (TUM), Ismaningerstrasse 22, 81675, Munich, Germany.
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3
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Baluszek S, Kober P, Rusetska N, Wągrodzki M, Mandat T, Kunicki J, Bujko M. DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment. Acta Neuropathol Commun 2023; 11:113. [PMID: 37434245 DOI: 10.1186/s40478-023-01610-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Chordomas are rare tumors of notochord remnants, occurring mainly in the sacrum and skull base. Despite of their unusually slow growth, chordomas are highly invasive and the involvement of adjacent critical structures causes treatment challenges. Due to the low incidence, the molecular pathogenesis of this entity remains largely unknown. This study aimed to investigate DNA methylation abnormalities and their impact on gene expression profiles in skull base chordomas. 32 tumor and 4 normal nucleus pulposus samples were subjected to DNA methylation and gene expression profiling with methylation microarrays and RNA sequencing. Genome-wide DNA methylation analysis revealed two distinct clusters for chordoma (termed subtypes C and I) with different patterns of aberrant DNA methylation. C Chordomas were characterized by general hypomethylation with hypermethylation of CpG islands, while I chordomas were generally hypermethylated. These differences were reflected by distinct distribution of differentially methylated probes (DMPs). Differentially methylated regions (DMRs) were identified, indicating aberrant methylation in known tumor-related genes in booth chordoma subtypes and regions encoding small RNAs in subtype C chordomas. Correlation between methylation and expression was observed in a minority of genes. Upregulation of TBXT in chordomas appeared to be related to lower methylation of tumor-specific DMR in gene promoter. Gene expression-based clusters of tumor samples did not overlap with DNA methylation-based subtypes. Nevertheless, they differ in transcriptomic profile that shows immune infiltration in I chordomas and up-regulation of cell cycle in C chordomas. Immune enrichment in chordomas I was confirmed with 3 independent deconvolution methods and immunohistochemistry. Copy number analysis showed higher chromosomal instability in C chordomas. Nine out of eight had deletion of CDKN2A/B loci and downregulation of genes encoded in related chromosomal band. No significant difference in patients' survival was observed between tumor subtypes, however, shorter survival was observed in patients with higher number of copy number alterations.
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Affiliation(s)
- Szymon Baluszek
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Rusetska
- Department of Experimental Immunotherapy, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Wągrodzki
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Tomasz Mandat
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
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Yamashita M, Kuroha M, Kinowawki Y, Kashiwagi N, Watanabe K, Nagase M, Niizato D, Mitsuiki N, Isoda T, Kamiya T, Arisaka A, Inaji M, Ohashi K, Imai K, Kanegane H, Morio T, Takagi M. A SAMD5-SASH1 fusion in solitary infantile myofibromatosis. Pediatr Blood Cancer 2023; 70:e30278. [PMID: 36861442 DOI: 10.1002/pbc.30278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Affiliation(s)
- Motoi Yamashita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masae Kuroha
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuko Kinowawki
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nao Kashiwagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kotaro Watanabe
- Department of Pediatrics, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Mika Nagase
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Daiki Niizato
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Noriko Mitsuiki
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiro Kamiya
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Atsuko Arisaka
- Department of Pediatrics, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Motoki Inaji
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kenichi Ohashi
- Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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5
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Zhao C, Tan T, Zhang E, Wang T, Gong H, Jia Q, Liu T, Yang X, Zhao J, Wu Z, Wei H, Xiao J, Yang C. A chronicle review of new techniques that facilitate the understanding and development of optimal individualized therapeutic strategies for chordoma. Front Oncol 2022; 12:1029670. [PMID: 36465398 PMCID: PMC9708744 DOI: 10.3389/fonc.2022.1029670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/19/2022] [Indexed: 09/01/2023] Open
Abstract
Chordoma is a rare malignant bone tumor that mainly occurs in the sacrum and the clivus/skull base. Surgical resection is the treatment of choice for chordoma, but the local recurrence rate is high with unsatisfactory prognosis. Compared with other common tumors, there is not much research and individualized treatment for chordoma, partly due to the rarity of the disease and the lack of appropriate disease models, which delay the discovery of therapeutic strategies. Recent advances in modern techniques have enabled gaining a better understanding of a number of rare diseases, including chordoma. Since the beginning of the 21st century, various chordoma cell lines and animal models have been reported, which have partially revealed the intrinsic mechanisms of tumor initiation and progression with the use of next-generation sequencing (NGS) techniques. In this study, we performed a systematic overview of the chordoma models and related sequencing studies in a chronological manner, from the first patient-derived chordoma cell line (U-CH1) to diverse preclinical models such as the patient-derived organoid-based xenograft (PDX) and patient-derived organoid (PDO) models. The use of modern sequencing techniques has discovered mutations and expression signatures that are considered potential treatment targets, such as the expression of Brachyury and overactivated receptor tyrosine kinases (RTKs). Moreover, computational and bioinformatics techniques have made drug repositioning/repurposing and individualized high-throughput drug screening available. These advantages facilitate the research and development of comprehensive and personalized treatment strategies for indicated patients and will dramatically improve their prognoses in the near feature.
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Affiliation(s)
- Chenglong Zhao
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Tao Tan
- Department of Orthopedics, 905 Hospital of People’s Liberation Army Navy, Shanghai, China
| | - E. Zhang
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Ting Wang
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Haiyi Gong
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Qi Jia
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Tielong Liu
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Xinghai Yang
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Jian Zhao
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Zhipeng Wu
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Haifeng Wei
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Jianru Xiao
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
| | - Cheng Yang
- Spinal Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Shanghai, China
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6
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Heft Neal ME, Michmerhuizen NL, Kovatch KJ, Owen JHJ, Zhai J, Jiang H, McKean EL, Prince ME, Brenner JC. Advancement of PI3 Kinase Inhibitor Combination Therapies for PI3K-Aberrant Chordoma. J Neurol Surg B Skull Base 2022; 83:87-98. [PMID: 35155075 PMCID: PMC8824629 DOI: 10.1055/s-0040-1716694] [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: 05/05/2020] [Accepted: 07/19/2020] [Indexed: 10/23/2022] Open
Abstract
Objectives Targeted inhibitors of the PI3 kinase (PI3K) pathway have shown promising but incomplete antitumor activity in preclinical chordoma models. The aim of this study is to advance methodology for a high-throughput drug screen using chordoma models to identify new combination therapies for chordoma. Study Design Present work is an in vitro study. Setting The study conducted at an academic research laboratory. Materials and Methods An in vitro study on automated high-throughput screening of chordoma cells was performed using a library of 1,406 drugs as both mono- and combination therapies with PI3K inhibitors. Combination indices were determined for dual therapies and synergistic outliers were identified as potential therapeutic agents. T (brachyury) siRNA knockdown in combination with PI3K pathway inhibition was also assessed. Results Fifty-nine combination therapies were identified as having potential therapeutic efficacy. Effective combinations included PI3K inhibitors with GSK1838705A (ALK/IGF-1R inhibitor), LY2874455 (VEGFR/FGFR inhibitor), El1 (selective Ezh2 inhibitor), and (-)-p-bromotetramisole oxalate (alkaline phosphatase inhibitor). The top ranking targets identified included ALK, PDGFR, VEGFR, aurora kinase, and BCL-2. T (brachyury) inhibition produced significant reduction in cell viability and growth; however PI3K inhibition in combination with T (brachyury) knockdown did not result in further reduction in growth and viability in vitro. Conclusion High throughput with in vitro combination screening is feasible with chordoma cells and allows for rapid identification of synergistic dual-therapies. Potential combination therapies and targetable pathways were identified. T (brachyury) knockdown produced significant reduction in cell viability, but did not show additional benefit with PI3K pathway inhibition in this model. Further in vitro and in vivo validation of these therapeutic combinations is warranted.
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Affiliation(s)
- Molly E. Heft Neal
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - Nicole L. Michmerhuizen
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Kevin J. Kovatch
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - John Henry J. Owen
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - Jingyi Zhai
- Department of Biostatistics, School of Public Heath, University of Michigan, Ann Arbor, Michigan, United States
| | - Hui Jiang
- Department of Biostatistics, School of Public Heath, University of Michigan, Ann Arbor, Michigan, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Erin L. McKean
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - Mark E.P. Prince
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
| | - J. Chad Brenner
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, United States
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7
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Zuccato JA, Patil V, Mansouri S, Liu JC, Nassiri F, Mamatjan Y, Chakravarthy A, Karimi S, Almeida JP, Bernat AL, Hasen M, Singh O, Khan S, Kislinger T, Sinha N, Froelich S, Adle-Biassette H, Aldape KD, De Carvalho DD, Zadeh G. DNA Methylation based prognostic subtypes of chordoma tumors in tissue and plasma. Neuro Oncol 2021; 24:442-454. [PMID: 34614192 DOI: 10.1093/neuonc/noab235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chordomas are rare malignant bone cancers of the skull-base and spine. Patient survival is variable and not reliably predicted using clinical factors or molecular features. This study identifies prognostic epigenetic chordoma subtypes that are detected non-invasively using plasma methylomes. METHODS Methylation profiles of 68 chordoma surgical samples were obtained between 1996-2018 across three international centres along with matched plasma methylomes where available. RESULTS Consensus clustering identified two stable tissue clusters with a disease-specific survival difference that was independent of clinical factors in a multivariate Cox analysis (HR=14.2, 95%CI: 2.1-94.8, p=0.0063). Immune-related pathways with genes hypomethylated at promoters and increased immune cell abundance were observed in the poor-performing "Immune-infiltrated" subtype. Cell-to-cell interaction plus extracellular matrix pathway hypomethylation and higher tumor purity was observed in the better-performing "Cellular" subtype. The findings were validated in additional DNA methylation and RNA sequencing datasets as well as with immunohistochemical staining. Plasma methylomes distinguished chordomas from other clinical differential diagnoses by applying fifty chordoma-versus-other binomial generalized linear models in random 20% testing sets (mean AUROC=0.84, 95%CI: 0.52-1.00). Tissue-based and plasma-based methylation signals were highly correlated in both prognostic clusters. Additionally, leave-one-out models accurately classified all tumors into their correct cluster based on plasma methylation data. CONCLUSIONS Here, we show the first identification of prognostic epigenetic chordoma subtypes and first use of plasma methylome-based biomarkers to non-invasively diagnose and subtype chordomas. These results may transform patient management by allowing treatment aggressiveness to be balanced with patient risk according to prognosis.
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Affiliation(s)
- Jeffrey A Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Sheila Mansouri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shirin Karimi
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Joao Paulo Almeida
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Laure Bernat
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Mohammed Hasen
- Section of Neurosurgery, Division of Surgery, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada.,Department of Neurosurgery, King Fahad University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Namita Sinha
- Department of Pathology, Shared Health, HSC, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sébastien Froelich
- Neurosurgery Department, Hôpital Lariboisiere, APHP, Université Paris Diderot, Paris, France
| | - Homa Adle-Biassette
- Department of Pathology, Lariboisière Hospital, Assistance Publique - Hôpitaux de Paris, Université de Paris, Paris, France
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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8
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Abstract
OBJECTIVE Comprehensive molecular profiling of radioresistant and cystic vestibular schwannoma (VS) subtypes. STUDY DESIGN Our study utilized whole-exome sequencing (WES), RNA-sequencing (RNAseq), and correlated clinical data from 12 samples (2 samples of solid sporadic subtype, 8 with cystic changes, and 2 previously irradiated). SETTING Academic medical center. PATIENTS Patients diagnosed with VS who required surgical treatment. Inclusion: Cystic and radioresistant tumors matched to age and tumor volume, with solid sporadic VS samples as control; Exclusion: NF-2 patients. INTERVENTION(S) WES using custom probes for copy number analysis. A modified version of the Agilent Human Whole Exome sequencing hybrid capture system was used to process samples. Recurrent variants were identified and compared between groups. Leukocyte-derived DNA was utilized as internal control to reduce false-positives. MAIN OUTCOME MEASURE(S) Analysis of genetic landscape of VS subtypes (naive solid VS, cystic VS, and previously irradiated VS) by performing deep next-generation sequencing. RESULTS WES data achieved a mean coverage of 202X and RNAseq generated an average of 74 million total reads. As a group, 25% of samples had 22q loss. Somatic analysis identified previously reported genes and multiple novel mutations across samples. Differential expression analysis of RNAseq data found significantly mutated genes such as COL6A3, CLMP, ART4, Lumican that were shared by both cystic VS and irradiated VS, but not seen in sporadic VS. CONCLUSIONS Using WES we were able to demonstrate that cystic and irradiated samples are subtypes of VS with an increased mutation burden and a unique genetic fingerprint. We identified differences between the genomic and molecular profile of cystic VS and radioresistant VS. Our results help advance the understanding of the pathophysiology of these tumor subtypes and suggest possible molecular targets for novel treatment strategies.
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9
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Lee E, Lee JW, Lee B, Park K, Shim J, Yoo KH, Koo HH, Sung KW, Park WY. Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma. BMC Med Genomics 2020; 13:171. [PMID: 33172452 PMCID: PMC7653769 DOI: 10.1186/s12920-020-00819-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
Background MYCN amplification is the most important genomic feature in neuroblastoma (NB). However, limited studies have been conducted on the MYCN non-amplified NB including low- and intermediate-risk NB. Here, the genomic characteristics of MYCN non-amplified NB were studied to allow for the identification of biomarkers for molecular stratification. Methods Fifty-eight whole exome sequencing (WES) and forty-eight whole transcriptome sequencing (WTS) samples of MYCN non-amplified NB were analysed. Forty-one patients harboured WES and WTS pairs. Results In the MYCN non-amplified NB WES data, maximum recurrent mutations were found in MUC4 (26%), followed by RBMXL3 (19%), ALB (17%), and MUC16 and SEPD8 (14% each). Two gene fusions, CCDC32-CBX3 (10%) and SAMD5-SASH1 (6%), were recurrent in WTS analysis, and these fusions were detected mostly in non-high-risk patients with ganglioneuroblastoma histology. Analysis of risk-group-specific biomarkers showed that several genes and gene sets were differentially expressed between the risk groups, and some immune-related pathways tended to be activated in the high-risk group. Mutational signatures 6 and 18, which represent DNA mismatch repair associated mutations, were commonly detected in 60% of the patients. In the tumour mutation burden (TMB) analysis, four patients showed high TMB (> 3 mutations/Mb), and had mutations in genes related to either MMR or homologous recombination. Excluding four outlier samples with TMB > 3 Mb, high-risk patients had significantly higher levels of TMB compared with the non-high-risk patients. Conclusions This study provides novel insights into the genomic background of MYCN non-amplified NB. Activation of immune-related pathways in the high-risk group and the results of TMB and mutational signature analyses collectively suggest the need for further investigation to discover potential immunotherapeutic strategies for NB.
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Affiliation(s)
- Eunjin Lee
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Boram Lee
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Joonho Shim
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Hong Hoe Koo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea. .,Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea. .,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.
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10
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Tallegas M, Miquelestorena-Standley É, Labit-Bouvier C, Badoual C, Francois A, Gomez-Brouchet A, Aubert S, Collin C, Tallet A, de Pinieux G. IDH mutation status in a series of 88 head and neck chondrosarcomas: different profile between tumors of the skull base and tumors involving the facial skeleton and the laryngotracheal tract. Hum Pathol 2019; 84:183-191. [DOI: 10.1016/j.humpath.2018.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/24/2018] [Accepted: 09/29/2018] [Indexed: 02/08/2023]
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11
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Liang WS, Dardis C, Helland A, Sekar S, Adkins J, Cuyugan L, Enriquez D, Byron S, Little AS. Identification of therapeutic targets in chordoma through comprehensive genomic and transcriptomic analyses. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003418. [PMID: 30322893 PMCID: PMC6318766 DOI: 10.1101/mcs.a003418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/04/2018] [Indexed: 01/12/2023] Open
Abstract
Chordoma is a rare, orphan cancer arising from embryonal precursors of bone. Surgery and radiotherapy (RT) provide excellent local control, often at the price of significant morbidity because of the structures involved and the need for relatively high doses of RT; however, recurrence remains high. Although our understanding of the genetic changes that occur in chordoma is evolving rapidly, this knowledge has yet to translate into treatments. We performed comprehensive DNA (paired tumor/normal whole-exome and shallow whole-genome) and RNA (tumor whole-transcriptome) next-generation sequencing analyses of archival sacral and clivus chordoma specimens. Incorporation of transcriptomic data enabled the identification of gene overexpression and expressed DNA alterations, thus providing additional support for potential therapeutic targets. In three patients, we identified alterations that may be amenable to off-label FDA-approved treatments for other tumor types. These alterations include FGFR1 overexpression (ponatinib, pazopanib) and copy-number duplication of CDK4 (palbociclib) and ERBB3 (gefitinib). In a third patient, germline DNA demonstrated predicted pathogenic changes in CHEK2 and ATM, which may have predisposed the patient to developing chordoma at a young age and may also be associated with potential sensitivity to PARP inhibitors because of homologous recombination repair deficiency. Last, in the fourth patient, a missense mutation in IGF1R was identified, suggesting potential activity for investigational anti-IGF1R strategies. Our findings demonstrate that chordoma patients present with aberrations in overlapping pathways. These results provide support for targeting the IGF1R/FGFR/EGFR and CDK4/6 pathways as treatment strategies for chordoma patients. This study underscores the value of comprehensive genomic and transcriptomic analysis in the development of rational, individualized treatment plans for chordoma.
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Affiliation(s)
- Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Christopher Dardis
- Division of Neurology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Adrienne Helland
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Shobana Sekar
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jonathan Adkins
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Lori Cuyugan
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Daniel Enriquez
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Sara Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Andrew S Little
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
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12
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Laetsch TW, Roy A, Xu L, Black JO, Coffin CM, Chi YY, Tian J, Spunt SL, Hawkins DS, Bridge JA, Parsons DW, Skapek SX. Undifferentiated Sarcomas in Children Harbor Clinically Relevant Oncogenic Fusions and Gene Copy-Number Alterations: A Report from the Children's Oncology Group. Clin Cancer Res 2018; 24:3888-3897. [PMID: 29691299 DOI: 10.1158/1078-0432.ccr-18-0672] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/27/2018] [Accepted: 04/20/2018] [Indexed: 01/14/2023]
Abstract
Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332.Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 × 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases.Results: Five-year overall survival for patients with UDS was 83% (95% CI, 69%-97%) with risk-adapted therapy (surgery, chemotherapy, and radiotherapy). Both focal and arm-level copy-number alterations were common including gain of 1q (8/32, 25%) and loss of 1p (7/32, 22%), both of which occurred more often in clinically defined high-risk tumors. Tumors with both loss of 1p and gain of 1q carried an especially poor prognosis with a 5-year event-free survival of 20%. GISTIC analysis identified recurrent amplification of FGF1 on 5q31.3 (q = 0.03) and loss of CDKN2A and CDKN2B on 9p21.3 (q = 0.07). Known oncogenic fusions were identified in eight of 10 cases analyzed by next-generation sequencing.Conclusions: Pediatric UDS generally has a good outcome with risk-adapted therapy. A high-risk subset of patients whose tumors have copy-number loss of 1p and gain of 1q was identified with only 20% survival. Oncogenic fusions are common in UDS, and next-generation sequencing should be considered for children with UDS to refine the diagnosis and identify potentially targetable drivers. Clin Cancer Res; 24(16); 3888-97. ©2018 AACR.
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Affiliation(s)
| | - Angshumoy Roy
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Lin Xu
- University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Cheryl M Coffin
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Jing Tian
- University of Florida, Gainesville, Florida
| | - Sheri L Spunt
- Stanford University School of Medicine, Stanford, California
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - D Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas
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13
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Establishment and genomic characterization of the new chordoma cell line Chor-IN-1. Sci Rep 2017; 7:9226. [PMID: 28835717 PMCID: PMC5569021 DOI: 10.1038/s41598-017-10044-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022] Open
Abstract
Chordomas are rare, slowly growing tumors with high medical need, arising in the axial skeleton from notochord remnants. The transcription factor “brachyury” represents a distinctive molecular marker and a key oncogenic driver of chordomas. Tyrosine kinase receptors are also expressed, but so far kinase inhibitors have not shown clear clinical efficacy in chordoma patients. The need for effective therapies is extremely high, but the paucity of established chordoma cell lines has limited preclinical research. Here we describe the isolation of the new Chor-IN-1 cell line from a recurrent sacral chordoma and its characterization as compared to other chordoma cell lines. Chor-IN-1 displays genomic identity to the tumor of origin and has morphological features, growth characteristics and chromosomal abnormalities typical of chordoma, with expression of brachyury and other relevant biomarkers. Chor-IN-1 gene variants, copy number alterations and kinome gene expression were analyzed in comparison to other four chordoma cell lines, generating large scale DNA and mRNA genomic data that can be exploited for the identification of novel pharmacological targets and candidate predictive biomarkers of drug sensitivity in chordoma. The establishment of this new, well characterized chordoma cell line provides a useful tool for the identification of drugs active in chordoma.
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14
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Genetic aberrations and molecular biology of skull base chordoma and chondrosarcoma. Brain Tumor Pathol 2017; 34:78-90. [PMID: 28432450 DOI: 10.1007/s10014-017-0283-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/27/2017] [Indexed: 12/20/2022]
Abstract
Chordomas and chondrosarcomas are two major malignant bone neoplasms located at the skull base. These tumors are rarely metastatic, but can be locally invasive and resistant to conventional chemotherapies and radiotherapies. Accordingly, therapeutic approaches for the treatment of these tumors can be difficult. Additionally, their location at the skull base makes them problematic. Although accurate diagnosis of these tumors is important because of their distinct prognoses, distinguishing between these tumor types is difficult due to overlapping radiological and histopathological findings. However, recent accumulation of molecular and genetic studies, including extracranial location analysis, has provided us clues for accurate diagnosis. In this report, we review the genetic aberrations and molecular biology of these two tumor types. Among the abundant genetic features of these tumors, brachyury immunohistochemistry and direct sequencing of IDH1/2 are simple and useful techniques that can be used to distinguish between these tumors. Although it is still unclear why these tumors, which have such distinct genetic backgrounds, show similar histopathological findings, comparison of their genetic backgrounds could provide essential information.
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15
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Yagai T, Matsui S, Harada K, Inagaki FF, Saijou E, Miura Y, Nakanuma Y, Miyajima A, Tanaka M. Expression and localization of sterile alpha motif domain containing 5 is associated with cell type and malignancy of biliary tree. PLoS One 2017; 12:e0175355. [PMID: 28388653 PMCID: PMC5384680 DOI: 10.1371/journal.pone.0175355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/07/2017] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma (CC) is a type of relatively rare neoplasm in adenocarcinoma. The characteristics of CCs as well as biliary epithelial cells are heterogeneous at the different portion of the biliary tree. There are two candidate stem/progenitor cells of the biliary tree, i.e., biliary tree stem/progenitor cell (BTSC) at the peribiliary gland (PBG) of large bile ducts and liver stem/progenitor cell (LPC) at the canals of Hering of peripheral small bile duct. Although previous reports suggest that intrahepatic CC (ICC) can arise from such stem/progenitor cells, the characteristic difference between BTSC and LPC in pathological process needs further investigation, and the etiology of CC remains poorly understood. Here we show that Sterile alpha motif domain containing 5 (SAMD5) is exclusively expressed in PBGs of large bile ducts in normal mice. Using a mouse model of cholestatic liver disease, we demonstrated that SAMD5 expression was upregulated in the large bile duct at the hepatic hilum, the extrahepatic bile duct and PBGs, but not in proliferating intrahepatic ductules, suggesting that SAMD5 is expressed in BTSC but not LPC. Intriguingly, human ICCs and extrahepatic CCs exhibited striking nuclear localization of SAMD5 while the normal hilar large bile duct displayed slight-to-moderate expression in cytoplasm. In vitro experiments using siRNA for SAMD5 revealed that SAMD5 expression was associated with the cell cycle regulation of CC cell lines. Conclusion: SAMD5 is a novel marker for PBG but not LPC in mice. In humans, the expression and location of SAMD5 could become a promising diagnostic marker for the cell type as well as malignancy of bile ducts and CCs.
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Affiliation(s)
- Tomoki Yagai
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Satoshi Matsui
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenichi Harada
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Fuyuki F. Inagaki
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Eiko Saijou
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yasushi Miura
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Department of Life Science and Medical Bio-Science, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yasuni Nakanuma
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Atsushi Miyajima
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Minoru Tanaka
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Laboratory of Stem Cell Regulation, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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