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Giesche J, Mellert K, Geißler S, Arndt S, Seeling C, von Baer A, Schultheiss M, Marienfeld R, Möller P, Barth TF. Epigenetic lockdown of CDKN1A (p21) and CDKN2A (p16) characterises the neoplastic spindle cell component of giant cell tumours of bone. J Pathol 2022; 257:687-696. [PMID: 35522566 DOI: 10.1002/path.5925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
Giant cell tumour of bone (GCTB) comprises the eponymous osteoclastic multinucleated giant cells eliciting bone lysis, a H3F3A-mutated neoplastic mononucleated fibroblast-like cell population and H3F3A-wild type mononucleated stromal cells. In this study, we characterised four new cell lines from GCTB. Furthermore, we compared the genome-wide DNA methylation profile of 13 such tumours and three further cell lines with giant cell rich lesions comprising three H3F3B-mutated chondroblastomas, three USP6-rearranged aneurysmal bone cysts, three non-ossifying fibromas, two hyperparathyroidism-associated brown tumours as well as mesenchymal stem cells, osteoblasts, and osteoclasts. In an unsupervised analysis, we delineated GCTB and chondroblastomas from the other analysed tumour entities. Using comparative methylation analysis, we demonstrated that the methylation pattern of the cell lines approximately equals that of H3F3A-mutated stromal cells in tissue. These patterns more resemble that of osteoblasts than that of mesenchymal stem cells, which argues for the osteoblast as the cell of origin of giant cell tumours of bone. Using enrichment analysis, we detected distinct hypermethylated clusters containing histone and collagen genes as well as target genes of the tumour suppressor p53. We found that the promotor regions of CDKN1A, CDKN2A and IGFBP3 are methylated more strongly in GCTB than in the other giant cell containing lesions, mesenchymal stem cells, osteoblasts, and osteoclasts (p<0.001). This hypermethylation correlates with the lower gene expression at the mRNA level for these three genes in the cell lines, the lack of p16 and p21 in these cell lines and the lower expression of p16 and p21 in GCTB. Overall, our analysis reveals characteristic DNA methylation patterns of giant cell tumours of bone and chondroblastomas and shows that cell lines of giant cell tumours of bone are a valid model for further analysis of H3F3A-mutated tumour cells. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Julian Giesche
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Kevin Mellert
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Sven Geißler
- Centre for Regenerative Therapies, Berlin Institute of Health, Charité University Hospital Berlin, Berlin, Germany
| | - Sophia Arndt
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Carolin Seeling
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | | | | | - Ralf Marienfeld
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Thomas Fe Barth
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
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Dai X, Chen X, Chen W, Chen Y, Zhao J, Zhang Q, Lu J. A Pan-cancer Analysis Reveals the Abnormal Expression and Drug Sensitivity of CSF1. Anticancer Agents Med Chem 2021; 22:1296-1312. [PMID: 34102987 DOI: 10.2174/1871520621666210608105357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/17/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Colony-stimulating factor-1 (CSF1) is a cytokine that is closely related to normal organ growth and development as well as tumor progression. OBJECTIVE We aimed to summarize and clarify the reasons for the abnormal expression of CSF1 in tumors and explore the role of CSF1 in tumor progression. Furthermore, drug response analysis may provide a reference for clinical medication. METHODS The expression of CSF1 was analyzed by TCGA and CCLE. Besides, cBioPortal and MethSurv databases were used to conduct mutation and DNA methylation analyses. Further, correlations between CSF1 expression and tumor stage, survival, immune infiltration, drug sensitivity and enrichment analyses were validated via UALCAN, Kaplan-Meier plotter, TIMER, CTRP and Coexperia databases. RESULTS CSF1 is expressed in a variety of tissues, meaningfully, it can be detected in blood. Compared with normal tissues, CSF1 expression was significantly decreased in most tumors. The missense mutation and DNA methylation of CSF1 may cause the downregulated expression. Moreover, decreased CSF1 expression was related with higher tumor stage and worse survival. Further, the promoter DNA methylation level of CSF1 was prognostically significant in most tumors. Besides, CSF1 was closely related to immune infiltration, especially macrophages. Importantly, CSF1 expression was associated with a good response to VEGFRs inhibitors, which may be due to the possible involvement of CSF1 in tumor angiogenesis and metastasis processes. CONCLUSION The abnormal expression of CSF1 could serve as a promising biomarker of tumor progression and prognosis in pan-cancer. Significantly, angiogenesis and metastasis inhibitors may show a good response to CSF1-related tumors.
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Affiliation(s)
- Xiaoshuo Dai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Xinhuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Wei Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Yihuan Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Jun Zhao
- Department of Oncology, Changzhi People's Hospital, Changzhi 046000, Shanxi, China
| | - Qiushuang Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
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Lutsik P, Baude A, Mancarella D, Öz S, Kühn A, Toth R, Hey J, Toprak UH, Lim J, Nguyen VH, Jiang C, Mayakonda A, Hartmann M, Rosemann F, Breuer K, Vonficht D, Grünschläger F, Lee S, Schuhmacher MK, Kusevic D, Jauch A, Weichenhan D, Zustin J, Schlesner M, Haas S, Park JH, Park YJ, Oppermann U, Jeltsch A, Haller F, Fellenberg J, Lindroth AM, Plass C. Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone. Nat Commun 2020; 11:5414. [PMID: 33110075 PMCID: PMC7591516 DOI: 10.1038/s41467-020-18955-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The neoplastic stromal cells of giant cell tumor of bone (GCTB) carry a mutation in H3F3A, leading to a mutant histone variant, H3.3-G34W, as a sole recurrent genetic alteration. We show that in patient-derived stromal cells H3.3-G34W is incorporated into the chromatin and associates with massive epigenetic alterations on the DNA methylation, chromatin accessibility and histone modification level, that can be partially recapitulated in an orthogonal cell line system by the introduction of H3.3-G34W. These epigenetic alterations affect mainly heterochromatic and bivalent regions and provide possible explanations for the genomic instability, as well as the osteolytic phenotype of GCTB. The mutation occurs in differentiating mesenchymal stem cells and associates with an impaired osteogenic differentiation. We propose that the observed epigenetic alterations reflect distinct differentiation stages of H3.3 WT and H3.3 MUT stromal cells and add to H3.3-G34W-associated changes. The histone variant mutation H3.3-G34W occurs in the majority of giant cell tumor of bone (GCTB). By profiling patient-derived GCTB tumor cells, the authors show that this mutation associates with epigenetic alterations in heterochromatic and bivalent regions that contribute to an impaired osteogenic differentiation and the osteolytic phenotype of GCTB.
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Affiliation(s)
- Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Annika Baude
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniela Mancarella
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Simin Öz
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexander Kühn
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Umut H Toprak
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jinyeong Lim
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Viet Ha Nguyen
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Chao Jiang
- Botnar Research Centre, Oxford NIHR BRC, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Mark Hartmann
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) & German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Felix Rosemann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kersten Breuer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Dominik Vonficht
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Grünschläger
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Suman Lee
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea
| | - Maren Kirstin Schuhmacher
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Denis Kusevic
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Anna Jauch
- Institute of Human Genetics, Ruprecht Karl University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jozef Zustin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251, Hamburg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Simon Haas
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine-HI-STEM gGmbH, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joo Hyun Park
- Department of Nutritional Science and Food Management, Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Yoon Jung Park
- Department of Nutritional Science and Food Management, Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRC, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.,FRIAS-Freiburg Institute of Advanced Studies, Albert Ludwig University of Freiburg, Alberstrasse 19, 79104, Freiburg, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nürnberg, Krankenstrasse 8, 91054, Erlangen, Germany
| | - Jörg Fellenberg
- Department of Experimental Orthopaedics, Orthopaedic University Hospital Heidelberg, Ruprecht Karl University of Heidelberg, Schlierbacher Landstrasse 200a, 69118, Heidelberg, Germany
| | - Anders M Lindroth
- Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea, Republic of Korea.
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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Gao F, Jiao F, Xia C, Zhao Y, Ying W, Xie Y, Guan X, Tao M, Zhang Y, Qin W, Qian X. A novel strategy for facile serum exosome isolation based on specific interactions between phospholipid bilayers and TiO 2. Chem Sci 2019; 10:1579-1588. [PMID: 30842820 PMCID: PMC6369439 DOI: 10.1039/c8sc04197k] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
Exosomes are cell-derived, phospholipid bilayer-enclosed vesicles that play important roles in intercellular interactions and regulate many biological processes. Accumulating evidence suggests that serum exosomes are potential biomarkers for the early diagnosis of cancer. To aid the downstream molecular analyses of tumour-secreted exosomes, purified exosomes are highly desirable. However, current techniques for exosome isolation are time-consuming and highly instrument-dependent, with limited specificity and recovery. Thus, rapid and efficient methods are strongly needed for both basic research and clinical applications. Here, we present a novel strategy for facile exosome isolation from human serum by taking advantage of the specific interaction of TiO2 with the phosphate groups on the lipid bilayer of exosomes. Due to their simplicity and highly affinitive binding, model exosomes can be reversibly isolated with a high recovery (93.4%). Downstream characterization and proteome profiling reveal that high-quality exosomes can be obtained from human serum by this TiO2-based isolation method in 5 min, which is a fraction of the time required for the commonly used ultracentrifugation method. We identified 59 significantly up-regulated proteins by comparing the serum exosomes of pancreatic cancer patients and healthy donors. In addition to the 30 proteins that were reported to be closely related to pancreatic cancer, we found an additional 29 proteins that had not previously been shown to be related to pancreatic cancer, indicating the potential of this novel method as a powerful tool for exosome isolation for health monitoring and disease diagnosis.
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Affiliation(s)
- Fangyuan Gao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Fenglong Jiao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
- School of Life Science and Technology , Beijing Institute of Technology , China
| | - Chaoshuang Xia
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Yang Zhao
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Wantao Ying
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Yuping Xie
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | | | - Ming Tao
- Peking University Third Hospital , China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Weijie Qin
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
| | - Xiaohong Qian
- State Key Laboratory of Proteomics , National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing Proteome Research Center , China . ; ;
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