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De Silva S, Alli-Shaik A, Gunaratne J. Machine Learning-Enhanced Extraction of Biomarkers for High-Grade Serous Ovarian Cancer from Proteomics Data. Sci Data 2024; 11:685. [PMID: 38918474 PMCID: PMC11199488 DOI: 10.1038/s41597-024-03536-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Comprehensive biomedical proteomic datasets are accumulating exponentially, warranting robust analytics to deconvolute them for identifying novel biological insights. Here, we report a strategic machine learning (ML)-based feature extraction workflow that was applied to unveil high-performing protein markers for high-grade serous ovarian carcinoma (HGSOC) from publicly available ovarian cancer tissue and serum proteomics datasets. Diagnosis of HGSOC, an aggressive form of ovarian cancer, currently relies on diagnostic methods based on tissue biopsy and/or non-specific biomarkers such as the cancer antigen 125 (CA125) and human epididymis protein 4 (HE4). Our newly developed ML-based approach enabled the identification of new serum proteomic biomarkers for HGSOC. The performance verification of these marker combinations using two independent cohorts affirmed their outperformance against known biomarkers for ovarian cancer including clinically used serum markers with >97% AUC. Our analysis also added novel biological insights such as enriched cancer-related processes associated with HGSOC.
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Affiliation(s)
- Senuri De Silva
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Asfa Alli-Shaik
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore.
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2
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Yue L, Gong T, Jiang W, Qian L, Gong W, Sun Y, Cai X, Xu H, Liu F, Wang H, Li S, Zhu Y, Zheng Z, Wu Q, Guo T. Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy. Proteomics 2024; 24:e2300242. [PMID: 38171885 DOI: 10.1002/pmic.202300242] [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: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32 patients with CCOC (H1 cohort) and characterized 8697 proteins using data-independent acquisition mass spectrometry (DIA-MS). We then performed proteomic analysis of 28 fresh frozen (FF) CCOC tissue specimens from an independent cohort of 24 patients with CCOC (H2 cohort), leading to the identification of 9409 proteins with DIA-MS. After bioinformatics analysis, we narrowed our focus to 15 proteins significantly correlated with the recurrence free survival (RFS) in both cohorts. These proteins are mainly involved in DNA damage response, extracellular matrix (ECM), and mitochondrial metabolism. Parallel reaction monitoring (PRM)-MS was adopted to validate the prognostic potential of the 15 proteins in the H1 cohort and an independent confirmation cohort (H3 cohort). Interferon-inducible transmembrane protein 1 (IFITM1) was observed as a robust prognostic marker for CCOC in both PRM data and immunohistochemistry (IHC) data. Taken together, this study presents a CCOC proteomic data resource and a single promising protein, IFITM1, which could potentially predict the recurrence and survival of CCOC.
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Affiliation(s)
- Liang Yue
- School of Life Sciences, Fudan University, Shanghai, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University
| | - Wenhao Jiang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Heli Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fanghua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - He Wang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qijun Wu
- Department of Clinical Epidemiology, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
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3
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Sun J, Li Q, Ding Y, Wei D, Hadisurya M, Luo Z, Gu Z, Chen B, Tao WA. Profiling Phosphoproteome Landscape in Circulating Extracellular Vesicles from Microliters of Biofluids through Functionally Tunable Paramagnetic Separation. Angew Chem Int Ed Engl 2023; 62:e202305668. [PMID: 37216424 PMCID: PMC11019431 DOI: 10.1002/anie.202305668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Many biological processes are regulated through dynamic protein phosphorylation. Monitoring disease-relevant phosphorylation events in circulating biofluids is highly appealing but also technically challenging. We introduce here a functionally tunable material and a strategy, extracellular vesicles to phosphoproteins (EVTOP), which achieves one-pot extracellular vesicles (EVs) isolation, extraction, and digestion of EV proteins, and enrichment of phosphopeptides, with only a trace amount of starting biofluids. EVs are efficiently isolated by magnetic beads functionalized with TiIV ions and a membrane-penetrating peptide, octa-arginine R8 + , which also provides the hydrophilic surface to retain EV proteins during lysis. Subsequent on-bead digestion concurrently converts EVTOP to TiIV ion-only surface for efficient enrichment of phosphopeptides for phosphoproteomic analyses. The streamlined, ultra-sensitive platform enabled us to quantify 500 unique EV phosphopeptides with only a few μL of plasma and over 1200 phosphopeptides with 100 μL of cerebrospinal fluid (CSF). We explored its clinical application of monitoring the outcome of chemotherapy of primary central nervous system lymphoma (PCNSL) patients with a small volume of CSF, presenting a powerful tool for broad clinical applications.
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Affiliation(s)
- Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Qing Li
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - Yajie Ding
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Marco Hadisurya
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhuojun Luo
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Bobin Chen
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - W. Andy Tao
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
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Okuda-Ashitaka E, Matsumoto KI. Tenascin-X as a causal gene for classical-like Ehlers-Danlos syndrome. Front Genet 2023; 14:1107787. [PMID: 37007968 PMCID: PMC10050494 DOI: 10.3389/fgene.2023.1107787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
Tenascin-X (TNX) is an extracellular matrix glycoprotein for which a deficiency results in a recessive form of classical-like Ehlers-Danlos syndrome (clEDS), a heritable connective tissue disorder with hyperextensible skin without atrophic scarring, joint hypermobility, and easy bruising. Notably, patients with clEDS also suffer from not only chronic joint pain and chronic myalgia but also neurological abnormalities such as peripheral paresthesia and axonal polyneuropathy with high frequency. By using TNX-deficient (Tnxb−/−) mice, well-known as a model animal of clEDS, we recently showed that Tnxb−/− mice exhibit hypersensitivity to chemical stimuli and the development of mechanical allodynia due to the hypersensitization of myelinated A-fibers and activation of the spinal dorsal horn. Pain also occurs in other types of EDS. First, we review the underlying molecular mechanisms of pain in EDS, especially that in clEDS. In addition, the roles of TNX as a tumor suppressor protein in cancer progression have been reported. Recent in silico large-scale database analyses have shown that TNX is downregulated in various tumor tissues and that high expression of TNX in tumor cells has a good prognosis. We describe what is so far known about TNX as a tumor suppressor protein. Furthermore, some patients with clEDS show delayed wound healing. Tnxb−/− mice also exhibit impairment of epithelial wound healing in corneas. TNX is also involved in liver fibrosis. We address the molecular mechanism for the induction of COL1A1 by the expression of both a peptide derived from the fibrinogen-related domain of TNX and integrin α11.
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Affiliation(s)
- Emiko Okuda-Ashitaka
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka, Japan
- *Correspondence: Emiko Okuda-Ashitaka, ; Ken-ichi Matsumoto,
| | - Ken-ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Head Office for Research and Academic Information, Shimane University, Izumo, Japan
- *Correspondence: Emiko Okuda-Ashitaka, ; Ken-ichi Matsumoto,
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Tucker RP, Degen M. Revisiting the Tenascins: Exploitable as Cancer Targets? Front Oncol 2022; 12:908247. [PMID: 35785162 PMCID: PMC9248440 DOI: 10.3389/fonc.2022.908247] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2022] [Indexed: 12/12/2022] Open
Abstract
For their full manifestation, tumors require support from the surrounding tumor microenvironment (TME), which includes a specific extracellular matrix (ECM), vasculature, and a variety of non-malignant host cells. Together, these components form a tumor-permissive niche that significantly differs from physiological conditions. While the TME helps to promote tumor progression, its special composition also provides potential targets for anti-cancer therapy. Targeting tumor-specific ECM molecules and stromal cells or disrupting aberrant mesenchyme-cancer communications might normalize the TME and improve cancer treatment outcome. The tenascins are a family of large, multifunctional extracellular glycoproteins consisting of four members. Although each have been described to be expressed in the ECM surrounding cancer cells, tenascin-C and tenascin-W are currently the most promising candidates for exploitability and clinical use as they are highly expressed in various tumor stroma with relatively low abundance in healthy tissues. Here, we review what is known about expression of all four tenascin family members in tumors, followed by a more thorough discussion on tenascin-C and tenascin-W focusing on their oncogenic functions and their potential as diagnostic and/or targetable molecules for anti-cancer treatment purposes.
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Affiliation(s)
- Richard P. Tucker
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Martin Degen
- Laboratory for Oral Molecular Biology, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
- *Correspondence: Martin Degen,
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Mendoza-Martinez AK, Loessner D, Mata A, Azevedo HS. Modeling the Tumor Microenvironment of Ovarian Cancer: The Application of Self-Assembling Biomaterials. Cancers (Basel) 2021; 13:5745. [PMID: 34830897 PMCID: PMC8616551 DOI: 10.3390/cancers13225745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer (OvCa) is one of the leading causes of gynecologic malignancies. Despite treatment with surgery and chemotherapy, OvCa disseminates and recurs frequently, reducing the survival rate for patients. There is an urgent need to develop more effective treatment options for women diagnosed with OvCa. The tumor microenvironment (TME) is a key driver of disease progression, metastasis and resistance to treatment. For this reason, 3D models have been designed to represent this specific niche and allow more realistic cell behaviors compared to conventional 2D approaches. In particular, self-assembling peptides represent a promising biomaterial platform to study tumor biology. They form nanofiber networks that resemble the architecture of the extracellular matrix and can be designed to display mechanical properties and biochemical motifs representative of the TME. In this review, we highlight the properties and benefits of emerging 3D platforms used to model the ovarian TME. We also outline the challenges associated with using these 3D systems and provide suggestions for future studies and developments. We conclude that our understanding of OvCa and advances in materials science will progress the engineering of novel 3D approaches, which will enable the development of more effective therapies.
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Affiliation(s)
- Ana Karen Mendoza-Martinez
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK;
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Daniela Loessner
- Department of Chemical Engineering, Faculty of Engineering, Monash University, Melbourne, VIC 3800, Australia;
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Melbourne, VIC 3800, Australia
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Bergmann Center of Biomaterials Dresden, Leibniz Institute of Polymer Research Dresden e.V., 01069 Dresden, Germany
| | - Alvaro Mata
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK;
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Helena S. Azevedo
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK;
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Matsumoto KI, Aoki H. The Roles of Tenascins in Cardiovascular, Inflammatory, and Heritable Connective Tissue Diseases. Front Immunol 2020; 11:609752. [PMID: 33335533 PMCID: PMC7736112 DOI: 10.3389/fimmu.2020.609752] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Tenascins are a family of multifunctional extracellular matrix (ECM) glycoproteins with time- and tissue specific expression patterns during development, tissue homeostasis, and diseases. There are four family members (tenascin-C, -R, -X, -W) in vertebrates. Among them, tenascin-X (TNX) and tenascin-C (TNC) play important roles in human pathologies. TNX is expressed widely in loose connective tissues. TNX contributes to the stability and maintenance of the collagen network, and its absence causes classical-like Ehlers-Danlos syndrome (clEDS), a heritable connective tissue disorder. In contrast, TNC is specifically and transiently expressed upon pathological conditions such as inflammation, fibrosis, and cancer. There is growing evidence that TNC is involved in inflammatory processes with proinflammatory or anti-inflammatory activity in a context-dependent manner. In this review, we summarize the roles of these two tenascins, TNX and TNC, in cardiovascular and inflammatory diseases and in clEDS, and we discuss the functional consequences of the expression of these tenascins for tissue homeostasis.
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Affiliation(s)
- Ken-Ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo, Japan
| | - Hiroki Aoki
- Cardiovascular Research Institute, Kurume University, Kurume, Japan
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Liot S, Aubert A, Hervieu V, Kholti NE, Schalkwijk J, Verrier B, Valcourt U, Lambert E. Loss of Tenascin-X expression during tumor progression: A new pan-cancer marker. Matrix Biol Plus 2020; 6-7:100021. [PMID: 33543019 PMCID: PMC7852205 DOI: 10.1016/j.mbplus.2020.100021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 12/13/2022] Open
Abstract
Cancer is a systemic disease involving multiple components produced from both tumor cells themselves and surrounding stromal cells. The pro- or anti-tumoral role of the stroma is still under debate. Indeed, it has long been considered the main physical barrier to the diffusion of chemotherapy by its dense and fibrous nature and its poor vascularization. However, in murine models, the depletion of fibroblasts, the main ExtraCellular Matrix (ECM)-producing cells, led to more aggressive tumors even though they were more susceptible to anti-angiogenic and immuno-modulators. Tenascin-C (TNC) is a multifunctional matricellular glycoprotein (i.e. an ECM protein also able to induce signaling pathway) and is considered as a marker of tumor expansion and metastasis. However, the status of other tenascin (TN) family members and particularly Tenascin-X (TNX) has been far less studied during this pathological process and is still controversial. Herein, through (1) in silico analyses of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases and (2) immunohistochemistry staining of Tissue MicroArrays (TMA), we performed a large and extensive study of TNX expression at both mRNA and protein levels (1) in the 6 cancers with the highest incidence and mortality in the world (i.e. lung, breast, colorectal, prostate, stomach and liver) and (2) in the cancers for which sparse data regarding TNX expression already exist in the literature. We thus demonstrated that, in most cancers, TNX expression is significantly downregulated during cancer progression and we also highlighted, when data were available, that high TNXB mRNA expression in cancer is correlated with a good survival prognosis.
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Key Words
- CAF, Cancer-Associated Fibroblast
- Cancers
- D.E.G., Differentially Expressed Genes
- ECM, Extracellular Matrix
- EDS, Ehlers-Danlos syndrome
- FBG, fibrinogen
- FNIII, fibronectin type III
- GEO, Gene Expression Omnibus
- GSE, GEO Series
- HDAC1, histone deacetylase-1
- MMP, Matrix Metalloproteinase
- MPNST, Malignant Peripheral Nerve Sheath Tumors
- Meta-analysis
- Prognosis marker
- TCGA, The Cancer Genome Atlas
- TMA, Tissue MicroArray
- TME, Tumor MicroEnvironment
- TN, Tenascin
- TNC, Tenascin-C
- TNR, Tenascin-R
- TNW, Tenascin-W
- TNX, Tenascin-X
- TSS, Transcription Start Site
- Tenascin-X
- Tissue MicroArray
- lncRNA, long non-coding RNA
- mRNA and protein levels
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Affiliation(s)
- Sophie Liot
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Alexandre Aubert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Valérie Hervieu
- Service d'Anatomopathologie, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - Naïma El Kholti
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Joost Schalkwijk
- Radboud Institute for Molecular Life Sciences, Faculty of Medical Sciences, 370 Geert Grooteplein-Zuid 26 28, 6525 GA Nijmegen, Netherlands
| | - Bernard Verrier
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Ulrich Valcourt
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Elise Lambert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7, passage du Vercors, F-69367 Lyon Cedex 07, France
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Lončar-Brzak B, Klobučar M, Veliki-Dalić I, Sabol I, Kraljević Pavelić S, Krušlin B, Mravak-Stipetić M. Expression of small leucine-rich extracellular matrix proteoglycans biglycan and lumican reveals oral lichen planus malignant potential. Clin Oral Investig 2017; 22:1071-1082. [PMID: 28779221 DOI: 10.1007/s00784-017-2190-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 07/21/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVES The aim of this study was to examine molecular alterations on the protein level in lesions of oral lichen planus (OLP), oral squamous cell carcinoma (OSCC) and healthy mucosa. MATERIALS AND METHODS Global protein profiling methods based on liquid chromatography coupled to mass spectrometry (LC-MS) were used, with a special emphasis on evaluation of deregulated extracellular matrix molecules expression, as well as on analyses of IG2F and IGFR2 expression in healthy mucosa, OLP and OSCC tissues by comparative semi-quantitative immunohistochemistry. RESULTS Mass spectrometry-based proteomics profiling of healthy mucosa, OLP and OSCC tissues (and accompanied histologically unaltered tissues, respectively) identified 55 extracellular matrix proteins. Twenty among identified proteins were common to all groups of samples. Expression of small leucine-rich extracellular matrix proteoglycans lumican and biglycan was found both in OSCC and OLP and they were validated by Western blot analysis as putative biomarkers. A significant increase (p < 0.05) of biglycan expression in OLP-AT group was determined in comparison with OLP-T group, while lumican showed significant up-regulation (p < 0.05) in OLP-T and OSCC-T groups vs. adjacent and control tissue groups. Biglycan expression was only determined in OSCC-AT group. Immunohistochemical analysis of IGF2 and IG2FR expression revealed no significant difference among groups of samples. CONCLUSION/CLINICAL RELEVANCE Biglycan and lumican were identified as important pathogenesis biomarkers of OLP that point to its malignant potential.
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Affiliation(s)
- Božana Lončar-Brzak
- School of Dental Medicine, Department of Oral Medicine, University of Zagreb, Zagreb, Croatia
| | - Marko Klobučar
- Department of Biotechnology and Centre for High-throughput technologies, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia
| | - Irena Veliki-Dalić
- Department of Pathology, Clinical Hospital for Tumours, Clinical Hospital Centre Sisters of Mercy, Zagreb, Croatia
| | - Ivan Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sandra Kraljević Pavelić
- Department of Biotechnology and Centre for High-throughput technologies, University of Rijeka, Radmile Matejčić 2, 51000, Rijeka, Croatia.
| | - Božo Krušlin
- School of Medicine, Department of Pathology, Clinical Hospital Centre Sisters of Mercy, University of Zagreb, Zagreb, Croatia
| | - Marinka Mravak-Stipetić
- School of Dental Medicine, Department of Oral Medicine, University of Zagreb, Zagreb, Croatia
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Chen JB, Neves MA, Thompson M. Biosensor surface attachment of the ovarian cancer biomarker HSP10 via His-tag modification. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Cho A, Howell VM, Colvin EK. The Extracellular Matrix in Epithelial Ovarian Cancer - A Piece of a Puzzle. Front Oncol 2015; 5:245. [PMID: 26579497 PMCID: PMC4629462 DOI: 10.3389/fonc.2015.00245] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/15/2015] [Indexed: 02/04/2023] Open
Abstract
Epithelial ovarian cancer is the fifth leading cause of cancer-related deaths in women and the most lethal gynecological malignancy. Extracellular matrix (ECM) is an integral component of both the normal and tumor microenvironment. ECM composition varies between tissues and is crucial for maintaining normal function and homeostasis. Dysregulation and aberrant deposition or loss of ECM components is implicated in ovarian cancer progression. The mechanisms by which tumor cells induce ECM remodeling to promote a malignant phenotype are yet to be elucidated. A thorough understanding of the role of the ECM in ovarian cancer is needed for the development of effective biomarkers and new therapies.
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Affiliation(s)
- Angela Cho
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, NSW, Australia
- Bill Walsh Translational Cancer Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW, Australia
| | - Viive M. Howell
- Bill Walsh Translational Cancer Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW, Australia
- Sydney Medical School Northern, University of Sydney, Sydney, NSW, Australia
| | - Emily K. Colvin
- Bill Walsh Translational Cancer Research Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW, Australia
- Sydney Medical School Northern, University of Sydney, Sydney, NSW, Australia
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