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Di Meo F, Kale B, Koomen JM, Perna F. Mapping the cancer surface proteome in search of target antigens for immunotherapy. Mol Ther 2024; 32:2892-2904. [PMID: 39068512 PMCID: PMC11403220 DOI: 10.1016/j.ymthe.2024.07.019] [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: 04/01/2024] [Revised: 06/26/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024] Open
Abstract
Immune-based therapeutic interventions recognizing proteins localized on the cell surface of cancer cells are emerging as a promising cancer treatment. Antibody-based therapies and engineered T cells are now approved by the Food and Drug Administration to treat some malignancies. These therapies utilize a few cell surface proteins highly expressed on cancer cells to release the negative regulation of immune activation that limits antitumor responses (e.g., PD-1, PD-L1, CTLA4) or to redirect the T cell specificity toward blood cancer cells (e.g., CD19 and B cell maturation antigen). One limitation preventing broader application of these novel therapeutic strategies to all cancer types is the lack of suitable target antigens for all indications owing in part to the challenges in identifying such targets. Ideal target antigens are cell surface proteins highly expressed on malignant cells and absent in healthy tissues. Technological advances in mass spectrometry, enrichment protocols, and computational tools for cell surface protein isolation and annotation have recently enabled comprehensive analyses of the cancer cell surface proteome, from which novel immunotherapeutic target antigens may emerge. Here, we review the most recent progress in this field.
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Affiliation(s)
- Francesco Di Meo
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - Brandon Kale
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Fabiana Perna
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA.
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Syafruddin SE, Nazarie WFWM, Moidu NA, Soon BH, Mohtar MA. Integration of RNA-Seq and proteomics data identifies glioblastoma multiforme surfaceome signature. BMC Cancer 2021; 21:850. [PMID: 34301218 PMCID: PMC8306276 DOI: 10.1186/s12885-021-08591-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is a highly lethal, stage IV brain tumour with a prevalence of approximately 2 per 10,000 people globally. The cell surface proteins or surfaceome serve as information gateway in many oncogenic signalling pathways and are important in modulating cancer phenotypes. Dysregulation in surfaceome expression and activity have been shown to promote tumorigenesis. The expression of GBM surfaceome is a case in point; OMICS screening in a cell-based system identified that this sub-proteome is largely perturbed in GBM. Additionally, since these cell surface proteins have ‘direct’ access to drugs, they are appealing targets for cancer therapy. However, a comprehensive GBM surfaceome landscape has not been fully defined yet. Thus, this study aimed to define GBM-associated surfaceome genes and identify key cell-surface genes that could potentially be developed as novel GBM biomarkers for therapeutic purposes. Methods We integrated the RNA-Seq data from TCGA GBM (n = 166) and GTEx normal brain cortex (n = 408) databases to identify the significantly dysregulated surfaceome in GBM. This was followed by an integrative analysis that combines transcriptomics, proteomics and protein-protein interaction network data to prioritize the high-confidence GBM surfaceome signature. Results Of the 2381 significantly dysregulated genes in GBM, 395 genes were classified as surfaceome. Via the integrative analysis, we identified 6 high-confidence GBM molecular signature, HLA-DRA, CD44, SLC1A5, EGFR, ITGB2, PTPRJ, which were significantly upregulated in GBM. The expression of these genes was validated in an independent transcriptomics database, which confirmed their upregulated expression in GBM. Importantly, high expression of CD44, PTPRJ and HLA-DRA is significantly associated with poor disease-free survival. Last, using the Drugbank database, we identified several clinically-approved drugs targeting the GBM molecular signature suggesting potential drug repurposing. Conclusions In summary, we identified and highlighted the key GBM surface-enriched repertoires that could be biologically relevant in supporting GBM pathogenesis. These genes could be further interrogated experimentally in future studies that could lead to efficient diagnostic/prognostic markers or potential treatment options for GBM. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08591-0.
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Affiliation(s)
- Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | | | - Nurshahirah Ashikin Moidu
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Bee Hong Soon
- Department of Surgery, Neurosurgery Division, Faculty of Medicine, Universiti Kebangsaan Malaysia, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia.
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Teneurins: Role in Cancer and Potential Role as Diagnostic Biomarkers and Targets for Therapy. Int J Mol Sci 2021; 22:ijms22052321. [PMID: 33652578 PMCID: PMC7956758 DOI: 10.3390/ijms22052321] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Teneurins have been identified in vertebrates as four different genes (TENM1-4), coding for membrane proteins that are mainly involved in embryonic and neuronal development. Genetic studies have correlated them with various diseases, including developmental problems, neurological disorders and congenital general anosmia. There is some evidence to suggest their possible involvement in cancer initiation and progression, and drug resistance. Indeed, mutations, chromosomal alterations and the deregulation of teneurins expression have been associated with several tumor types and patient survival. However, the role of teneurins in cancer-related regulatory networks is not fully understood, as both a tumor-suppressor role and pro-tumoral functions have been proposed, depending on tumor histotype. Here, we summarize and discuss the literature data on teneurins expression and their potential role in different tumor types, while highlighting the possibility of using teneurins as novel molecular diagnostic and prognostic biomarkers and as targets for cancer treatments, such as immunotherapy, in some tumors.
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S100A4 is a Biomarker of Tumorigenesis, EMT, Invasion, and Colonization of Host Organs in Experimental Malignant Mesothelioma. Cancers (Basel) 2020; 12:cancers12040939. [PMID: 32290283 PMCID: PMC7226589 DOI: 10.3390/cancers12040939] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
Recent findings suggest that S100A4, a protein involved in communication between stromal cells and cancer cells, could be more involved than previously expected in cancer invasiveness. To investigate its cumulative value in the multistep process of the pathogenesis of malignant mesothelioma (MM), SWATH-MS (sequential window acquisition of all theoretical fragmentation spectra), an advanced and robust technique of quantitative proteomics, was used to analyze a collection of 26 preneoplastic and neoplastic rat mesothelial cell lines and models of MM with increasing invasiveness. Secondly, proteomic and histological analyses were conducted on formalin-fixed paraffin-embedded sections of liver metastases vs. primary tumor, and spleen from tumor-bearing rats vs. controls in the most invasive MM model. We found that S100A4, along with 12 other biomarkers, differentiated neoplastic from preneoplastic mesothelial cell lines, and invasive vs. non-invasive tumor cells in vitro, and MM tumors in vivo. Additionally, S100A4 was the only protein differentiating preneoplastic mesothelial cell lines with sarcomatoid vs. epithelioid morphology in relation to EMT (epithelial-to-mesenchymal transition). Finally, S100A4 was the most significantly increased biomarker in liver metastases vs. primary tumor, and in the spleen colonized by MM cells. Overall, we showed that S100A4 was the only protein that showed increased abundance in all situations, highlighting its crucial role in all stages of MM pathogenesis.
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Bastías-Candia S, Martínez M, Zolezzi JM, Inestrosa NC. Wnt Signaling Upregulates Teneurin-3 Expression via Canonical and Non-canonical Wnt Pathway Crosstalk. Front Neurosci 2019; 13:505. [PMID: 31156379 PMCID: PMC6534050 DOI: 10.3389/fnins.2019.00505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/02/2019] [Indexed: 01/09/2023] Open
Abstract
Teneurins (Tens) are a highly conserved family of proteins necessary for cell-cell adhesion. Tens can be cleaved, and some of their proteolytic products, such as the teneurin c-terminal associated-peptide (TCAP) and the intracellular domain (ICD), have been demonstrated to be biologically active. Although Tens are considered critical for central nervous system development, they have also been demonstrated to play important roles in adult tissues, suggesting a potential link between their deregulation and various pathological processes, including neurodegeneration and cancer. However, knowledge regarding how Ten expression is modulated is almost absent. Relevantly, the functions of Tens resemble several of the effects of canonical and non-canonical Wnt pathway activation, including the effects of the Wnt pathways on neuronal development and function as well as their pivotal roles during carcinogenesis. Accordingly, in this initial study, we decided to evaluate whether Wnt signaling can modulate the expression of Tens. Remarkably, in the present work, we used a specific inhibitor of porcupine, the key enzyme for Wnt ligand secretion, to not only demonstrate the involvement of Wnt signaling in regulating Ten-3 expression for the first time but also reveal that Wnt3a, a canonical Wnt ligand, increases the expression of Ten-3 through a mechanism dependent on the secretion and activity of the non-canonical ligand Wnt5a. Although our work raises several new questions, our findings seem to demonstrate the upregulation of Ten-3 by Wnt signaling and also suggest that Ten-3 modulation is possible because of crosstalk between the canonical and non-canonical Wnt pathways.
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Affiliation(s)
- Sussy Bastías-Candia
- Basal Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center of Excellence of Biomedicine of Magallanes, Universidad de Magallanes, Punta Arenas, Chile
| | - Milka Martínez
- Basal Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan M Zolezzi
- Basal Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center of Excellence of Biomedicine of Magallanes, Universidad de Magallanes, Punta Arenas, Chile
| | - Nibaldo C Inestrosa
- Basal Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center of Excellence of Biomedicine of Magallanes, Universidad de Magallanes, Punta Arenas, Chile.,School of Psychiatry, Centre for Healthy Brain Ageing, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Bausch-Fluck D, Goldmann U, Müller S, van Oostrum M, Müller M, Schubert OT, Wollscheid B. The in silico human surfaceome. Proc Natl Acad Sci U S A 2018; 115:E10988-E10997. [PMID: 30373828 PMCID: PMC6243280 DOI: 10.1073/pnas.1808790115] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% of approved human drugs listed in the DrugBank database target a cell-surface protein. Despite this biomedical relevance, there has been no comprehensive assessment of the human surfaceome, and only a fraction of the predicted 5,000 human transmembrane proteins have been shown to be located at the plasma membrane. To enable analysis of the human surfaceome, we developed the surfaceome predictor SURFY, based on machine learning. As a training set, we used experimentally verified high-confidence cell-surface proteins from the Cell Surface Protein Atlas (CSPA) and trained a random forest classifier on 131 features per protein and, specifically, per topological domain. SURFY was used to predict a human surfaceome of 2,886 proteins with an accuracy of 93.5%, which shows excellent overlap with known cell-surface protein classes (i.e., receptors). In deposited mRNA data, we found that between 543 and 1,100 surfaceome genes were expressed in cancer cell lines and maximally 1,700 surfaceome genes were expressed in embryonic stem cells and derivative lines. Thus, the surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome. To make the predicted surfaceome readily accessible to the research community, we provide visualization tools for intuitive interrogation (wlab.ethz.ch/surfaceome). The in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization.
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Affiliation(s)
- Damaris Bausch-Fluck
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrich Goldmann
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Sebastian Müller
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Marc van Oostrum
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Maik Müller
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Olga T Schubert
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology at the Department of Biology, ETH Zurich, 8093 Zurich, Switzerland;
- Biomedical Proteomics Platform, Department of Health Sciences and Technology, ETH Zurich, 8093 Zurich, Switzerland
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Oehl K, Kresoja-Rakic J, Opitz I, Vrugt B, Weder W, Stahel R, Wild P, Felley-Bosco E. Live-Cell Mesothelioma Biobank to Explore Mechanisms of Tumor Progression. Front Oncol 2018. [PMID: 29527515 PMCID: PMC5829086 DOI: 10.3389/fonc.2018.00040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Experimental models closely representing in vivo conditions allow investigating mechanisms of resistance. Our aims were to establish a live-cell biobank of malignant pleural mesothelioma (MPM) samples and to obtain proof of principle that primary culture chemoresistant models, mimicking tumor progression observed in patients, can be obtained in vitro, providing a useful tool to investigate underlying mechanisms. Primary mesothelioma cultures were established from 235 samples between 2007 and 2014. Of two MPM patients, primary cultures obtained at different time points: at initial diagnosis, after neoadjuvant treatment at surgery and/or after tumor recurrence, were deeply investigated. Cells and corresponding tumor tissue were characterized by mesothelial protein and gene expression analysis. In addition, primary cultures from chemo naive patients were exposed to increasing doses of cisplatin/pemetrexed during three months and compared with non-treated cells in a cytotoxicity assay, and by selected profiling of senescence markers. In vitro chemoresistance in the primary mesothelioma cell cultures was associated with increased Thy1 (CD90) expression. Thy1 expression in MPM samples was significantly associated with poor overall survival in the TCGA MPM cohort. Our results illustrate that the establishment of a large live-cell MPM biobank contributes to a better understanding of therapy resistance observed in vivo, which eventually may lead to a more logical approach for developing new treatment strategies.
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Affiliation(s)
- Kathrin Oehl
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Jelena Kresoja-Rakic
- Laboratory of Molecular Oncology, Division of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Isabelle Opitz
- Laboratory of Molecular Oncology, Division of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Bart Vrugt
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Walter Weder
- Laboratory of Molecular Oncology, Division of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Rolf Stahel
- Cancer Center Zürich, University Hospital Zürich, Zürich, Switzerland
| | - Peter Wild
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Division of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
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Graumann R, Di Capua GA, Oyarzún JE, Vásquez MA, Liao C, Brañes JA, Roa I, Casanello P, Corvalán AH, Owen GI, Delgado I, Zangemeister-Wittke U, Ziegler A. Expression of teneurins is associated with tumor differentiation and patient survival in ovarian cancer. PLoS One 2017; 12:e0177244. [PMID: 28472127 PMCID: PMC5417686 DOI: 10.1371/journal.pone.0177244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Teneurins are a family of highly conserved pair-rule proteins involved in morphogenesis and development of the central nervous system. Their function in adult tissues and in disease is largely unknown. Recent evidence suggests a role for dysregulated expression of Teneurins in human tumors, but systematic investigations are missing. Here, we investigated Teneurin-2 and Teneurin-4 expression in various cancer cell lines and in ovarian tumor tissues. Teneurin-2 and Teneurin-4 were expressed in most of the breast cancer cell lines tested. Teneurin-4 was also detected in ovarian cancer cell lines, and throughout ovarian tumors and normal ovary tissue. Ovarian tumors with low Teneurin-4 expression showed less differentiated phenotypes and these patients had shorter mean overall survival. Similarly, Teneurin-2 expression correlated with overall survival as well, especially in patients with serous tumors. In the various cell lines, 5-Aza-cytidine-induced changes in DNA methylation did not alter expression of Teneurin-2 and Teneurin-4, despite the existence of predicted CpG islands in both genes. Interestingly, however, we found evidence for the control of Teneurin-2 expression by the oncogenic growth factor FGF8. Furthermore, we identified multiple transcript splicing variants for Teneurin-2 and Teneurin-4, indicating complex gene expression patterns in malignant cells. Finally, downregulation of Teneurin-4 expression using siRNA caused a cell-type dependent increase in proliferation and resistance to cisplatin. Altogether, our data suggest that low Teneurin-4 expression provides a growth advantage to cancer cells and marks an undifferentiated state characterized by increased drug resistance and clinical aggressiveness. We conclude that Teneurin-2 and Teneurin-4 expression levels could be of prognostic value in ovarian cancer.
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Affiliation(s)
- Rebecca Graumann
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Gabriella A. Di Capua
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Juan E. Oyarzún
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Marcos A. Vásquez
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Christine Liao
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Jorge A. Brañes
- Division of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iván Roa
- Division of Pathology, Clínica Alemana de Santiago, Santiago, Chile
| | - Paola Casanello
- Perinatology Research Laboratory, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro H. Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I. Owen
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iris Delgado
- Center for Epidemiology and Health Policies, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | | | - Annemarie Ziegler
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
- * E-mail:
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Sahin N, Akatli AN, Celik MR, Ulutas H, Samdanci ET, Colak C. The Role of CD90 in the Differential Diagnosis of Pleural Malignant Mesothelioma, Pulmonary Carcinoma and Comparison with Calretının. Pathol Oncol Res 2016; 23:487-491. [PMID: 27761727 DOI: 10.1007/s12253-016-0135-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/12/2016] [Indexed: 01/05/2023]
Abstract
Pleural Malignant Mesothelioma (MM) is a fatal disease that has been associated with asbestos exposure. Differential diagnosis between the pleural infiltration of pulmonary carcinomas and MM is rather difficult particularly for epitheloid type mesothelioma.We aimed to investigate the utility of CD90, a cancer stem cell marker, in the differential diagnosis of MM and lung carcinoma, its prognostic significance and compare its value with that of Calretinin. Ninety pathology specimens including MM (n:30), pulmonary adenocarcinoma (n:30) and pulmonary squamous cell carcinoma (n:30) were used in this study. Immunohistochemical comparision of CD 90 and Calretinin was made in all groups. Calretinin was positive in 20 cases with MM (64.5 %), and was negative in 10 (32.3 %). CD 90 was positive in 25 of these cases (80 %) and negative in 5 (16 %). On the other hand pulmonary adenocarcinomas and squamous cell carcinomas showed positivity with CD90, 63,6 % and 73 %, respectively. We think that CD 90 has no place in the differential diagnosis between mesothelioma and pulmonary carcinoma because of the low specificity in spite of the high sensitivity.
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Affiliation(s)
- Nurhan Sahin
- Turgut Ozal Medical Center, Department of Pathology, Inonu University, 44280, Malatya, Turkey.
| | - Ayse Nur Akatli
- Turgut Ozal Medical Center, Department of Pathology, Inonu University, 44280, Malatya, Turkey
| | - Muhammet Reha Celik
- Turgut Ozal Medical Center, Department of Thoracic Surgery, Inonu University, Malatya, Turkey
| | - Hakkı Ulutas
- Turgut Ozal Medical Center, Department of Thoracic Surgery, Inonu University, Malatya, Turkey
| | - Emine Turkmen Samdanci
- Turgut Ozal Medical Center, Department of Pathology, Inonu University, 44280, Malatya, Turkey
| | - Cemil Colak
- Medical Faculty, Department of Biostatistic, Inonu University, Malatya, Turkey
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Manfredi M, Martinotti S, Gosetti F, Ranzato E, Marengo E. The secretome signature of malignant mesothelioma cell lines. J Proteomics 2016; 145:3-10. [DOI: 10.1016/j.jprot.2016.02.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/18/2016] [Accepted: 02/21/2016] [Indexed: 12/17/2022]
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Multiple roles of CD90 in cancer. Tumour Biol 2016; 37:11611-11622. [DOI: 10.1007/s13277-016-5112-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/09/2016] [Indexed: 12/26/2022] Open
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de Jong K, Vonk JM, Timens W, Bossé Y, Sin DD, Hao K, Kromhout H, Vermeulen R, Postma DS, Boezen HM. Genome-wide interaction study of gene-by-occupational exposure and effects on FEV1 levels. J Allergy Clin Immunol 2015; 136:1664-1672.e14. [PMID: 25979521 DOI: 10.1016/j.jaci.2015.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by impaired lung function and airway obstruction resulting from interactions between multiple genes and multiple environmental exposures. Thus far, genome-wide association studies have largely disregarded environmental factors that might trigger the development of lung function impairment and COPD, such as occupational exposures, which are thought to contribute to 15% to 20% of the COPD prevalence. OBJECTIVES We performed a genome-wide interaction study to identify novel susceptibility loci for occupational exposure to biological dust, mineral dust, and gases and fumes in relation to FEV1 levels. METHODS We performed an identification analysis in 12,400 subjects from the LifeLines cohort study and verified our findings in 1436 subjects from a second independent cohort, the Vlagtwedde-Vlaardingen cohort. Additionally, we assessed whether replicated single nucleotide polymorphisms (SNPs) were cis-acting expression (mRNA) quantitative trait loci in lung tissue. RESULTS Of the 7 replicated SNPs that interacted with one of the occupational exposures, several identified loci were plausible candidates that might be involved in biological pathways leading to lung function impairment, such as PCDH9 and GALNT13. Two of the 7 replicated SNPs were cis-acting expression quantitative trait loci associated with gene expression of PDE4D and TMEM176A in lung tissue. CONCLUSION This genome-wide interaction study on occupational exposures in relation to the level of lung function identified several novel genes. Further research should determine whether the identified genes are true susceptibility loci for occupational exposures and whether these SNP-by-exposure interactions consequently contribute to the development of COPD.
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Affiliation(s)
- Kim de Jong
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Don D Sin
- Department of Medicine and Center for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hans Kromhout
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Utrecht, The Netherlands
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Utrecht, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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The established and future biomarkers of malignant pleural mesothelioma. Cancer Treat Rev 2015; 41:486-95. [DOI: 10.1016/j.ctrv.2015.05.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/27/2015] [Accepted: 05/02/2015] [Indexed: 12/18/2022]
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14
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Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, Bourquin JP, Aebersold R, Boheler KR, Zandstra P, Wollscheid B. A mass spectrometric-derived cell surface protein atlas. PLoS One 2015; 10:e0121314. [PMID: 25894527 PMCID: PMC4404347 DOI: 10.1371/journal.pone.0121314] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/30/2015] [Indexed: 01/08/2023] Open
Abstract
Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.
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Affiliation(s)
- Damaris Bausch-Fluck
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Andreas Hofmann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Bock
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas P. Frei
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ferdinando Cerciello
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Molecular Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Andrea Jacobs
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hansjoerg Moest
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ulrich Omasits
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Wisconsin, Milwaukee, United States of America
| | - Charles Yoon
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Ralph Schiess
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paulina Mirkowska
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Anetta Härtlová
- Centre of Advanced Studies, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czech Republic
| | - Jennifer E. Van Eyk
- Department of Medicine, Biological Chemistry and Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jean-Pierre Bourquin
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Kenneth R. Boheler
- SCRMC, LKS Faculty of Medicine, Hong Kong University, Hong Kong, Hong Kong SAR
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Peter Zandstra
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
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15
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Mermelekas G, Zoidakis J. Mass spectrometry-based membrane proteomics in cancer biomarker discovery. Expert Rev Mol Diagn 2014; 14:549-63. [DOI: 10.1586/14737159.2014.917965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Giusti L, Da Valle Y, Bonotti A, Donadio E, Ciregia F, Ventroni T, Foddis R, Giannaccini G, Guglielmi G, Cristaudo A, Lucacchini A. Comparative proteomic analysis of malignant pleural mesothelioma evidences an altered expression of nuclear lamin and filament-related proteins. Proteomics Clin Appl 2014; 8:258-68. [PMID: 24415579 DOI: 10.1002/prca.201300052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/11/2013] [Accepted: 11/12/2013] [Indexed: 12/28/2022]
Abstract
PURPOSE Malignant mesothelioma is a neoplastic disease linked to asbestos exposure whose diagnosis is limited, so detection methods for an early diagnosis and treatment result essential. Here, we compared proteomic profiles of malignant pleural mesothelioma (MPM) and benign biopsies to search potential biomarkers useful in differential diagnosis. EXPERIMENTAL DESIGN Tissue biopsies were obtained from 53 patients who were subjected to a diagnostic thoracoscopy. 2DE/MS based approach was used for proteomic analysis and protein validation was carried out by Western blot analysis versus benign and lung carcinoma samples. RESULTS Among the proteins identified we confirmed known MPM biomarkers such as calretinin and suggested the new ones as prelamin A/C, desmin, vimentin, calretinin, fructose-bisphosphate aldolase A, myosin regulatory light chain 2, ventricular/cardiac muscle isoform, myosin light chain 3 and myosin light chain 6B. Ingenuity software was used to identify the biological processes to which these proteins belong and to construct a potential network. CONCLUSIONS AND CLINICAL RELEVANCE Overall, our results suggest potential biomarkers that can be useful in occupational medicine for the early identification of the onset of disease in health surveillance of past asbestos-exposed workers, for monitoring the progress of disease and for assessing the response to treatment.
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Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Pisa, Italy
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17
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Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clin Proteomics 2013; 10:16. [PMID: 24207061 PMCID: PMC3827840 DOI: 10.1186/1559-0275-10-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 10/22/2013] [Indexed: 01/22/2023] Open
Abstract
Background Serum biomarkers can improve diagnosis and treatment of malignant pleural mesothelioma (MPM). However, the evaluation of potential new serum biomarker candidates is hampered by a lack of assay technologies for their clinical evaluation. Here we followed a hypothesis-driven targeted proteomics strategy for the identification and clinical evaluation of MPM candidate biomarkers in serum of patient cohorts. Results Based on the hypothesis that cell surface exposed glycoproteins are prone to be released from tumor-cells to the circulatory system, we screened the surfaceome of model cell lines for potential MPM candidate biomarkers. Selected Reaction Monitoring (SRM) assay technology allowed for the direct evaluation of the newly identified candidates in serum. Our evaluation of 51 candidate biomarkers in the context of a training and an independent validation set revealed a reproducible glycopeptide signature of MPM in serum which complemented the MPM biomarker mesothelin. Conclusions Our study shows that SRM assay technology enables the direct clinical evaluation of protein-derived candidate biomarker panels for which clinically reliable ELISA’s currently do not exist.
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Kawamura K, Hiroshima K, Suzuki T, Chai K, Yamaguchi N, Shingyoji M, Yusa T, Tada Y, Takiguchi Y, Tatsumi K, Shimada H, Tagawa M. CD90 is a diagnostic marker to differentiate between malignant pleural mesothelioma and lung carcinoma with immunohistochemistry. Am J Clin Pathol 2013; 140:544-9. [PMID: 24045552 DOI: 10.1309/ajcpm2z4ngiipbge] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES To pathologically distinguish mesothelioma from lung carcinoma, particularly adenocarcinoma. METHODS We conducted immunohistochemical analyses on clinical specimens, including 26 cases of mesothelioma, 28 cases of lung adenocarcinoma, and 33 cases of lung squamous cell carcinoma. RESULTS We found that CD90 expression was useful in making a differential diagnosis between epithelioid mesothelioma and lung adenocarcinoma, whereas sarcomatoid mesothelioma and lung carcinoma specimens, irrespective of the histologic types, were negative in general. The sensitivity and specificity of CD90 expression in epithelioid mesothelioma and lung adenocarcinoma were comparable to those of well-established markers used for the differential diagnosis. CONCLUSIONS These data collectively indicate that CD90 is a novel diagnostic marker that contributes to a diagnosis of epithelioid mesothelioma.
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Affiliation(s)
- Kiyoko Kawamura
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Kenzo Hiroshima
- Department of Pathology, Tokyo Women’s Medical University Yachiyo Medical Center,Yachiyo, Japan
| | - Takeo Suzuki
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kuan Chai
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoto Yamaguchi
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masato Shingyoji
- Department of Thoracic Disease, Chiba Cancer Center, Chiba, Japan
| | - Toshikazu Yusa
- Department of General Thoracic Surgery and Asbestos Disease Center, Chiba Rosai Hospital, Ichihara, Japan
| | - Yuji Tada
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Takiguchi
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koichiro Tatsumi
- Department of Respirology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideaki Shimada
- Department of Surgery, School of Medicine, Toho University, Tokyo, Japan
| | - Masatoshi Tagawa
- Division of Pathology and Cell Therapy, Chiba Cancer Center Research Institute, Chiba, Japan
- Department of Molecular Biology and Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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Kupcova Skalnikova H. Proteomic techniques for characterisation of mesenchymal stem cell secretome. Biochimie 2013; 95:2196-211. [PMID: 23880644 DOI: 10.1016/j.biochi.2013.07.015] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 07/13/2013] [Indexed: 02/06/2023]
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells with a substantial potential in human regenerative medicine due to their ability to migrate to sites of injury, capability to suppress immune response and accessibility in large amount from patient's own bone marrow or fat tissue. It has been increasingly observed that the transplanted MSCs did not necessarily engraft and differentiate at the site of injury but might exert their therapeutic effects through secreted trophic signals. The MSCs secrete a variety of autocrine/paracrine factors, called secretome, that support regenerative processes in the damaged tissue, induce angiogenesis, protect cells from apoptotic cell death and modulate immune system. The cell culture medium conditioned by MSCs or osteogenic, chondrogenic as well as adipogenic precursors derived from MSCs has become a subject of intensive proteomic profiling in the search for and identification of released factors and microvesicles that might be applicable in regenerative medicine. Jointly with the methods for MSC isolation, expansion and differentiation, proteomic analysis of MSC secretome was enabled recently mainly due to the extensive development in protein separation techniques, mass spectrometry, immunological methods and bioinformatics. This review describes proteomic techniques currently applied or prospectively applicable in MSC secretomics, with a particular focus on preparation of the secretome sample, protein/peptide separation, mass spectrometry and protein quantification techniques, analysis of posttranslational modifications, immunological techniques, isolation and characterisation of secreted vesicles and exosomes, analysis of cytokine-encoding mRNAs and bioinformatics.
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Affiliation(s)
- Helena Kupcova Skalnikova
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Rumburska 89, 277 21 Libechov, Czech Republic.
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Armengaud J, Christie-Oleza JA, Clair G, Malard V, Duport C. Exoproteomics: exploring the world around biological systems. Expert Rev Proteomics 2013. [PMID: 23194272 DOI: 10.1586/epr.12.52] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The term 'exoproteome' describes the protein content that can be found in the extracellular proximity of a given biological system. These proteins arise from cellular secretion, other protein export mechanisms or cell lysis, but only the most stable proteins in this environment will remain in abundance. It has been shown that these proteins reflect the physiological state of the cells in a given condition and are indicators of how living systems interact with their environments. High-throughput proteomic approaches based on a shotgun strategy, and high-resolution mass spectrometers, have modified the authors' view of exoproteomes. In the present review, the authors describe how these new approaches should be exploited to obtain the maximum useful information from a sample, whatever its origin. The methodologies used for studying secretion from model cell lines derived from eukaryotic, multicellular organisms, virulence determinants of pathogens and environmental bacteria and their relationships with their habitats are illustrated with several examples. The implication of such data, in terms of proteogenomics and the discovery of novel protein functions, is discussed.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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Ziegler A, Corvalán A, Roa I, Brañes JA, Wollscheid B. Teneurin protein family: An emerging role in human tumorigenesis and drug resistance. Cancer Lett 2012; 326:1-7. [DOI: 10.1016/j.canlet.2012.07.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/12/2012] [Accepted: 07/13/2012] [Indexed: 01/15/2023]
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Application of proteomics to soft tissue sarcomas. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:876401. [PMID: 22778956 PMCID: PMC3388341 DOI: 10.1155/2012/876401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/21/2012] [Indexed: 01/27/2023]
Abstract
Soft tissue sarcomas are rare and account for less than 1% of all malignant cancers. Other than development of intensive therapies, the clinical outcome of patients with soft tissue sarcoma remains very poor, particularly when diagnosed at a late stage. Unique mutations have been associated with certain soft tissue sarcomas, but their etiologies remain unknown. The proteome is a functional translation of a genome, which directly regulates the malignant features of tumors. Thus, proteomics is a promising approach for investigating soft tissue sarcomas. Various proteomic approaches and clinical materials have been used to address clinical and biological issues, including biomarker development, molecular target identification, and study of disease mechanisms. Several cancer-associated proteins have been identified using conventional technologies such as 2D-PAGE, mass spectrometry, and array technology. The functional backgrounds of proteins identified were assessed extensively using in vitro experiments, thus supporting expression analysis. These observations demonstrate the applicability of proteomics to soft tissue sarcoma studies. However, the sample size in each study was insufficient to allow conclusive results. Given the low frequency of soft tissue sarcomas, multi-institutional collaborations are required to validate the results of proteomic approaches.
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