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Yang H, Xu F, Xiao K, Chen Y, Tian Z. N-Glycoproteomics Study of Putative N-Glycoprotein Biomarkers of Drug Resistance in MCF-7/ADR Cells. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:269-284. [PMID: 36939756 PMCID: PMC9590513 DOI: 10.1007/s43657-021-00029-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 01/13/2023]
Abstract
Currently, drug resistance of anti-cancer therapy has become the main cause of low survival rate and poor prognosis. Full understanding of drug resistance mechanisms is an urgent request for further development of anti-cancer therapy and improvement of prognosis. Here we present our N-glycoproteomics study of putative N-glycoprotein biomarkers of drug resistance in doxorubicin resistance breast cancer cell line michigan cancer foundation-7 (MCF-7/ADR) relative to parental michigan cancer foundation-7 (MCF-7) cells. Intact N-glycopeptides (IDs) from MCF-7/ADR and MCF-7 cells were enriched with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC), labeled with stable isotopic diethylation (SIDE), and analyzed with C18-RPLC-MS/MS (HCD with stepped normalized collision energies); these IDs were identified with database search engine GPSeeker, and the differentially expressed intact N-glycopeptides (DEGPs) were quantified with GPSeekerQuan. With target-decoy searches and control of spectrum-level FDR ≤ 1%, 322 intact N-glycopeptides were identified; these intact N-glycopeptides come from the combination of 249 unique peptide backbones (corresponding to 234 intact N-glycoproteins) and 90 monosaccharide compositions (corresponding to 248 putative N-glycosites). The sequence structures of 165 IDs were confirmed with structure-diagnostic fragment ions. With the criteria of observation at least twice among the three technical replicates, ≥ 1.5-fold change and p value < 0.05, 20 DEGPs were quantified, where five of them were up-regulated and 15 of them were down-regulated; the corresponding intact N-glycoproteins as putative markers of drug resistance were discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-021-00029-8.
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Affiliation(s)
- Hailun Yang
- grid.24516.340000000123704535Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092 China
| | - Feifei Xu
- grid.89957.3a0000 0000 9255 8984School of Pharmacy, Nanjing Medical University, Nanjing, 211166 China
| | - Kaijie Xiao
- grid.24516.340000000123704535Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092 China
| | - Yun Chen
- grid.89957.3a0000 0000 9255 8984School of Pharmacy, Nanjing Medical University, Nanjing, 211166 China
| | - Zhixin Tian
- grid.24516.340000000123704535Shanghai Key Laboratory of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092 China
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2
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Huizer K, Zhu C, Chirifi I, Krist B, Zorgman D, van der Weiden M, van den Bosch TPP, Dumas J, Cheng C, Kros JM, Mustafa DA. Periostin Is Expressed by Pericytes and Is Crucial for Angiogenesis in Glioma. J Neuropathol Exp Neurol 2021; 79:863-872. [PMID: 32647861 DOI: 10.1093/jnen/nlaa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/12/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
The expression of the matricellular protein periostin has been associated with glioma progression. In previous work we found an association of periostin with glioma angiogenesis. Here, we screen gliomas for POSTN expression and identify the cells that express periostin in human gliomas. In addition, we study the role of periostin in an in vitro model for angiogenesis. The expression of periostin was investigated by RT-PCR and by immunohistochemistry. In addition, we used double labeling and in situ RNA techniques to identify the expressing cells. To investigate the function of periostin, we silenced POSTN in a 3D in vitro angiogenesis model. Periostin expression was elevated in pilocytic astrocytoma and glioblastoma, but not in grade II/III astrocytomas and oligodendrogliomas. The expression of periostin colocalized with PDGFRβ+ cells, but not with OLIG2+/SOX2+ glioma stem cells. Silencing of periostin in pericytes in coculture experiments resulted in attenuation of the numbers and the length of the vessels formation and in a decrease in endothelial junction formation. We conclude that pericytes are the main source of periostin in human gliomas and that periostin plays an essential role in the growth and branching of blood vessels. Therefore, periostin should be explored as a novel target for developing anti-angiogenic therapy for glioma.
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Affiliation(s)
- Karin Huizer
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Changbin Zhu
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ihsan Chirifi
- Laboratory for Experimental Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Krist
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Denise Zorgman
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marcel van der Weiden
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thierry P P van den Bosch
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jasper Dumas
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline Cheng
- Laboratory for Experimental Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Johan M Kros
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dana A Mustafa
- From the Laboratory for Tumor Immunopathology, Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
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3
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Hao R, Liu Y, Du Q, Liu L, Chen S, You H, Dong Y. Transgelin-2 expression in breast cancer and its relationships with clinicopathological features and patient outcome. Breast Cancer 2019; 26:776-783. [PMID: 31144206 DOI: 10.1007/s12282-019-00981-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND Transgelin-2 is an actin-binding protein that is widely expressed in various tissues and organs of the body, and reportedly may participate in the development and progression of multiple cancers. However, the clinical significance of transgelin-2 still remains controversial. We, therefore, aimed to determine the expression of transgelin-2 in breast cancer as well as its correlation with the tumorigenesis, progression and prognosis of human breast cancer. METHODS We collected tissues of 58 breast cancer patients from our hospital and 1090 samples from The Cancer Genome Atlas (TCGA) database. X-tile software was used to divide the transgelin-2 mRNA expression level in the database, logistic regression model was used to identify independent factors influencing transgelin-2 mRNA expression, and then Cox regression and Kaplan-Meier analysis were used to find factors that influence survival of breast cancer. RESULTS Transgelin-2 was significantly overexpressed in breast cancer tissues from our hospital and receiver operating characteristic (ROC) curve indicated that transgelin-2 may have diagnostic value. Meanwhile, estrogen receptor (ER) was in inverse correlation with transgelin-2 protein and mRNA expression, and transgelin-2 expression was positively correlated with Ki67 in breast cancer tissues. Logistic regression model revealed that TNM stage, ER and progesterone receptor (PR) status were independent factors for transgelin-2 mRNA expression. Patients with high transgelin-2 mRNA expression showed a poor survival and the trend was statistically significant only in ER-negative patients. CONCLUSIONS Transgelin-2 was expressed significantly higher in breast cancer cells and correlated with some clinicopathological factors. High transgelin-2 expression might predict poor prognosis for ER-negative patients.
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Affiliation(s)
- Ruifang Hao
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qian Du
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Leichao Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Siying Chen
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haisheng You
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yalin Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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4
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Liang X, Jin Y, Wang H, Meng X, Tan Z, Huang T, Fan S. Transgelin 2 is required for embryo implantation by promoting actin polymerization. FASEB J 2019; 33:5667-5675. [PMID: 30702937 DOI: 10.1096/fj.201802158rrr] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Infertility has been a great challenge in reproductive medicine. At least 40% of human pregnancy losses are clinically unrecognized and occur because of embryo implantation failure. Identification of the proteins and biochemical factors involved in embryo implantation and that are essential for crosstalk between the embryo and uterus can further increase female fertility rates. The actin cytoskeleton and actin-binding proteins (ABPs) are of great importance for cell morphology and rearrangement, which is crucial for trophoblast adhesion and invasion. However, the research on ABPs in embryo implantation is insufficient. In this report, we found that transgelin (TAGLN)2 is highly expressed in mouse blastocyst trophoblasts. Notably, inhibition of mouse blastocyst trophoblast TAGLN2 by lentivirus-mediated RNA interference significantly impaired embryo adhesion and implantation ability. Further in vitro experiments demonstrated that TAGLN2 knockdown with small interfering RNA observably decreased the invasion and migration abilities of human trophoblast cells. Immunofluorescence colocalization and microscale thermophoresis analysis showed that TAGLN2 directly binds to actin. In addition, knockdown of TAGLN2 in trophoblast cells resulted in a remarkable reduction in F-actin rather than G-actin. Our findings reveal an unidentified role of TAGLN2 in regulation of trophoblast invasion and adhesion by promoting actin polymerization.-Liang, X., Jin, Y., Wang, H., Meng, X., Tan, Z., Huang, T., Fan, S. Transgelin 2 is required for embryo implantation by promoting actin polymerization.
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Affiliation(s)
- Xiaoling Liang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Shenzhen, China
| | - Yimei Jin
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Hao Wang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Shenzhen, China
| | - Xinlu Meng
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Zhongzhou Tan
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Tao Huang
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Shangrong Fan
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological Diseases, Shenzhen, China
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5
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Uzozie AC, Aebersold R. Advancing translational research and precision medicine with targeted proteomics. J Proteomics 2018; 189:1-10. [PMID: 29476807 DOI: 10.1016/j.jprot.2018.02.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 12/21/2022]
Abstract
Remarkable advances in quantitative mass spectrometry have shifted the focus of proteomics from the characterization of protein expression profiles to detailed investigations on the spatial and temporal organization of the proteome. Demands for precision therapy and personalized medicine are challenged by heterogeneity in the larger population, which have led to drawbacks in biomarker performance and therapeutic efficacy. The consistent adaptation of the cellular proteome in response to distinctive signals defines a phenotype. Acquisition of quantitative multi-layered omics data on multiple individuals over defined time scales has made it possible to establish means to probe the extent to which the genome, transcriptome and environment influence the variability of the proteome in given conditions, over time. Comprehensive, reproducible datasets generated with contemporary quantitative, massively parallel, targeted proteomic approaches offer as yet untapped benefits for biomarker discovery, development, and validation. The objective of this review is to recapitulate on advances in targeted proteomics approaches for quantifying the cellular proteome and to address ways to incorporate these data towards improving present day methodologies for biomarker evaluation and precision medicine. SIGNIFICANCE: Advances in quantitative mass spectrometry have shifted the focus of proteomics from the characterization of protein expression profiles to detailed investigations on the spatial and temporal organization of the proteome. This review expounds on avenues through which targeted proteomic methodologies can be constructively implemented in translational research and precision medicine to overcome existing challenges that hinder the success of protein biomarkers in clinics, and to develop precise therapeutics for future applications.
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Affiliation(s)
- Anuli Christiana Uzozie
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; BC Children's Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
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6
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Zhong JM, Li J, Kang AD, Huang SQ, Liu WB, Zhang Y, Liu ZH, Zeng L. Protein S100-A8: A potential metastasis-associated protein for breast cancer determined via iTRAQ quantitative proteomic and clinicopathological analysis. Oncol Lett 2018; 15:5285-5293. [PMID: 29552168 DOI: 10.3892/ol.2018.7958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Breast cancer is the most common malignancy in females, with metastasis of this type of cancer frequently proving lethal. However, there are still no effective biomarkers to predict breast cancer metastasis. The aim of the present study was, therefore, to analyze breast cancer metastasis-associated proteins and evaluate the association between protein S100-A8 and the prognosis of breast cancer. The isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technique was used to analyze the differential expression of proteins between fresh primary breast tumor (PBT) tissue and fresh paired metastatic lymph nodes (PMLN) tissue. Subsequently, immunohistochemical staining was used to locate and assess the expression of protein S100-A8 in benign breast disease (n=15), primary breast cancer with (n=109) or without (n=83) metastasis, and in paired metastatic lymph nodes (n=109) formalin fixed paraffin embedded (FFPE) tissue. Staining scores were evaluated and the association between protein S100-A8 expression levels and the clinicopathological characteristics of 192 patients with breast cancer were evaluated using the χ2 test. Kaplan-Meier and Cox hazards regression analyses were utilized to investigate the association between the expression of protein S100-A8 and the prognosis of patients with breast cancer. A total of 4,837 proteins were identified using the iTRAQ proteomic technique. Among these proteins, 643 differentially expressed proteins were revealed. Protein S100-A8 expression levels were identified to differ between PBT and PMLN tissues. Immunohistochemical staining suggested a significant difference between NMBT and PMLN (P=0.002), and also between PBT and PMLN (P<0.001). Cox hazards regression model analyses suggested that histological grade (P=0.031) and nodal status (P=0.001) were risk factors for lymph nodes metastasis of breast cancer. Kaplan-Meier analyses revealed no significant relationship between protein S100-A8 expression level and overall survival rate of patients with breast cancer. In conclusion, by using the iTRAQ proteomic technique and immunohistochemistry staining, it was identified that protein S100-A8 may be associated with lymph nodes metastasis of breast cancer and be a marker for progression of breast cancer.
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Affiliation(s)
- Jing-Min Zhong
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.,Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Jing Li
- Department of Breast Internal Medicine, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - An-Ding Kang
- Department of Intestinal Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - San-Qian Huang
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wen-Bin Liu
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Yun Zhang
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Zhi-Hong Liu
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Liang Zeng
- Department of Pathology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China.,Department of Pathology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, P.R. China
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7
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Braakman RBH, Stingl C, Tilanus-Linthorst MMA, van Deurzen CHM, Timmermans MAM, Smid M, Foekens JA, Luider TM, Martens JWM, Umar A. Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation. Proteomics 2017; 17. [PMID: 28058811 PMCID: PMC5347865 DOI: 10.1002/pmic.201600213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/23/2016] [Accepted: 01/03/2017] [Indexed: 01/26/2023]
Abstract
Both healthy and cancerous breast tissue is heterogeneous, which is a bottleneck for proteomics‐based biomarker analysis, as it obscures the cellular origin of a measured protein. We therefore aimed at obtaining a protein‐level interpretation of malignant transformation through global proteome analysis of a variety of laser capture microdissected cells originating from benign and malignant breast tissues. We compared proteomic differences between these tissues, both from cells of epithelial origin and the stromal environment, and performed string analysis. Differences in protein abundances corresponded with several hallmarks of cancer, including loss of cell adhesion, transformation to a migratory phenotype, and enhanced energy metabolism. Furthermore, despite enriching for (tumor) epithelial cells, many changes to the extracellular matrix were detected in microdissected cells of epithelial origin. The stromal compartment was heterogeneous and richer in the number of fibroblast and immune cells in malignant sections, compared to benign tissue sections. Furthermore, stroma could be clearly divided into reactive and nonreactive based on extracellular matrix disassembly proteins. We conclude that proteomics analysis of both microdissected epithelium and stroma gives an additional layer of information and more detailed insight into malignant transformation.
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Affiliation(s)
- René B H Braakman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | | | - Mieke A M Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Arzu Umar
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
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8
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An Essential Role for TAGLN2 in Phagocytosis of Lipopolysaccharide-activated Macrophages. Sci Rep 2017; 7:8731. [PMID: 28821818 PMCID: PMC5562783 DOI: 10.1038/s41598-017-09144-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/28/2017] [Indexed: 01/27/2023] Open
Abstract
Activated macrophages have a greater ability of phagocytosis against pathogens that is mediated by large-scale actin rearrangement. However, molecular machineries that conduct this task have not been fully identified. Here, we demonstrate an unanticipated role of TAGLN2, a 22-kDa actin-binding protein, in Toll-like receptor (TLR)-stimulated phagocytosis. TAGLN2 was greatly induced in macrophages in response to lipopolysaccharide (LPS), a ligand for TLR4, partly via the NF-κB pathway. TAGLN2-deficient macrophages (TAGLN2−/−) showed defective phagocytic functions of IgM- and IgG-coated sheep red blood cells as well as bacteria. Cell signaling pathways involved in actin rearrangement—PI3 kinase/AKT and Ras-ERK—were also down-regulated in LPS-stimulated TAGLN2-deficient macrophages. Moreover, TAGLN2−/− mice showed higher mortality after bacterial infection than wild-type littermates. Thus, our results revealed a novel function of TAGLN2 as a molecular armament required for host defense.
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9
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Papiewska-Pająk I, Balcerczyk A, Stec-Martyna E, Koziołkiewicz W, Boncela J. Vascular endothelial growth factor-D modulates oxidant-antioxidant balance of human vascular endothelial cells. J Cell Mol Med 2016; 21:1139-1149. [PMID: 27957793 PMCID: PMC5431135 DOI: 10.1111/jcmm.13045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/24/2016] [Indexed: 01/13/2023] Open
Abstract
Vascular endothelial growth factor‐D (VEGF‐D) is an angiogenic and lymphangiogenic glycoprotein that facilitates tumour growth and distant organ metastasis. Our previous studies showed that VEGF‐D stimulates the expression of proteins involved in cell–matrix interactions and promoting the migration of endothelial cells. In this study, we focused on the redox homoeostasis of endothelial cells, which is significantly altered in the process of tumour angiogenesis. Our analysis revealed up‐regulated expression of proteins that form the antioxidant barrier of the cell in VEGF‐D‐treated human umbilical endothelial cells and increased production of reactive oxygen and nitrogen species in addition to a transient elevation in the total thiol group content. Despite a lack of changes in the total antioxidant capacity, modification of the antioxidant barrier induced by VEGF‐D was sufficient to protect cells against the oxidative stress caused by hypochlorite and paraquat. These results suggest that exogenous stimulation of endothelial cells with VEGF‐D induces an antioxidant response of cells that maintains the redox balance. Additionally, VEGF‐D‐induced changes in serine/threonine kinase mTOR shuttling between the cytosol and nucleus and its increased phosphorylation at Ser‐2448, lead us to the conclusion that the observed shift in redox balance is regulated via mTOR kinase signalling.
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Affiliation(s)
| | - Aneta Balcerczyk
- Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | | | - Wiktor Koziołkiewicz
- Department of Cytobiology and Proteomics, Medical University of Lodz, Lodz, Poland
| | - Joanna Boncela
- Institute of Medical Biology, Polish Academy of Science, Lodz, Poland
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10
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Dvořáková M, Jeřábková J, Procházková I, Lenčo J, Nenutil R, Bouchal P. Transgelin is upregulated in stromal cells of lymph node positive breast cancer. J Proteomics 2015; 132:103-11. [PMID: 26639304 DOI: 10.1016/j.jprot.2015.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022]
Abstract
UNLABELLED Transgelin and transgelin-2 have been discussed as potential markers of various cancers. Here we identified increased transgelin level in lymph node positive vs. negative, low grade primary breast cancer tissues using 2-DE in the cohort of 12 patients. We further clinically validated 2-DE results in an independent cohort of 48 low grade breast cancer patients through untargeted and targeted proteomics analysis (iTRAQ-2D-LC-MS/MS, mTRAQ-SRM), at transcript level and using immunohistochemistry. Another group of 48 high grade tumors of different breast cancer subtypes was analyzed together with the low grade samples to test transgelin specificity for low grade tumors and to study transgelin relation to known molecular markers and histological features. The results confirmed transgelin connection with the lymph node metastasis. As a marker of a reactive tumor stroma, transgelin can be connected with the higher risk of metastasis development. Moreover, we observed significant down-regulation of transgelin in high vs. low grade tumors caused by decreased content of stromal cells (mainly expressing transgelin) in high grade tumor tissue. We also analyzed expression of transgelin-2 in the second cohort using proteomics and immunohistochemistry. Transgelin-2 was mainly expressed by epithelial cancer cells and its levels were increased in metastatic and poorly differentiated tumors. BIOLOGICAL SIGNIFICANCE Both transgelin and transgelin-2 have been previously described as potential markers of many types of cancer. We are specifying this connection to metastatic affection of lymph nodes and cell differentiation in breast cancer. In the wider context, the results of our study highlight tumor stroma as a source of cancer biomarkers and point out how measured levels of tissue markers can actually reflect cellular feature of cancer mass.
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Affiliation(s)
- Monika Dvořáková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jarmila Jeřábková
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Iva Procházková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic
| | - Juraj Lenčo
- Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Rudolf Nenutil
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic
| | - Pavel Bouchal
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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11
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Chen CL, Chung T, Wu CC, Ng KF, Yu JS, Tsai CH, Chang YS, Liang Y, Tsui KH, Chen YT. Comparative Tissue Proteomics of Microdissected Specimens Reveals Novel Candidate Biomarkers of Bladder Cancer. Mol Cell Proteomics 2015; 14:2466-78. [PMID: 26081836 DOI: 10.1074/mcp.m115.051524] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 12/22/2022] Open
Abstract
More than 380,000 new cases of bladder cancer are diagnosed worldwide, accounting for ∼150,200 deaths each year. To discover potential biomarkers of bladder cancer, we employed a strategy combining laser microdissection, isobaric tags for relative and absolute quantitation labeling, and liquid chromatography-tandem MS (LC-MS/MS) analysis to profile proteomic changes in fresh-frozen bladder tumor specimens. Cellular proteins from four pairs of surgically resected primary bladder cancer tumor and adjacent nontumorous tissue were extracted for use in two batches of isobaric tags for relative and absolute quantitation experiments, which identified a total of 3220 proteins. A DAVID (database for annotation, visualization and integrated discovery) analysis of dysregulated proteins revealed that the three top-ranking biological processes were extracellular matrix organization, extracellular structure organization, and oxidation-reduction. Biological processes including response to organic substances, response to metal ions, and response to inorganic substances were highlighted by up-expressed proteins in bladder cancer. Seven differentially expressed proteins were selected as potential bladder cancer biomarkers for further verification. Immunohistochemical analyses showed significantly elevated levels of three proteins-SLC3A2, STMN1, and TAGLN2-in tumor cells compared with noncancerous bladder epithelial cells, and suggested that TAGLN2 could be a useful tumor tissue marker for diagnosis (AUC = 0.999) and evaluating lymph node metastasis in bladder cancer patients. ELISA results revealed significantly increased urinary levels of both STMN1 and TAGLN2 in bladder cancer subgroups compared with control groups. In comparisons with age-matched hernia urine specimens, urinary TAGLN2 in bladder cancer samples showed the largest fold change (7.13-fold), with an area-under-the-curve value of 0.70 (p < 0.001, n = 205). Overall, TAGLN2 showed the most significant overexpression in individual bladder cancer tissues and urine specimens, and thus represents a potential biomarker for noninvasive screening for bladder cancer. Our findings highlight the value of bladder tissue proteome in providing valuable information for future validation studies of potential biomarkers in urothelial carcinoma.
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Affiliation(s)
- Chien-Lun Chen
- From the ‡Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; §School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting Chung
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‖Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kwai-Fong Ng
- **Department of Pathology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jau-Song Yu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ying Liang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ke-Hung Tsui
- From the ‡Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; §School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Chen
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; §§Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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12
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Panis C, Pizzatti L, Corrêa S, Binato R, Lemos GF, da Silva do Amaral Herrera AC, Seixas TF, Cecchini R, Abdelhay E. The positive is inside the negative: HER2-negative tumors can express the HER2 intracellular domain and present a HER2-positive phenotype. Cancer Lett 2015; 357:186-195. [DOI: 10.1016/j.canlet.2014.11.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023]
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13
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Turiák L, Shao C, Meng L, Khatri K, Leymarie N, Wang Q, Pantazopoulos H, Leon DR, Zaia J. Workflow for combined proteomics and glycomics profiling from histological tissues. Anal Chem 2014; 86:9670-8. [PMID: 25203838 DOI: 10.1021/ac5022216] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular matrixes comprise glycoproteins, glycosaminoglycans and proteoglycans that order the environment through which cells receive signals and communicate. Proteomic and glycomic molecular signatures from tissue surfaces can add diagnostic power to the immunohistochemistry workflows. Acquired in a spatially resolved manner, such proteomic and glycomic information can help characterize disease processes and be easily applied in a clinical setting. Our aim toward obtaining integrated omics datasets was to develop the first workflow applicable for simultaneous analysis of glycosaminoglycans, N-glycans and proteins/peptides from tissue surface areas as small as 1.5 mm in diameter. Targeting small areas is especially important in the case of glycans, as their distribution can be very heterogeneous between different tissue regions. We first established reliable and reproducible digestion protocols for the individual compound classes by applying standards on the tissue using microwave irradiation to achieve reduced digestion times. Next, we developed a multienzyme workflow suitable for analysis of the different compound classes. Applicability of the workflow was demonstrated on serial mouse brain and liver sections, both fresh frozen and formalin-fixed. The glycomics data from the 1.5 mm diameter tissue surface area was consistent with data published on bulk mouse liver and brain tissues, which demonstrates the power of the workflow in obtaining combined molecular signatures from very small tissue regions.
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Affiliation(s)
- Lilla Turiák
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
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14
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Gurski LA, Knowles LM, Basse PH, Maranchie JK, Watkins SC, Pilch J. Relocation of CLIC1 promotes tumor cell invasion and colonization of fibrin. Mol Cancer Res 2014; 13:273-80. [PMID: 25205595 DOI: 10.1158/1541-7786.mcr-14-0249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Chloride intracellular channel 1 (CLIC1) has been shown to be upregulated in various malignancies but its exact function remains unclear. Here, it is revealed that CLIC1 is critical for the stability of invadopodia in endothelial and tumor cells embedded in a 3-dimensional (3D) matrix of fibrin. Invadopodia stability was associated with the capacity of CLIC1 to induce stress fiber and fibronectin matrix formation following its β3 integrin (ITGB3)-mediated recruitment into invadopodia. This pathway, in turn, was relevant for fibrin colonization as well as slug (SNAI2) expression and correlated with a significant role of CLIC1 in metastasis in vivo. Mechanistically, a reduction of myosin light chain kinase (MYLK) in CLIC1-depleted as well as β3 integrin-depleted cells suggests an important role of CLIC1 for integrin-mediated actomyosin dynamics in cells embedded in fibrin. Overall, these results indicate that CLIC1 is an important contributor to tumor invasion, metastasis, and angiogenesis. IMPLICATIONS This study uncovers an important new function of CLIC1 in the regulation of cell-extracellular matrix interactions and ability of tumor cells to metastasize to distant organs.
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Affiliation(s)
- Lisa A Gurski
- Department of Urology, University of Pittsburgh School of Medicine, Shadyside Medical Center, Pittsburgh, Pennsylvania
| | - Lynn M Knowles
- Department of Urology, University of Pittsburgh School of Medicine, Shadyside Medical Center, Pittsburgh, Pennsylvania
| | - Per H Basse
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Jodi K Maranchie
- Department of Urology, University of Pittsburgh School of Medicine, Shadyside Medical Center, Pittsburgh, Pennsylvania. University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Simon C Watkins
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania. Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jan Pilch
- Department of Urology, University of Pittsburgh School of Medicine, Shadyside Medical Center, Pittsburgh, Pennsylvania. University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania. Institute of Clinical Hemostaseology and Transfusion Medicine, Saarland University Medical Center, Homburg, Saarland, Germany.
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15
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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16
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Dvorakova M, Nenutil R, Bouchal P. Transgelins, cytoskeletal proteins implicated in different aspects of cancer development. Expert Rev Proteomics 2014; 11:149-65. [PMID: 24476357 DOI: 10.1586/14789450.2014.860358] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Transgelin is an abundant protein of smooth muscle cells, where its role has been primarily studied. As a protein affecting dynamics of the actin cytoskeleton via stabilization of actin filaments, transgelin is both directly and indirectly involved in many cancer-related processes such as migration, proliferation, differentiation or apoptosis. Transgelin was previously reviewed as a tumor suppressor; however, recent data based on a number of proteomics studies indicate its pro-tumorigenic role, for example, in colorectal or hepatocellular cancer. We summarize these contradictory observations in both clinical and functional proteomics projects and analyze the role of transgelin in tumors in detail. Generally, the expression and biological role of transgelin seem to differ among various types of tumor cells and stroma, and possibly change during tumor progression. We also overview the recent data on transgelin-2, a sequence homolog of transgelin, whose role in the tumor development might be contradictory to the role of transgelin.
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Affiliation(s)
- Monika Dvorakova
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic
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17
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Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 2014; 12:343-59. [DOI: 10.1586/erm.12.31] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Megger DA, Pott LL, Ahrens M, Padden J, Bracht T, Kuhlmann K, Eisenacher M, Meyer HE, Sitek B. Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:967-76. [PMID: 23954498 DOI: 10.1016/j.bbapap.2013.07.017] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/10/2013] [Accepted: 07/29/2013] [Indexed: 12/31/2022]
Abstract
Within the past decade numerous methods for quantitative proteome analysis have been developed of which all exhibit particular advantages and disadvantages. Here, we present the results of a study aiming for a comprehensive comparison of ion-intensity based label-free proteomics and two label-based approaches using isobaric tags incorporated at the peptide and protein levels, respectively. As model system for our quantitative analysis we used the three hepatoma cell lines HepG2, Hep3B and SK-Hep-1. Four biological replicates of each cell line were quantitatively analyzed using an RPLC-MS/MS setup. Each quantification experiment was performed twice to determine technical variances of the different quantification techniques. We were able to show that the label-free approach by far outperforms both TMT methods regarding proteome coverage, as up to threefold more proteins were reproducibly identified in replicate measurements. Furthermore, we could demonstrate that all three methods show comparable reproducibility concerning protein quantification, but slightly differ in terms of accuracy. Here, label-free was found to be less accurate than both TMT approaches. It was also observed that the introduction of TMT labels at the protein level reduces the effect of underestimation of protein ratios, which is commonly monitored in case of TMT peptide labeling. Previously reported differences in protein expression between the particular cell lines were furthermore reproduced, which confirms the applicability of each investigated quantification method to study proteomic differences in such biological systems. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Dominik A Megger
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
| | - Leona L Pott
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Maike Ahrens
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Juliet Padden
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Katja Kuhlmann
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Helmut E Meyer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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19
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Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1581-90. [DOI: 10.1016/j.bbapap.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
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20
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Candidate biomarker discovery for angiogenesis by automatic integration of Orbitrap MS1 spectral- and X!Tandem MS2 sequencing information. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:182-94. [PMID: 23557902 PMCID: PMC4357783 DOI: 10.1016/j.gpb.2013.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/21/2013] [Accepted: 02/28/2013] [Indexed: 02/06/2023]
Abstract
Candidate protein biomarker discovery by full automatic integration of Orbitrap full MS1 spectral peptide profiling and X!Tandem MS2 peptide sequencing is investigated by analyzing mass spectra from brain tumor samples using Peptrix. Potential protein candidate biomarkers found for angiogenesis are compared with those previously reported in the literature and obtained from previous Fourier transform ion cyclotron resonance (FT-ICR) peptide profiling. Lower mass accuracy of peptide masses measured by Orbitrap compared to those measured by FT-ICR is compensated by the larger number of detected masses separated by liquid chromatography (LC), which can be directly linked to protein identifications. The number of peptide sequences divided by the number of unique sequences is 9248/6911 ≈ 1.3. Peptide sequences appear 1.3 times redundant per up-regulated protein on average in the peptide profile matrix, and do not seem always up-regulated due to tailing in LC retention time (40%), modifications (40%) and mass determination errors (20%). Significantly up-regulated proteins found by integration of X!Tandem are described in the literature as tumor markers and some are linked to angiogenesis. New potential biomarkers are found, but need to be validated independently. Eventually more proteins could be found by actively involving MS2 sequence information in the creation of the MS1 peptide profile matrix.
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21
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A mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer. J Proteomics 2013; 81:135-47. [DOI: 10.1016/j.jprot.2012.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/01/2012] [Accepted: 11/04/2012] [Indexed: 01/19/2023]
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22
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Soloviev M, Esteves MP, Amiri F, Crompton MR, Rider CC. Elevated transcription of the gene QSOX1 encoding quiescin Q6 sulfhydryl oxidase 1 in breast cancer. PLoS One 2013; 8:e57327. [PMID: 23460839 PMCID: PMC3583868 DOI: 10.1371/journal.pone.0057327] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
The q arm of chromosome 1 is frequently amplified at the gene level in breast cancer. Since the significance of this is unclear we investigated whether 1q genes are overexpressed in this disease. The cDNA levels of 1q-located genes were analysed in a search for overexpressed genes. 26 genes mapping to the 1q arm show highly significant (P≤0.01) overexpression of transcripts in breast cancer compared to normal breast tissue. Amongst those showing the highest levels of overexpression in both expressed sequence tag (EST) and serial analysis of gene expression (SAGE) databases was enzyme quiescin Q6 sulfhydryl oxidase 1 (QSOX1). We investigated QSOX1 cDNA derived from T47D breast carcinoma cells by RT-PCR and 3′-RACE PCR and identified a novel extended form of QSOX1 transcript, containing a long 3′UTR, nearly double the size of the previously reported QSOX1 cDNA, and confirmed its 3′ end nucleotide sequence using RACE-PCR. We also used quantitative real-time PCR to analyse a panel of cDNAs derived from 50 clinically-graded normal and malignant breast tissue samples for the expression of QSOX1 mRNAs. QSOX1 transcription was elevated in an increasing proportion in the grade 2 and grade 3 tumours (graded according to the Nottingham prognostic index), with 10 of the 15 grade 3 tumours (67%) examined exceeding the normal range. There was a significant correlation between relative transcript level and clinical grade (P≤0.01) for all qPCR primer sets tested. QSOX1 mRNA levels, based on SAGE expression data, did not correlate with either Estrogen Receptor (ER) or Epidermal Growth Factor Receptor 2 (ErbB-2 or HER2/neu) expression. Our data indicate that QSOX1 is a potential new prognostic marker which may prove of use in the staging of breast tumours and the stratification of breast cancer patients.
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MESH Headings
- Alternative Splicing/genetics
- Base Sequence
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Carcinoma, Ductal, Breast/enzymology
- Carcinoma, Ductal, Breast/genetics
- Cell Line, Tumor
- DNA, Complementary/genetics
- Expressed Sequence Tags
- Female
- Gene Expression Regulation, Neoplastic
- Genes, Neoplasm/genetics
- Humans
- Molecular Sequence Data
- Open Reading Frames/genetics
- Oxidoreductases Acting on Sulfur Group Donors/genetics
- Oxidoreductases Acting on Sulfur Group Donors/metabolism
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Transcription, Genetic
- Up-Regulation/genetics
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Affiliation(s)
- Mikhail Soloviev
- School of Biological Sciences, Centre for Biomedical Sciences, Royal Holloway University of London, London, United Kingdom.
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23
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Mitra S, Stemke-Hale K, Mills GB, Claerhout S. Interactions between tumor cells and microenvironment in breast cancer: a new opportunity for targeted therapy. Cancer Sci 2012; 103:400-7. [PMID: 22151725 DOI: 10.1111/j.1349-7006.2011.02183.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Breast cancer remains the leading cause of morbidity and second-leading cause of death in women. Despite efforts to uncover new targeted therapies, a vast number of women die due to refractory or recurrent breast tumors. Most breast cancer studies have focused on the intrinsic characteristics of breast tumor cells, including altered growth, proliferation, and metabolism. However, emerging research suggests that the tumor microenvironment can substantially affect relapse rates and therapeutic responses. In this review, we discuss the interactions between the tumor and microenvironment in breast cancer, with regard to mutational profiles and altered metabolism that could serve as potential therapeutic targets. We also describe current technologies available to study these interactions.
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Affiliation(s)
- Shreya Mitra
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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24
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CLT1 targets angiogenic endothelium through CLIC1 and fibronectin. Angiogenesis 2011; 15:115-29. [PMID: 22203240 DOI: 10.1007/s10456-011-9247-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/15/2011] [Indexed: 12/21/2022]
Abstract
Angiogenesis is important for tumor growth and metastasis. CLT1 (CGLIIQKNEC), a peptide that binds to tumor interstitial spaces in the presence of fibrin-fibronectin, has structural similarity to the anti-angiogenic β-sheet peptides anastellin and anginex. This similarity is reflected in the ability of CLT1 to form co-aggregates with fibronectin that induce an unfolded protein response and cause autophagic cell death in proliferating endothelial cells. CLT1 cytotoxicity is mediated at least in parts by a novel CLT1 binding protein, Chloride Intracellular Channel 1 (CLIC1), which promotes internalization of CLT1-fibronectin co-aggregates in a mechanism that depends on the LIIQK amino acid sequence of CLT1. LIIQK encompasses amino acid residues relevant for CLT1 binding to CLIC1 and in addition, facilitates the formation of CLT1-fibronectin co-aggregates, which in turn promote translocation of CLIC1 to the endothelial cell surface through ligation of integrin αvβ3. Paralleling the in vitro results, we found that CLT1 co-localizes with CLIC1 and fibronectin in angiogenic blood vessels in vivo, and that CLT1 treatment inhibited angiogenesis and tumor growth. Our findings show that CLT1 is a new anti-angiogenic compound, and its mechanism of action is to form co-aggregates with fibronectin, which bind to angiogenic endothelial cells through integrins, become internalized through CLIC1 and elicit a cytotoxic unfolded protein response. The simple structure and high potency of CLT1 make it a potentially useful compound for anti-angiogenic treatments.
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25
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Goodchild SC, Angstmann CN, Breit SN, Curmi PMG, Brown LJ. Transmembrane extension and oligomerization of the CLIC1 chloride intracellular channel protein upon membrane interaction. Biochemistry 2011; 50:10887-97. [PMID: 22082111 DOI: 10.1021/bi2012564] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloride intracellular channel proteins (CLICs) differ from most ion channels as they can exist in both soluble and integral membrane forms. The CLICs are expressed as soluble proteins but can reversibly autoinsert into the membrane to form active ion channels. For CLIC1, the interaction with the lipid bilayer is enhanced under oxidative conditions. At present, little evidence is available characterizing the structure of the putative oligomeric CLIC integral membrane form. Previously, fluorescence resonance energy transfer (FRET) was used to monitor and model the conformational transition within CLIC1 as it interacts with the membrane bilayer. These results revealed a large-scale unfolding between the C- and N-domains of CLIC1 as it interacts with the membrane. In the present study, FRET was used to probe lipid-induced structural changes arising in the vicinity of the putative transmembrane region of CLIC1 (residues 24-46) under oxidative conditions. Intramolecular FRET distances are consistent with the model in which the N-terminal domain inserts into the bilayer as an extended α-helix. Further, intermolecular FRET was performed between fluorescently labeled CLIC1 monomers within membranes. The intermolecular FRET shows that CLIC1 forms oligomers upon oxidation in the presence of the membranes. Fitting the data to symmetric oligomer models of the CLIC1 transmembrane form indicates that the structure is large and most consistent with a model comprising approximately six to eight subunits.
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Affiliation(s)
- Sophia C Goodchild
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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26
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Advances in tenascin-C biology. Cell Mol Life Sci 2011; 68:3175-99. [PMID: 21818551 PMCID: PMC3173650 DOI: 10.1007/s00018-011-0783-6] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 07/19/2011] [Accepted: 07/19/2011] [Indexed: 12/11/2022]
Abstract
Tenascin-C is an extracellular matrix glycoprotein that is specifically and transiently expressed upon tissue injury. Upon tissue damage, tenascin-C plays a multitude of different roles that mediate both inflammatory and fibrotic processes to enable effective tissue repair. In the last decade, emerging evidence has demonstrated a vital role for tenascin-C in cardiac and arterial injury, tumor angiogenesis and metastasis, as well as in modulating stem cell behavior. Here we highlight the molecular mechanisms by which tenascin-C mediates these effects and discuss the implications of mis-regulated tenascin-C expression in driving disease pathology.
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