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Moreira RS, Calomeno NA, das Neves GB, do Nascimento LFN, Filho VB, Wagner G, Miletti LC. Trypanosoma evansi secretome carries potential biomarkers for Surra diagnosis. J Proteomics 2023; 272:104789. [PMID: 36464092 DOI: 10.1016/j.jprot.2022.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Trypanosoma evansi is a parasite that is phylogenetically close to Trypanosoma brucei and is the causative agent of a disease known as surra. Surra is responsible for a high mortality rate in livestock and large economic losses in the Americas, Africa, and Asia. This work aimed to analyze in vitro secreted proteins from T. evansi and identify potential treatment and diagnostic biomarkers for surra diagnosis. Two groups were used. In one group the parasites were purified using a DEAE-Cellulose column and maintained in a secretion medium while in the other group the parasites were not purified. Each group was further divided to be maintained at either 37 °C or 27 °C. We identified 246 proteins through mass spectrometry and found that the temperature appears to modulate protein secretion. We found minimal variations in the protein pools from pure and non-purified sets. We observed an emphasis on proteins associated to vesicles, glycolysis, and cellular homeostasis through the enrichment of GO. Also, we found that most secretome proteins share homologous proteins with T. b. brucei, T. b. gambiense, T. vivax, T. equiperdum, and T. b. rhodesiense secretome but unique T. evansi epitopes with potential biomarkers for surra diagnosis were detected. SIGNIFICANCE: Trypanosoma evansi is a parasite of African origin that is phylogenetically close to Trypanosoma brucei. As with other trypanosomatids and blood parasites, its infection causes non-pathognomonic symptoms, which makes its diagnosis difficult. One great problem is the fact that no diagnostic test differentiates between Trypanosoma equiperdum and T. evansi, which is a problem in South America and Asia, and Africa. Thus, it is urgent to study the biochemistry of the parasite to discover proteins that can be used for differential diagnosis or be possible therapeutic targets. In addition, the study of the secretome can point out proteins that are used by the parasite in its interactions with the host, helping to understand the progression of the disease.
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Affiliation(s)
- Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil; Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510 - Bela Vista, Gaspar, SC 89111-009, Brazil
| | - Nathália Anderson Calomeno
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Gabriella Bassi das Neves
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Luiz Flávio Nepomuceno do Nascimento
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil.
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Poplawski P, Alseekh S, Jankowska U, Skupien-Rabian B, Iwanicka-Nowicka R, Kossowska H, Fogtman A, Rybicka B, Bogusławska J, Adamiok-Ostrowska A, Hanusek K, Hanusek J, Koblowska M, Fernie AR, Piekiełko-Witkowska A. Coordinated reprogramming of renal cancer transcriptome, metabolome and secretome associates with immune tumor infiltration. Cancer Cell Int 2023; 23:2. [PMID: 36604669 PMCID: PMC9814214 DOI: 10.1186/s12935-022-02845-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer. The molecules (proteins, metabolites) secreted by tumors affect their extracellular milieu to support cancer progression. If secreted in amounts detectable in plasma, these molecules can also serve as useful, minimal invasive biomarkers. The knowledge of ccRCC tumor microenvironment is fragmentary. In particular, the links between ccRCC transcriptome and the composition of extracellular milieu are weakly understood. In this study, we hypothesized that ccRCC transcriptome is reprogrammed to support alterations in tumor microenvironment. Therefore, we comprehensively analyzed ccRCC extracellular proteomes and metabolomes as well as transcriptomes of ccRCC cells to find molecules contributing to renal tumor microenvironment. METHODS Proteomic and metabolomics analysis of conditioned media isolated from normal kidney cells as well as five ccRCC cell lines was performed using mass spectrometry, with the following ELISA validation. Transcriptomic analysis was done using microarray analysis and validated using real-time PCR. Independent transcriptomic and proteomic datasets of ccRCC tumors were used for the analysis of gene and protein expression as well as the level of the immune infiltration. RESULTS Renal cancer secretome contained 85 proteins detectable in human plasma, consistently altered in all five tested ccRCC cell lines. The top upregulated extracellular proteins included SPARC, STC2, SERPINE1, TGFBI, while downregulated included transferrin and DPP7. The most affected extracellular metabolites were increased 4-hydroxy-proline, succinic acid, cysteine, lactic acid and downregulated glutamine. These changes were associated with altered expression of genes encoding the secreted proteins (SPARC, SERPINE1, STC2, DPP7), membrane transporters (SLC16A4, SLC6A20, ABCA12), and genes involved in protein trafficking and secretion (KIF20A, ANXA3, MIA2, PCSK5, SLC9A3R1, SYTL3, and WNTA7). Analogous expression changes were found in ccRCC tumors. The expression of SPARC predicted the infiltration of ccRCC tumors with endothelial cells. Analysis of the expression of the 85 secretome genes in > 12,000 tumors revealed that SPARC is a PanCancer indicator of cancer-associated fibroblasts' infiltration. CONCLUSIONS Transcriptomic reprogramming of ccRCC supports the changes in an extracellular milieu which are associated with immune infiltration. The proteins identified in our study represent valuable cancer biomarkers detectable in plasma.
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Affiliation(s)
- Piotr Poplawski
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Saleh Alseekh
- grid.418390.70000 0004 0491 976XMax-Planck Institute of Molecular Plant Physiology, Golm, 14476 Potsdam, Germany ,grid.510916.a0000 0004 9334 5103Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Urszula Jankowska
- grid.5522.00000 0001 2162 9631Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Bozena Skupien-Rabian
- grid.5522.00000 0001 2162 9631Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Roksana Iwanicka-Nowicka
- grid.12847.380000 0004 1937 1290Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland ,grid.413454.30000 0001 1958 0162Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Helena Kossowska
- grid.12847.380000 0004 1937 1290Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Anna Fogtman
- grid.413454.30000 0001 1958 0162Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Beata Rybicka
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Joanna Bogusławska
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Anna Adamiok-Ostrowska
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Karolina Hanusek
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Jan Hanusek
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Marta Koblowska
- grid.12847.380000 0004 1937 1290Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland ,grid.413454.30000 0001 1958 0162Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Alisdair R. Fernie
- grid.418390.70000 0004 0491 976XMax-Planck Institute of Molecular Plant Physiology, Golm, 14476 Potsdam, Germany ,grid.510916.a0000 0004 9334 5103Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Agnieszka Piekiełko-Witkowska
- grid.414852.e0000 0001 2205 7719Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
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Liang W, Zuo J, Liu M, Su Y, Guo B, Hou J, Xing Q, Peng Y, Fang L, Cao Y, Shan J, Sun R, Zhao J, Wang J. VASN promotes colorectal cancer progression by activating the YAP/TAZ and AKT signaling pathways via YAP. FASEB J 2023; 37:e22688. [PMID: 36468780 DOI: 10.1096/fj.202201181r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/07/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal malignancies. Vasorin (VASN) has been reported to be critical in tumor development and angiogenesis. However, VASN has not been reported in CRC, and its role is unclear. In this study, VASN expression is upregulated in CRC compared with the normal tissues, and VASN expression positively correlates with N stage and poor overall survival by analysis of different datasets and 32 CRC clinicopathologic samples. Overexpression of VASN significantly promotes CRC cell progression, including proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT), while knockdown of VASN inhibits CRC progression. We found that VASN was associated with the YAP/TAZ and PI3K/AKT pathways by gene set enrichment analysis (GSEA) and gene ontology (GO) analysis. Notably, western blotting, immunofluorescence staining and co-immunofluorescence (co-IP) confirmed that VASN could interact with YAP and activate the YAP/TAZ and PTEN/PI3K/AKT pathways, and knockdown of YAP reversed this effect. Importantly, our findings indicate that VASN interacts with YAP to inhibit YAP phosphorylation and stimulates CRC proliferation, migration, and invasion through activation of the YAP/TAZ-TEAD target gene CTGF and PTEN/PI3K/AKT pathways. Our results also show that knockdown of YAP reverses the cellular phenotype induced by increased VASN. In conclusion, our study reveals that VASN acts as an oncogene to stimulate tumor progression in CRC, providing new insights into the molecular mechanisms of CRC development and representing a possible novel biomarker for CRC.
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Affiliation(s)
- Weiye Liang
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jia Zuo
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mingkai Liu
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuling Su
- Center for Pancreatic Cancer Research, School of Medicine, South China University of Technology, Guangzhou, China
| | - Baoyin Guo
- Department of Pathology, Guangzhou First People's Hospital, Guangzhou, China
| | - Jiangtao Hou
- Department of Gastroenterology, The First Affiliated Hospital of Guangzhou University of TCM, Guangzhou, China
| | - Qi Xing
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yinglong Peng
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lian Fang
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yihui Cao
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiajie Shan
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ruixia Sun
- Bioscience Laboratory, BIOS Bioscience and Technology Limited Company, Guangzhou, China
| | - Jie Zhao
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jian Wang
- Department of Neurobiology, School of Medicine, South China University of Technology, Guangzhou, China.,Bioscience Laboratory, BIOS Bioscience and Technology Limited Company, Guangzhou, China
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Zhang S, Wang C, Ju J, Wang C. Extracellular Hsp90α Supports the ePKM2-GRP78-AKT Axis to Promote Tumor Metastasis. Front Oncol 2022; 12:906080. [PMID: 35847880 PMCID: PMC9280132 DOI: 10.3389/fonc.2022.906080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Tumor-secreted proteins can provide numerous molecular targets for cancer diagnosis and treatment. Of note, pyruvate kinase M2 (PKM2) is secreted by tumor cells to promote malignant progression, while its regulatory mechanism or the interacting network remains uncovered. In the present study, we identified extracellular heat shock protein 90 alpha (eHsp90α) as one potential interacting protein of ePKM2 by mass spectrometry (MS), which was further verified by pull-down and co-immunoprecipitation analysis. Later, we found that eHsp90α enhanced the effect of ePKM2 on migration and invasion of lung cancer cells. Blocking of Hsp90α activity, on the other hand, attenuated tumor migration or invasion induced by ePKM2. Eventually, the in vivo role of Hsp90α in regulating ePKM2 activity was validated by the mouse xenograft tumor model. Mechanistically, we found that eHsp90α binds to and stabilizes ePKM2 to protect it from degradation in the extracellular environment. Besides, eHsp90α promoted the interaction of ePKM2 with cell surface receptor GRP78, which leads to the activation of the ePKM2/GRP78/AKT axis. Collectively, we unraveled the novel molecular mechanism of eHsp90α in regulating ePKM2 activity during tumor progression, which is beneficial for the development of new treatments against lung cancer.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Caihong Wang
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jiujun Ju
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
| | - Caixia Wang
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, China
- *Correspondence: Caixia Wang,
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Abstract
PURPOSE OF REVIEW This article reviews the latest proteomic research on uveal melanoma. RECENT FINDINGS Proteomic analysis of uveal melanoma cell lines and tissue specimens has improved our understanding of the pathophysiology of uveal melanoma and helped identify potential prognostic biomarkers. Circulating proteins in patient serum may aid in the surveillance of metastatic disease. The proteomes of aqueous and vitreous biopsy specimens may provide safer biomarkers for metastatic risk and candidate therapeutic targets in uveal melanoma. Proteomic analysis has the potential to benefit patient outcomes by improving diagnosis, prognostication, surveillance, and treatment of uveal melanoma. SUMMARY These recent findings demonstrate that proteomic analysis is an important area of research to better understand the pathophysiology of uveal melanoma and improve the personalized management of our patients.
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Affiliation(s)
- Michael J. Heiferman
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Vinit B. Mahajan
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304 USA
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Department of Radiation Oncology, Stanford University, Palo Alto, CA, USA
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De Morais JA, Zelanis A. Bioinformatic reanalysis of public proteomics data reveals that nuclear proteins are recurrent in cancer secretomes. Traffic 2021; 23:98-108. [PMID: 34806804 DOI: 10.1111/tra.12827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/05/2021] [Accepted: 11/18/2021] [Indexed: 11/27/2022]
Abstract
Proteins secreted by tumoral cells (cancer secretomes) have been continuously associated with cancer development and progression processes. In this context, secreted proteins contribute to the signaling mechanisms related to tumor growth and spreading and studies on tumor secretomes provide valuable clues on putative tumor biomarkers. Although the in vitro identification of intracellular proteins in cancer secretome studies has usually been associated with contamination derived from cell lysis or fetal bovine serum, accumulated evidence reports on intracellular proteins with moonlighting functions in the extracellular environment. In this study, we performed a systematic reanalysis of public proteomics data regarding different cancer secretomes, aiming to identify intracellular proteins potentially secreted by tumor cells via unconventional secretion pathways. We found a similar repertoire of unconventionally secreted proteins, including the recurrent identification of nuclear proteins secreted by different cancer cells. In addition, in some cancer types, immunohistochemical data were in line with proteomics identifications and suggested that nuclear proteins might relocate from the nucleus to the cytoplasm. Both the presence of nuclear proteins and the likely unconventional secretion of such proteins may comprise biological signatures of malignant transformation in distinct cancer types and may be targeted for further analysis aiming at the prognostic/therapeutic value of such features.
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Affiliation(s)
- Juliana A De Morais
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Institute of Science and Technology, Federal University of São Paulo, UNIFESP, São José dos Campos, São Paulo, Brazil
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Dihazi GH, Eltoweissy M, Jahn O, Tampe B, Zeisberg M, Wülfrath HS, Müller GA, Dihazi H. The Secretome Analysis of Activated Human Renal Fibroblasts Revealed Beneficial Effect of the Modulation of the Secreted Peptidyl-Prolyl Cis-Trans Isomerase A in Kidney Fibrosis. Cells 2020; 9:cells9071724. [PMID: 32708451 PMCID: PMC7407823 DOI: 10.3390/cells9071724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
The secretome is an important mediator in the permanent process of reciprocity between cells and their environment. Components of secretome are involved in a large number of physiological mechanisms including differentiation, migration, and extracellular matrix modulation. Alteration in secretome composition may therefore trigger cell transformation, inflammation, and diseases. In the kidney, aberrant protein secretion plays a central role in cell activation and transition and in promoting renal fibrosis onset and progression. Using comparative proteomic analyses, we investigated in the present study the impact of cell transition on renal fibroblast cells secretome. Human renal cell lines were stimulated with profibrotic hormones and cytokines, and alterations in secretome were investigated using proteomic approaches. We identified protein signatures specific for the fibrotic phenotype and investigated the impact of modeling secretome proteins on extra cellular matrix accumulation. The secretion of peptidyl-prolyl cis-trans isomerase A (PPIA) was demonstrated to be associated with fibrosis phenotype. We showed that the in-vitro inhibition of PPIA with ciclosporin A (CsA) resulted in downregulation of PPIA and fibronectin (FN1) expression and significantly reduced their secretion. Knockdown studies of PPIA in a three-dimensional (3D) cell culture model significantly impaired the secretion and accumulation of the extracellular matrix (ECM), suggesting a positive therapeutic effect on renal fibrosis progression.
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Affiliation(s)
- Gry H. Dihazi
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Marwa Eltoweissy
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21500, Egypt;
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Hermann-Rein-Strasse 3, D-37075 Göttingen, Germany;
| | - Björn Tampe
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Michael Zeisberg
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hauke S. Wülfrath
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Gerhard A. Müller
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37075 Göttingen, Germany
- Correspondence: ; Tel.: +49-551-399-1221; Fax: +49-551-399-1039
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Rehman AU, Olof Olsson P, Khan N, Khan K. Identification of Human Secretome and Membrane Proteome-Based Cancer Biomarkers Utilizing Bioinformatics. J Membr Biol 2020; 253:257-270. [PMID: 32415382 DOI: 10.1007/s00232-020-00122-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/02/2020] [Indexed: 12/12/2022]
Abstract
Cellular secreted proteins (secretome), together with cellular membrane proteins, collectively referred to as secretory and membrane proteins (SMPs) are a large potential source of biomarkers as they can be used to indicate cell types and conditions. SMPs have been shown to be ideal candidates for several clinically approved drug regimens including for cancer. This study aimed at performing a functional analysis of SMPs within different cancer subtypes to provide great clinical targets for potential prognostic, diagnostic and the therapeutics use. Using an innovative majority decision-based algorithm and transcriptomic data spanning 5 cancer types and over 3000 samples, we quantified the relative difference in SMPs gene expression compared to normal adjacent tissue. A detailed deep data mining analysis revealed a consistent group of downregulated SMP isoforms, enriched in hematopoietic cell lineages (HCL), in multiple cancer types. HCL-associated genes were frequently downregulated in successive cancer stages and high expression was associated with good patient prognosis. In addition, we suggest a potential mechanism by which cancer cells suppress HCL signaling by reducing the expression of immune-related genes. Our data identified potential biomarkers for the cancer immunotherapy. We conclude that our approach may be applicable for the delineation of other types of cancer and illuminate specific targets for therapeutics and diagnostics.
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Affiliation(s)
- Adeel Ur Rehman
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | | | - Naveed Khan
- Max Plank Partner Institute of Computational Biology, Shanghai Institute of Biological Sciences, Shanghai, 200032, China
| | - Khalid Khan
- Department of Respiratory and Critical Care Medicine, The Second Clinical Medical College (Shenzhen People's Hospital) of Jinan University, Shenzhen Institute of Respiratory Diseases, Shenzhen, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
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Wang C, Zhang S, Liu J, Tian Y, Ma B, Xu S, Fu Y, Luo Y. Secreted Pyruvate Kinase M2 Promotes Lung Cancer Metastasis through Activating the Integrin Beta1/FAK Signaling Pathway. Cell Rep 2020; 30:1780-1797.e6. [PMID: 32049010 DOI: 10.1016/j.celrep.2020.01.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/01/2019] [Accepted: 01/10/2020] [Indexed: 12/31/2022] Open
Abstract
Cancer cell-derived secretomes have been documented to play critical roles in cancer progression. Intriguingly, alternative extracellular roles of intracellular proteins are involved in various steps of tumor progression, which can offer strategies to fight cancer. Herein, we identify lung cancer progression-associated secretome signatures using mass spectrometry analysis. Among them, PKM2 is verified to be highly expressed and secreted in lung cancer cells and clinical samples. Functional analyses demonstrates that secreted PKM2 facilitates tumor metastasis. Furthermore, mass spectrometry analysis and functional validation identify integrin β1 as a receptor of secreted PKM2. Mechanistically, secreted PKM2 directly bound to integrin β1 and subsequently activated the FAK/SRC/ERK axis to promote tumor metastasis. Collectively, our findings suggest that PKM2 is a potential serum biomarker for diagnosing lung cancer and that targeting the secreted PKM2-integrin β1 axis can inhibit lung cancer development, which provides evidence of a potential therapeutic strategy in lung cancer.
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Affiliation(s)
- Caihong Wang
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Shaosen Zhang
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Jie Liu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yang Tian
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Boyuan Ma
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Siran Xu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yan Fu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yongzhang Luo
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China.
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10
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Gong Y, Wang C, Jiang Y, Zhang S, Feng S, Fu Y, Luo Y. Metformin Inhibits Tumor Metastasis through Suppressing Hsp90α Secretion in an AMPKα1-PKCγ Dependent Manner. Cells 2020; 9:cells9010144. [PMID: 31936169 PMCID: PMC7016760 DOI: 10.3390/cells9010144] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Metformin has been documented in epidemiological studies to mitigate tumor progression. Previous reports show that metformin inhibits tumor migration in several cell lines, such as MCF-7 and H1299, but the mechanisms whereby metformin exerts its inhibitory effects on tumor metastasis remain largely unknown. The secreted proteins in cancer cell-derived secretome have been reported to play important roles in tumor metastasis, but whether metformin has an effect on tumor secretome remains unclear. Here we show that metformin inhibits tumor metastasis by suppressing Hsp90α (heat shock protein 90α) secretion. Mass spectrometry (MS) analysis and functional validation identify that eHsp90α (extracellular Hsp90α) is one of the most important secreted proteins for metformin to inhibit tumor cells migration, invasion and metastasis both in vitro and in vivo. Moreover, we find that metformin inhibits Hsp90α secretion in an AMPKα1 dependent manner. Our data elucidate that AMPKα1 (AMP-activated protein kinase α1) decreases the phosphorylation level of Hsp90α by inhibiting the kinase activity of PKCγ (protein kinase Cγ), which suppresses the membrane translocation and secretion of Hsp90α. Collectively, our results illuminate that metformin inhibits tumor metastasis by suppressing Hsp90α secretion in an AMPKα1 dependent manner.
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Affiliation(s)
- Yuanchao Gong
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Caihong Wang
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi Jiang
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shaosen Zhang
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi Feng
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Fu
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yongzhang Luo
- The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; (Y.G.); (C.W.); (Y.J.); (S.Z.); (S.F.); (Y.F.)
- Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Correspondence: ; Tel.: +86-10-6277-2897; Fax: +86-10-6279-4691
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11
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Chen W, Wang Q, Xu X, Saxton B, Tessema M, Leng S, Choksi S, Belinsky SA, Liu ZG, Lin Y. Vasorin/ATIA Promotes Cigarette Smoke-Induced Transformation of Human Bronchial Epithelial Cells by Suppressing Autophagy-Mediated Apoptosis. Transl Oncol 2020; 13:32-41. [PMID: 31760267 PMCID: PMC6883318 DOI: 10.1016/j.tranon.2019.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Escaping cell death pathways is an important event during carcinogenesis. We previously identified anti-TNFα-induced apoptosis (ATIA, also known as vasorin) as an antiapoptotic factor that suppresses reactive oxygen species (ROS) production. However, the role of vasorin in lung carcinogenesis has not been investigated. METHODS Vasorin expression was examined in human lung cancer tissues with immunohistochemistry and database analysis. Genetic and pharmacological approaches were used to manipulate protein expression and autophagy activity in human bronchial epithelial cells (HBECs). ROS generation was measured with fluorescent indicator, apoptosis with release of lactate dehydrogenase, and cell transformation was assessed with colony formation in soft agar. RESULTS Vasorin expression was increased in human lung cancer tissues and cell lines, which was inversely associated with lung cancer patient survival. Cigarette smoke extract (CSE) and benzo[a]pyrene diol epoxide (BPDE)-induced vasorin expression in HBECs. Vasorin knockdown in HBECs significantly suppressed CSE-induced transformation in association with enhanced ROS accumulation and autophagy. Scavenging ROS attenuated autophagy and cytotoxicity in vasorin knockdown cells, suggesting that vasorin potentiates transformation by impeding ROS-mediated CSE cytotoxicity and improving survival of the premalignant cells. Suppression of autophagy effectively inhibited CSE-induced apoptosis, suggesting that autophagy was pro-apoptotic in CSE-treated cells. Importantly, blocking autophagy strongly potentiated CSE-induced transformation. CONCLUSION These results suggest that vasorin is a potential lung cancer-promoting factor that facilitates cigarette smoke-induced bronchial epithelial cell transformation by suppressing autophagy-mediated apoptosis, which could be exploited for lung cancer prevention.
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Affiliation(s)
- Wenshu Chen
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Qiong Wang
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Xiuling Xu
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Bryanna Saxton
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Mathewos Tessema
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Shuguang Leng
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Swati Choksi
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
| | - Steven A Belinsky
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA
| | - Zheng-Gang Liu
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
| | - Yong Lin
- Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, 2425 Ridgecrest DR. SE, Albuquerque, NM, 87108, USA.
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12
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Bonnet AL, Chaussain C, Broutin I, Rochefort GY, Schrewe H, Gaucher C. From Vascular Smooth Muscle Cells to Folliculogenesis: What About Vasorin? Front Med (Lausanne) 2018; 5:335. [PMID: 30564578 PMCID: PMC6288187 DOI: 10.3389/fmed.2018.00335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/15/2018] [Indexed: 01/18/2023] Open
Abstract
First described in 1988, vasorin (VASN) is a transmembrane glycoprotein expressed during early mouse development, and with a less extent, in various organs and tissues (e.g., kidney, aorta, and brain) postnatally. Vasn KO mice die after 3 weeks of life from unknown cause(s). No human disease has been associated with variants of this gene so far, but VASN seems to be a potential biomarker for nephropathies and tumorigenesis. Its interactions with the TGF-β and Notch1 pathways offer the most serious assumptions regarding VASN functions. In this review, we will describe current knowledge about this glycoprotein and discuss its implication in various organ pathophysiology.
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Affiliation(s)
- Anne-Laure Bonnet
- EA 2496 Orofacial Pathologies, Imaging and Biotherapies, Dental School Faculty, University Paris Descartes and Life Imaging Platform (PIV), Montrouge, France.,Department of Odontology, University Hospitals Charles Foix, PNVS, and Henri Mondor, AP-HP, Paris, France
| | - Catherine Chaussain
- EA 2496 Orofacial Pathologies, Imaging and Biotherapies, Dental School Faculty, University Paris Descartes and Life Imaging Platform (PIV), Montrouge, France.,Department of Odontology, University Hospitals Charles Foix, PNVS, and Henri Mondor, AP-HP, Paris, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015, CNRS), Pharmacy Faculty, University Paris Descartes, USPC, Paris, France
| | - Gaël Y Rochefort
- EA 2496 Orofacial Pathologies, Imaging and Biotherapies, Dental School Faculty, University Paris Descartes and Life Imaging Platform (PIV), Montrouge, France
| | - Heinrich Schrewe
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Céline Gaucher
- EA 2496 Orofacial Pathologies, Imaging and Biotherapies, Dental School Faculty, University Paris Descartes and Life Imaging Platform (PIV), Montrouge, France.,Department of Odontology, University Hospitals Charles Foix, PNVS, and Henri Mondor, AP-HP, Paris, France
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13
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Li D, Zhang T, Yang X, Geng J, Li S, Ding H, Li H, Huang A, Wang C, Sun L, Bai C, Zhang H, Li J, Dong J, Shao N. Identification of Functional mimotopes of human Vasorin Ectodomain by Biopanning. Int J Biol Sci 2018; 14:461-470. [PMID: 29725267 PMCID: PMC5930478 DOI: 10.7150/ijbs.22692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/25/2018] [Indexed: 01/11/2023] Open
Abstract
Human vasorin (VASN) as a type I transmembrane protein, is a potential biomarker of hepatocellular carcinoma, which could expedite HepG2 cell proliferation and migration significantly in vitro. The ectodomain of VASN was proteolytically released to generate soluble VASN (sVASN), which was validated to be the active form. Among several monoclonal antibodies produced against sVASN, the clone V21 was found to bind with the recombinant human sVASN (rhsVASN) with the highest affinity and specificity, and also have inhibitory effects on proliferation and migration of HepG2 cells. Hence the phage-displayed peptide library was screened against the antibody V21. The positive phage clones were isolated and sequenced, and one unique consensus motifs was obtained. The result of sequence alignment showed that the conserved motif had similarity to VASN(Cys432-Cys441), embedded in the epidermal growth factor (EGF)-like domain. The synthetic mimotope peptide V21P1 and V21P2 were confirmed to bind with V21 and could compete with rhsVASN in ELISA assay. And they could also almost completely reverse the inhibitory effect of V21 on HepG2 migration and proliferation. Furthermore, the antibodies produced against V21P1 were able to bind not only with the peptide V21P1, but also with rhsVASN and the natural VASN from HepG2 cell. Our results showed that V21 seemed to be a functional antibody. The mimotopes toward V21 might mimic the functional domain of VASN, which would be helpful to exploit VASN functions and act as a candidate target for developing therapeutic antibodies against VASN.
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Affiliation(s)
- Da Li
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Tan Zhang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiqin Yang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jie Geng
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Shaohua Li
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hongmei Ding
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hui Li
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Aixue Huang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Chaonan Wang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Leqiao Sun
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Chenjun Bai
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Heqiu Zhang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jie Li
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jie Dong
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
| | - Ningsheng Shao
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, China
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14
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Angi M, Kalirai H, Prendergast S, Simpson D, Hammond DE, Madigan MC, Beynon RJ, Coupland SE. In-depth proteomic profiling of the uveal melanoma secretome. Oncotarget 2018; 7:49623-49635. [PMID: 27391064 PMCID: PMC5226534 DOI: 10.18632/oncotarget.10418] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/09/2016] [Indexed: 12/23/2022] Open
Abstract
Uveal melanoma (UM), the most common primary intraocular tumour in adults, is characterised by a high frequency of metastases to the liver, typically with a fatal outcome. Proteins secreted from cancer cells (‘secretome’) are biologically important molecules thought to contribute to tumour progression. We examined the UM secretome by applying a label-free nanoLCMS/MS proteomic approach to profile proteins secreted into culture media by primary UM tumours with a high− (HR; n = 11) or low− (LR; n = 4) metastatic risk, compared to normal choroidal melanocytes (NCM) from unaffected post-mortem eyes. Across the three groups, 1843 proteins were identified at a 1% false discovery rate; 758 of these by at least 3 unique peptides, and quantified. The majority (539/758, 71%) of proteins were classified as secreted either by classical (144, 19%), non-classical (43, 6%) or exosomal (352, 46%) mechanisms. Bioinformatic analyzes showed that the secretome composition reflects biological differences and similarities of the samples. Ingenuity® pathway analysis of the secreted protein dataset identified abundant proteins involved in cell proliferation-, growth- and movement. Hepatic fibrosis/hepatic stellate cell activation and the mTORC1-S6K signalling axis were among the most differentially regulated biological processes in UM as compared with NCM. Further analysis of proteins upregulated ≥ 2 in HR-UM only, identified exosomal proteins involved in extracellular matrix remodelling and cancer cell migration/invasion; as well as classically secreted proteins, possibly representing novel biomarkers of metastatic disease. In conclusion, UM secretome analysis identifies novel proteins and pathways that may contribute to metastatic development at distant sites, particularly in the liver.
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Affiliation(s)
- Martina Angi
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Samuel Prendergast
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Deborah Simpson
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Dean E Hammond
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Michele C Madigan
- School of Optometry, University of New South Wales, New South Wales, Australia.,Save Sight Institute, Ophthalmology, University of Sydney, New South Wales, Australia
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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15
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Bozzi F, Mogavero A, Varinelli L, Belfiore A, Manenti G, Caccia C, Volpi CC, Beznoussenko GV, Milione M, Leoni V, Gloghini A, Mironov AA, Leo E, Pilotti S, Pierotti MA, Bongarzone I, Gariboldi M. MIF/CD74 axis is a target for novel therapies in colon carcinomatosis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:16. [PMID: 28114961 PMCID: PMC5260021 DOI: 10.1186/s13046-016-0475-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/13/2016] [Indexed: 12/16/2022]
Abstract
Background Strategies aimed at obtaining a complete cytoreduction are needed to improve long-term survival for patients with colorectal cancer peritoneal carcinomatosis (CRC-pc). Methods We established organoid models from peritoneal metastases of two naïve CRC patients. A standard paraffin inclusion was conducted to compare their 3D structure and immunohistochemical profile with that of the corresponding surgical samples. RNA expression levels of the CRC stem cell marker LGR5 was measured by in situ hybridization. The secretome of organoids was profiled by mass spectrometry. Energy homeostasis of organoids was interfered with 4-IPP and metformin. Biochemical and metabolic changes after drug treatments were investigated by western blot and mass spectrometry. Mitochondria impairment was evaluated by electron microscopy and mitotraker staining. Results The two organoids recapitulated their corresponding clinical samples in terms of 3D structure and immmunoistochemical profile and were positive for the cancer stem cells marker LGR5. Proteomic analyses of organoids highlighted their strong dependence on energy producing pathways, which suggest that their targeting could be an effective therapeutic approach. To test this hypothesis, we treated organoids with two drugs that target metabolism acting on AMP-activated protein kinase (AMPK), the main regulator of cellular energy homeostasis, which may act as metabolic tumour suppressor in CRC. Organoids were treated with 4-IPP, an inhibitor of MIF/CD74 signalling axis which activates AMPK function, or metformin that inhibits mitochondrial respiratory chain complex I. As a new finding we observed that treatment with 4-IPP downregulated AMPK signalling activity, reduced AKT phosphorylation and activated a JNK-mediated stress-signalling response, thus generating mitochondrial impairment and cell death. Metformin treatment enhanced AMPK activation, decreasing the activity of the anabolic factors ribosomal protein S6 and p4EBP-1 and inducing mitochondrial depolarization. Conclusion We provide evidence that the modulation of AMPK activity may be a strategy for targeting metabolism of CRC-pc organoids. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0475-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabio Bozzi
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Angela Mogavero
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Amadeo 42, Milan, 20133, Italy.,Molecular Genetics of Cancer, Fondazione Istituto FIRC di Oncologia Molecolare, via Adamello 16, Milan, 20139, Italy
| | - Luca Varinelli
- Proteomics Laboratory Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Amadeo 42, Milan, 20133, Italy
| | - Antonino Belfiore
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Giacomo Manenti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Amadeo 42, Milan, 20133, Italy
| | - Claudio Caccia
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS 'Carlo Besta' Istituto Neurologico, via G. Amadeo 42, Milan, 20133, Italy
| | - Chiara C Volpi
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Galina V Beznoussenko
- Fondazione Istituto FIRC di Oncologia Molecolare, via Adamello 16, Milan, 20139, Italy
| | - Massimo Milione
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Valerio Leoni
- Laboratory of Clinical Pathology and Medical Genetics, Fondazione IRCCS 'Carlo Besta' Istituto Neurologico, via G. Amadeo 42, Milan, 20133, Italy
| | - Annunziata Gloghini
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Alexandre A Mironov
- Fondazione Istituto FIRC di Oncologia Molecolare, via Adamello 16, Milan, 20139, Italy
| | - Ermanno Leo
- Colorectal Cancer Unit-Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Silvana Pilotti
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Venezian 1, Milan, 20133, Italy
| | - Marco A Pierotti
- Molecular Genetics of Cancer, Fondazione Istituto FIRC di Oncologia Molecolare, via Adamello 16, Milan, 20139, Italy
| | - Italia Bongarzone
- Proteomics Laboratory Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Amadeo 42, Milan, 20133, Italy.
| | - Manuela Gariboldi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, via G. Amadeo 42, Milan, 20133, Italy.,Molecular Genetics of Cancer, Fondazione Istituto FIRC di Oncologia Molecolare, via Adamello 16, Milan, 20139, Italy
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16
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Shin J, Kim G, Lee JW, Lee JE, Kim YS, Yu JH, Lee ST, Ahn SH, Kim H, Lee C. Identification of ganglioside GM2 activator playing a role in cancer cell migration through proteomic analysis of breast cancer secretomes. Cancer Sci 2016; 107:828-35. [PMID: 27002480 PMCID: PMC4968593 DOI: 10.1111/cas.12935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/28/2022] Open
Abstract
Cancer cell secretomes are considered a potential source for the discovery of cancer markers. In this study, the secretomes of four breast cancer (BC) cell lines (Hs578T, MCF‐7, MDA‐MB‐231, and SK‐BR‐3) were profiled with liquid chromatography–tandem mass spectrometry analysis. A total of 1410 proteins were identified with less than 1% false discovery rate, of which approximately 55% (796 proteins) were predicted to be secreted from cells. To find BC‐specific proteins among the secreted proteins, data of immunohistochemical staining compiled in the Human Protein Atlas were investigated by comparing the data of BC tissues with those of normal tissues. By applying various criteria, including higher expression level in BC tissues, higher predicted potential of secretion, and sufficient number of tandem mass spectra, 12 biomarker candidate proteins including ganglioside GM2 activator (GM2A) were selected for confirmation. Western blot analysis and ELISA for plasma samples of healthy controls and BC patients revealed elevation of GM2A in BC patients, especially those who were estrogen receptor‐negative. Additionally, siRNA‐mediated knockdown of GM2A in BC cells decreased migration in vitro, whereas the overexpression of GM2A led to an increase in cell migration. Although GM2A as a diagnostic and prognostic marker in BC should be carefully verified further, this study has established the potential role of GM2A in BC progression.
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Affiliation(s)
- Jihye Shin
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea.,Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Gamin Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea.,Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Won Lee
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea
| | - Yoo Seok Kim
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jong-Han Yu
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Seung-Taek Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Sei Hyun Ahn
- Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Cheolju Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea.,Department of Biological Chemistry, Korea University of Science and Technology, Daejeon, Korea
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17
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Li S, Li H, Yang X, Wang W, Huang A, Li J, Qin X, Li F, Lu G, Ding H, Su X, Hou L, Xia W, Shi M, Zhang H, Zhao Q, Dong J, Ge X, Sun L, Bai C, Wang C, Shen X, Fang T, Wang F, Zhang H, Shao N. Vasorin is a potential serum biomarker and drug target of hepatocarcinoma screened by subtractive-EMSA-SELEX to clinic patient serum. Oncotarget 2016; 6:10045-59. [PMID: 25826090 PMCID: PMC4496339 DOI: 10.18632/oncotarget.3541] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/13/2015] [Indexed: 11/25/2022] Open
Abstract
We report a new biomarker of hepatocarcinoma, vasorin (VASN), screened by a subtractive EMSA-SELEX strategy from AFP negative serum of hepatocellular carcinoma (HCC) patients with extrahepatic metastases. VASN was verified to be highly expressed in sera of 100 cases of HCC patients compared with 97 cases of normal persons and 129 cases of hepatitis patients. Further validation by Q-PCR, IFA and Western blot showed higher expression of VASN at mRNA and protein levels in HCC cell lines and HCC tissues than in normal controls. RNA interference and forced overexpression assays verified that VASN promotes cell proliferation and migration and inhibits apoptosis. Down-regulation of microRNA miR145 and miR146a is an important mechanism leading to high expression of VASN. Conclusion: As a membrane protein and/or as free protein, VASN may be an effective target for biological treatment of liver cancer and is a potential biomarker for HCC diagnosis. Small molecular nucleotides targeting VASN are promising biological therapies to HCC.
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Affiliation(s)
- Shaohua Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiqin Yang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Wei Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Aixue Huang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jie Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xingliang Qin
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Fei Li
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Guanyi Lu
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Hongmei Ding
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xueting Su
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Lvbin Hou
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Wei Xia
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Ming Shi
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Hongwen Zhang
- Department of Interventional Radiology, General Hospital of Fuzhou, Fuzhou, China
| | - Qiang Zhao
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jie Dong
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xingfeng Ge
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Leqiao Sun
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chenjun Bai
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chaonan Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xuelian Shen
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Tao Fang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Fusheng Wang
- Center of Infectous Disease, Beijing 302 Hospital, Beijing, China
| | - Heqiu Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing, China
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18
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Soluble CD109 binds TGF-β and antagonizes TGF-β signalling and responses. Biochem J 2015; 473:537-47. [PMID: 26621871 DOI: 10.1042/bj20141488] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
Transforming growth factor-β (TGF-β) is a multifunctional cytokine implicated in many diseases, including tissue fibrosis and cancer. TGF-β mediates diverse biological responses by signalling through type I and II TGF-β receptors (TβRI and TβRII). We have previously identified CD109, a glycosylphosphatidylinositol (GPI)-anchored protein, as a novel TGF-β co-receptor that negatively regulates TGF-β signalling and responses and demonstrated that membrane-anchored CD109 promotes TGF-β receptor degradation via a SMAD7/Smurf2-mediated mechanism. To determine whether CD109 released from the cell surface (soluble CD109 or sCD109) also acts as a TGF-β antagonist, we determined the efficacy of recombinant sCD109 to interact with TGF-β and inhibit TGF-β signalling and responses. Our results demonstrate that sCD109 binds TGF-β with high affinity as determined by surface plasmon resonance (SPR) and cell-based radioligand binding and affinity labelling competition assays. SPR detected slow dissociation kinetics between sCD109 and TGF-β at low concentrations, indicating a stable and effective interaction. In addition, sCD109 antagonizes TGF-β-induced Smad2/3 phosphorylation, transcription and cell migration. Together, our results suggest that sCD109 can bind TGF-β, inhibit TGF-β binding to its receptors and decrease TGF-β signalling and TGF-β-induced cellular responses.
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19
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Varinelli L, Caccia D, Volpi CC, Caccia C, De Bortoli M, Taverna E, Gualeni AV, Leoni V, Gloghini A, Manenti G, Bongarzone I. 4-IPP, a selective MIF inhibitor, causes mitotic catastrophe in thyroid carcinomas. Endocr Relat Cancer 2015. [PMID: 26206776 DOI: 10.1530/erc-15-0299] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine that is over-expressed in several human neoplastic cells. When MIF binds its receptor (CD74) and co-receptor (CD44), it initiates signaling cascades that orchestrate cell proliferation and survival, and it can directly modulate the activity of AMPK. These activities indicate that MIF potentially regulates cell survival and metabolism. We found that MIF was primarily co-expressed with CD74 in 16 out of 23 papillary thyroid carcinoma (PTC) and in all the 27 available anaplastic thyroid carcinoma (ATC) biopsy samples. MIF and CD74 were co-expressed in TPC-1 and HTC-C3 cell lines. The selective MIF inhibitor, 4-iodo-6-phenylpyrimidine (4-IPP), blocked MIF/CD74 internalization, activated JNK, and dose-dependently inhibited proliferation inducing apoptosis and mitotic cell death. In two CD74-negative cell lines, NIM-1 and K1, 4-IPP treatment partially reduced proliferation. Coordinated MIF and CD74 expression appeared to confer in tumor cells the plasticity necessary to escape cell cycle regulation, metabolic changes, and stress conditions. MIF/CD74 signaling removal made cells susceptible to apoptosis and mitotic cell death. This finding suggests a possible avenue for targeting DNA endoreduplication, thus preventing the proliferation of therapy-resistant cell subpopulations. This study highlights MIF/CD74 axis as an important player in the biology of aggressive thyroid neoplasms.
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Affiliation(s)
- Luca Varinelli
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Dario Caccia
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Chiara C Volpi
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Claudio Caccia
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Maida De Bortoli
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Elena Taverna
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Ambra V Gualeni
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Valerio Leoni
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Annunziata Gloghini
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Giacomo Manenti
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
| | - Italia Bongarzone
- Proteomics LaboratoryDepartment of Experimental Oncology and Molecular MedicineDepartment of Diagnostic Pathology and Laboratory MedicineDepartment of Predictive and Preventive MedicineFondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milan, ItalyLaboratory of Clinical Pathology and Medical GeneticsFondazione IRCCS 'Carlo Besta' Istituto Neurologico, Via Amadeo 42, 20133 Milan, Italy
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20
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Feizi A, Banaei-Esfahani A, Nielsen J. HCSD: the human cancer secretome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav051. [PMID: 26078477 PMCID: PMC4480035 DOI: 10.1093/database/bav051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/04/2015] [Indexed: 12/11/2022]
Abstract
The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology. The secreted proteins from cancer cells are believed to play a deterministic role in cancer progression and therefore may be the key to find novel therapeutic targets and biomarkers for many cancers. Consequently, huge data on cancer secretome have been generated in recent years and the lack of a coherent database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer types. It has a simple and user friendly query system for basic and advanced search based on gene name, cancer type and data type as the three main query options. The results are visualized in an explicit and interactive manner. An example of a result page includes annotations, cross references, cancer secretome data and secretory features for each identified protein. Database URL:www.cancersecretome.org.
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Affiliation(s)
- Amir Feizi
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Amir Banaei-Esfahani
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Fremtidsvej 3, DK-2970 Hørsholm, Denmark and Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
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21
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Huang A, Dong J, Li S, Wang C, Ding H, Li H, Su X, Ge X, Sun L, Bai C, Shen X, Fang T, Li J, Shao N. Exosomal transfer of vasorin expressed in hepatocellular carcinoma cells promotes migration of human umbilical vein endothelial cells. Int J Biol Sci 2015; 11:961-9. [PMID: 26157350 PMCID: PMC4495413 DOI: 10.7150/ijbs.11943] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 02/07/2023] Open
Abstract
Vasorin (VASN) is a type I transmembrane protein that plays important roles in tumor development and vasculogenesis. In this paper, we showed that VASN could be a key mediator of communication between tumor cells and endothelial cells. We confirmed for the first time that HepG2-derived VASN can be transferred to human umbilical vein endothelial cells (HUVECs) via receptor mediated endocytosis of exosomes, at least in part through HSPGs. The HepG2-derived VASN containing exosomes promote migration of recipient HUVECs cells. Our results identify a novel pathway by which a functional protein expressed in tumor cells affects the biological fate of endothelial cells via exosomes.
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Affiliation(s)
- Aixue Huang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jie Dong
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Shaohua Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Chaonan Wang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hongmei Ding
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xueting Su
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xingfeng Ge
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Leqiao Sun
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Chenjun Bai
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xuelian Shen
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Tao Fang
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Jie Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
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22
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Gloghini A, Bongarzone I. Cell-secreted signals shape lymphoma identity. Semin Cancer Biol 2015; 34:81-91. [PMID: 25837156 DOI: 10.1016/j.semcancer.2015.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/21/2015] [Accepted: 02/05/2015] [Indexed: 12/12/2022]
Abstract
Sequencing data show that both specific genes and a number of signaling pathways are recurrently mutated in various types of lymphoma. DNA sequencing analyses of lymphoma have identified several aberrations that might affect the interaction between malignant cells and the tumor microenvironment. Microenvironmental functions are essential to lymphoma; they provide survival and proliferation signals and license immune evasion. It is plausible that interventions that aim to destroy tumor-microenvironment interactions may improve responses to therapeutics. Accordingly, the identification of extrinsic factors and their downstream intracellular signaling targets has led to much progress in understanding tumor-microenvironment interactions. Lymphoma cells are differently influenced by cells' interactions with components of their microenvironment; these cell extrinsic factors include soluble and immobilized factors, the extracellular matrix, and signals presented by neighboring cells. Soluble factors, which are often cell-secreted autocrine and paracrine factors, comprise a significant fraction of targetable molecules. To begin to understand how intercellular communication is conducted in lymphoma, a first order of study is deciphering the soluble factors secreted by malignant cells and microenvironmental cells. These soluble factors are shed into the interstitial fluid in lymphoma and can be conveniently explored using mass spectrometry. Protein components can be detected and quantified, thus enabling the routine navigation of the soluble part of the microenvironment. Elucidating functional and signaling states affords a new paradigm for understanding cancer biology and devising new therapies. This review summarizes knowledge in this field and discusses the utility of studying tumor-secreted factors.
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Affiliation(s)
- Annunziata Gloghini
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
| | - Italia Bongarzone
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
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23
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Klein-Scory S, Tehrani MM, Eilert-Micus C, Adamczyk KA, Wojtalewicz N, Schnölzer M, Hahn SA, Schmiegel W, Schwarte-Waldhoff I. New insights in the composition of extracellular vesicles from pancreatic cancer cells: implications for biomarkers and functions. Proteome Sci 2014; 12:50. [PMID: 25469109 PMCID: PMC4251850 DOI: 10.1186/s12953-014-0050-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pancreatic cancer development is associated with characteristic alterations like desmoplastic reaction and immune escape which are mediated by the cell-cell communication mechanism and by the microenvironment of the cells. The whole of released components are important determinants in these processes. Especially the extracellular vesicles released by pancreatic cancer cells play a role in cell communication and modulate cell growth and immune responses. RESULTS Here, we present the proteomic description of affinity purified extracellular vesicles from pancreatic tumour cells, compared to the secretome, defined as the whole of the proteins released by pancreatic cancer cells. The proteomic data provide comprehensive catalogues of hundreds of proteins, and the comparison reveals a special proteomic composition of pancreatic cancer cell derived extracellular vesicles. The functional analysis of the protein composition displayed that membrane proteins, glycoproteins, small GTP binding proteins and a further, heterogeneous group of proteins are enriched in vesicles, whereas proteins derived from proteasomes and ribosomes, as well as metabolic enzymes, are not components of the vesicles. Furthermore proteins playing a role in carcinogenesis and modulators of the extracellular matrix (ECM) or cell-cell interactions are components of affinity purified extracellular vesicles. CONCLUSION The data deepen the knowledge of extracellular vesicle composition by hundreds of proteins that have not been previously described as vesicle components released by pancreatic cancer cells. Extracellular vesicles derived from pancreatic cancer cells show common proteins shared with other vesicles as well as cell type specific proteins indicating biomarker candidates and suggesting functional roles in cancer cell stroma interactions.
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Affiliation(s)
- Susanne Klein-Scory
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Mahnaz Moradian Tehrani
- />Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christina Eilert-Micus
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Kamila A Adamczyk
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Nathalie Wojtalewicz
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Martina Schnölzer
- />Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stephan A Hahn
- />Molecular Gastrointestinal Oncology MGO, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Wolff Schmiegel
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
- />Medical Department, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Irmgard Schwarte-Waldhoff
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
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24
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Lecht S, Gerstenhaber JA, Stabler CT, Pimton P, Karamil S, Marcinkiewicz C, Schulman ES, Lelkes PI. Heterogeneous Mixed-Lineage Differentiation of Mouse Embryonic Stem Cells Induced by Conditioned Media from A549 Cells. Stem Cells Dev 2014; 23:1923-36. [DOI: 10.1089/scd.2014.0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shimon Lecht
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Jonathan A. Gerstenhaber
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Collin T. Stabler
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Pimchanok Pimton
- Department of Biology, School of Science, Walailak University, Thammarat, Thailand
| | - Seda Karamil
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Cezary Marcinkiewicz
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
| | - Edward S. Schulman
- Division of Pulmonary, Critical Care and Sleep Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Peter I. Lelkes
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
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25
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Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LCJ, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics 2014; 13:1753-68. [PMID: 24741114 PMCID: PMC4083113 DOI: 10.1074/mcp.m114.038273] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/04/2014] [Indexed: 12/31/2022] Open
Abstract
The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) will address the urgent clinical need to minimize the general overtreatment of patients with non-aggressive PCa, who account for the majority of PCa cases. Here, we isolated formerly N-linked glycopeptides from normal prostate (n = 10) and from non-aggressive (n = 24), aggressive (n = 16), and metastatic (n = 25) PCa tumor tissues and analyzed the samples using SWATH mass spectrometry, an emerging data-independent acquisition method that generates a single file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy in which an a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH mass spectrometry data. On average we identified 1430 N-glycosites from each sample. Out of those, 220 glycoproteins showed significant quantitative changes associated with diverse biological processes involved in PCa aggressiveness and metastasis and indicated functional relationships. Two glycoproteins, N-acylethanolamine acid amidase and protein tyrosine kinase 7, that were significantly associated with aggressive PCa in the initial sample cohort were further validated in an independent set of patient tissues using tissue microarray analysis. The results suggest that N-acylethanolamine acid amidase and protein tyrosine kinase 7 may be used as potential tissue biomarkers to avoid overtreatment of non-aggressive PCa.
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Affiliation(s)
- Yansheng Liu
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jing Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Atul Sethi
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Qing K Li
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Lijun Chen
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231
| | - Ben Collins
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ludovic C J Gillet
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bernd Wollscheid
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Hui Zhang
- ¶Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231;
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; **Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
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SWATH™- and iTRAQ-based quantitative proteomic analyses reveal an overexpression and biological relevance of CD109 in advanced NSCLC. J Proteomics 2014; 102:125-36. [PMID: 24667143 DOI: 10.1016/j.jprot.2014.03.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 02/28/2014] [Accepted: 03/04/2014] [Indexed: 02/07/2023]
Abstract
UNLABELLED To identify cancer-related proteins, we used isobaric tags in a relative and absolute quantitation (iTRAQ) proteomic approach and SWATH™ quantification approach to analyze the secretome of an isogenic pair of highly metastatic and low metastatic non-small-cell lung cancer (NSCLC) cell lines. In addition, we compared two groups of pooled serum samples (12 early-stage and 12 late-stage patients) to mine data for candidates screened by iTRAQ-labeled proteomic analysis. A total of 110 proteins and 71 proteins were observed to be significantly differentially expressed in the cell line secretome and NSCLC sera, respectively. Among these proteins, CD109 was found to be highly expressed in both the highly metastatic cell line secretome and the group of late-stage patients. A sandwich ELISA assay also demonstrated an elevation of serum CD109 levels in individual NSCLC patients (n=30) compared with healthy subjects (n=19). Furthermore, CD109 displayed higher expression in lung cancer tissues compared with their matched noncancerous lung tissues (n=72). In addition, the knockdown of CD109 influenced several NSCLC cell bio-functions, for instance, depressing cell growth, affecting cell cycle phases. These phenomena suggest that CD109 plays a critical role in NSCLC progression. BIOLOGICAL SIGNIFICANCE We simultaneously applied two quantitative proteomic approaches-iTRAQ-labeling and SWATH™-to analyze the secretome of metastatic cell lines, in order to explore the cancer-associated proteins in conditioned media. In this study, our results indicate that CD109 plays a critical role in non-small-cell lung cancer (NSCLC) progression, and is overexpressed in advanced NSCLC.
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Gloghini A, Volpi CC, Caccia D, Gualeni AV, Cilia AM, Carbone A, Bongarzone I. Primary effusion lymphoma: secretome analysis reveals novel candidate biomarkers with potential pathogenetic significance. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:618-30. [PMID: 24521760 DOI: 10.1016/j.ajpath.2013.11.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 10/25/2013] [Accepted: 11/26/2013] [Indexed: 12/14/2022]
Abstract
Primary effusion lymphoma (PEL) is a rare B-cell neoplasm in which tumor cells are consistently infected by Kaposi's sarcoma-associated herpesvirus and usually grow in body cavities without tumor mass formation. To detect new proteins related to pathogenesis, four established cell lines from PEL (CRO-AP2, CRO-AP3, CRO-AP5, and CRO-AP6) were characterized by proteomics analysis of the secretome. The secretomes were analyzed using two complementary mass spectrometry platforms: liquid chromatography-mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight-based approaches. Among 266 proteins identified from the proteomics analysis, 139 were considered as predicted secreted. Twenty proteins were specifically secreted by PEL cell lines after comparison with secretomes of human cell lines representative of diverse solid tumors and leukemias. More important, 27 additional proteins were shared by all CRO-AP PEL cell lines. The presence of these proteins was confirmed by IHC in CRO-AP cell lines and in six other PEL cell lines, four PEL clinical samples, and three extracavitary Kaposi's sarcoma-associated herpesvirus-positive solid lymphomas included for comparative analysis. Functional classification showed that PEL cell secretomes were enriched in proteins specifically involved in inflammation/immune response, growth/cell cycle, and mRNA processing, in addition to structural/matrix proteins and proteins with enzymatic activity.
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Affiliation(s)
- Annunziata Gloghini
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milano
| | - Chiara C Volpi
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milano
| | - Dario Caccia
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milano
| | - Ambra V Gualeni
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milano
| | - Anna M Cilia
- Department of Pathology, Centro di Riferimento Oncologico Aviano (CRO Aviano National Cancer Institute), Istituto Nazionale Tumori (National Cancer Institute), IRCCS, Aviano, Italy
| | - Antonino Carbone
- Department of Pathology, Centro di Riferimento Oncologico Aviano (CRO Aviano National Cancer Institute), Istituto Nazionale Tumori (National Cancer Institute), IRCCS, Aviano, Italy.
| | - Italia Bongarzone
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milano
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Zawadzka AM, Schilling B, Cusack MP, Sahu AK, Drake P, Fisher SJ, Benz CC, Gibson BW. Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma. Mol Cell Proteomics 2014; 13:1034-49. [PMID: 24505115 PMCID: PMC3977182 DOI: 10.1074/mcp.m113.035485] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Breast cancer is a heterogeneous disease whose molecular diversity is not well reflected in clinical and pathological markers used for prognosis and treatment selection. As tumor cells secrete proteins into the extracellular environment, some of these proteins reach circulation and could become suitable biomarkers for improving diagnosis or monitoring response to treatment. As many signaling pathways and interaction networks are altered in cancerous tissues by protein phosphorylation, changes in the secretory phosphoproteome of cancer tissues could reflect both disease progression and subtype. To test this hypothesis, we compared the phosphopeptide-enriched fractions obtained from proteins secreted into conditioned media (CM) derived from five luminal and five basal type breast cancer cell lines using label-free quantitative mass spectrometry. Altogether over 5000 phosphosites derived from 1756 phosphoproteins were identified, several of which have the potential to qualify as phosphopeptide plasma biomarker candidates for the more aggressive basal and also the luminal-type breast cancers. The analysis of phosphopeptides from breast cancer patient plasma and controls allowed us to construct a discovery list of phosphosites under rigorous collection conditions, and second to qualify discovery candidates generated from the CM studies. Indeed, a set of basal-specific phosphorylation CM site candidates derived from IBP3, CD44, OPN, FSTL3, LAMB1, and STC2, and luminal-specific candidates derived from CYTC and IBP5 were selected and, based on their presence in plasma, quantified across all cell line CM samples using Skyline MS1 intensity data. Together, this approach allowed us to assemble a set of novel cancer subtype specific phosphopeptide candidates for subsequent biomarker verification and clinical validation.
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Affiliation(s)
- Anna M Zawadzka
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, California 94945
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Lecht S, Stabler CT, Rylander AL, Chiaverelli R, Schulman ES, Marcinkiewicz C, Lelkes PI. Enhanced reseeding of decellularized rodent lungs with mouse embryonic stem cells. Biomaterials 2014; 35:3252-62. [PMID: 24439414 DOI: 10.1016/j.biomaterials.2013.12.093] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/24/2013] [Indexed: 12/23/2022]
Abstract
Repopulation of decellularized lung scaffolds (DLS) is limited due to alterations in the repertoire and ratios of the residual extracellular matrix (ECM) proteins, characterized by e.g., the retention of type I collagen and loss of glycoproteins. We hypothesized that pre-treatment of decellularized matrices with defined ECM proteins, which match the repertoire of integrin receptors expressed by the cells to be seeded (e.g., embryonic stem cells) can increase the efficacy of the reseeding process. To test this hypothesis, we first determined the integrin receptors profile of mouse embryonic stem cells (mESCs). Mouse ESCs express α3, α5, α6, α9 and β1, but not α1, α2 and α4 integrin subunits, as established by Western blotting and adhesion to laminin and fibronectin, but not to collagens type I and IV. Reseeding of DLS with mESCs was inefficient (6.9 ± 0.5%), but was significantly enhanced (2.3 ± 0.1 fold) by pre-treating the scaffolds with media conditioned by A549 human lung adenocarcinoma cells, which we found to contain ∼5 μg/ml laminin. Furthermore, pre-treatment with A549-conditioned media resulted in a significantly more uniform distribution of the seeded mESCs throughout the engineered organ as compared to untreated DLS. Our study may advance whole lung engineering by stressing the importance of matching the integrin receptor repertoire of the seeded cells and the cell binding motifs of DLS.
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Affiliation(s)
- Shimon Lecht
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Collin T Stabler
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Alexis L Rylander
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Rachel Chiaverelli
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Edward S Schulman
- Division of Pulmonary, Critical Care and Sleep Medicine, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Cezary Marcinkiewicz
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA
| | - Peter I Lelkes
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA 19122, USA.
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30
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Sakakura H, Murakumo Y, Mii S, Hagiwara S, Kato T, Asai M, Hoshino A, Yamamoto N, Sobue S, Ichihara M, Ueda M, Takahashi M. Detection of a soluble form of CD109 in serum of CD109 transgenic and tumor xenografted mice. PLoS One 2014; 9:e83385. [PMID: 24400073 PMCID: PMC3882221 DOI: 10.1371/journal.pone.0083385] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/26/2013] [Indexed: 12/25/2022] Open
Abstract
CD109, a glycosylphosphatidylinositol-anchored glycoprotein, is expressed at high levels in some human tumors including squamous cell carcinomas. As CD109 is reportedly cleaved by furin and its soluble form is secreted into culture medium in vitro, we hypothesized that CD109 could serve as a tumor marker in vivo. In this study, we investigated CD109 as a novel serum tumor marker using transgenic mice that overexpress mouse CD109 (mCD109-TG mice) and tumor xenografted mice inoculated with human CD109 (hCD109)-overexpressing HEK293 cells. In sera and urine of mCD109-TG mice, mCD109 was detected using western blotting. In xenografted mice, hCD109 secreted from inoculated tumors was detected in sera, using western blotting and CD109 ELISA. Concentrations of tumor-secreted CD109 increased proportionally as tumors enlarged. Concentrations of secreted CD109 decreased notably by 17 h after tumor resection, and became undetectable 48 h after resection. The half-life of tumor-secreted CD109 was about 5.86±0.17 h. These results indicate that CD109 is present in serum as a soluble form, and suggest its potential as a novel tumor marker in patients with cancers that express CD109.
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Affiliation(s)
- Hiroki Sakakura
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yoshiki Murakumo
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Shinji Mii
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Sumitaka Hagiwara
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takuya Kato
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masato Asai
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akiyoshi Hoshino
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Noriyuki Yamamoto
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Sayaka Sobue
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Masatoshi Ichihara
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Minoru Ueda
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masahide Takahashi
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- * E-mail:
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Burrows GG, Van't Hof W, Newell LF, Reddy A, Wilmarth PA, David LL, Raber A, Bogaerts A, Pinxteren J, Deans RJ, Maziarz RT. Dissection of the human multipotent adult progenitor cell secretome by proteomic analysis. Stem Cells Transl Med 2013; 2:745-57. [PMID: 23981727 DOI: 10.5966/sctm.2013-0031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Multipotent adult progenitor cells (MAPCs) are adult adherent stromal stem cells currently being assessed in acute graft versus host disease clinical trials with demonstrated immunomodulatory capabilities and the potential to ameliorate detrimental autoimmune and inflammation-related processes. Our previous studies documented that MAPCs secrete factors that play a role in regulating T-cell activity. Here we expand our studies using a proteomics approach to characterize and quantify MAPC secretome components secreted over 72 hours in vitro under steady-state conditions and in the presence of the inflammatory triggers interferon-γ and lipopolysaccharide, or a tolerogenic CD74 ligand, RTL1000. MAPCs differentially responded to each of the tested stimuli, secreting molecules that regulate the biological activity of the extracellular matrix (ECM), including proteins that make up the ECM itself, proteins that regulate its construction/deconstruction, and proteins that serve to attach and detach growth factors from ECM components for redistribution upon appropriate stimulation. MAPCs secreted a wide array of proteases, some detectable in their zymogen forms. MAPCs also secreted protease inhibitors that would regulate protease activity. MAPCs secreted chemokines and cytokines that could provide molecular guidance cues to various cell types, including neutrophils, macrophages, and T cells. In addition, MAPCs secreted factors involved in maintenance of a homeostatic environment, regulating such diverse programs as innate immunity, angiogenesis/angiostasis, targeted delivery of growth factors, and the matrix-metalloprotease cascade.
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32
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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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33
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Caccia D, Dugo M, Callari M, Bongarzone I. Bioinformatics tools for secretome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2442-53. [PMID: 23395702 DOI: 10.1016/j.bbapap.2013.01.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/23/2013] [Accepted: 01/29/2013] [Indexed: 12/29/2022]
Abstract
Over recent years, analyses of secretomes (complete sets of secreted proteins) have been reported in various organisms, cell types, and pathologies and such studies are quickly gaining popularity. Fungi secrete enzymes can break down potential food sources; plant secreted proteins are primarily parts of the cell wall proteome; and human secreted proteins are involved in cellular immunity and communication, and provide useful information for the discovery of novel biomarkers, such as for cancer diagnosis. Continuous development of methodologies supports the wide identification and quantification of secreted proteins in a given cellular state. The role of secreted factors is also investigated in the context of the regulation of major signaling events, and connectivity maps are built to describe the differential expression and dynamic changes of secretomes. Bioinformatics has become the bridge between secretome data and computational tasks for managing, mining, and retrieving information. Predictions can be made based on this information, contributing to the elucidation of a given organism's physiological state and the determination of the specific malfunction in disease states. Here we provide an overview of the available bioinformatics databases and software that are used to analyze the biological meaning of secretome data, including descriptions of the main functions and limitations of these tools. The important challenges of data analysis are mainly related to the integration of biological information from dissimilar sources. Improvements in databases and developments in software will likely substantially contribute to the usefulness and reliability of secretome studies. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Dario Caccia
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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34
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Lin Q, Tan HT, Lim HSR, Chung MCM. Sieving through the cancer secretome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2360-71. [PMID: 23376431 DOI: 10.1016/j.bbapap.2013.01.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/03/2013] [Accepted: 01/24/2013] [Indexed: 12/22/2022]
Abstract
Cancer is among the most prevalent and serious health problems worldwide. Therefore, there is an urgent need for novel cancer biomarkers with high sensitivity and specificity for early detection and management of the disease. The cancer secretome, encompassing all the proteins that are secreted by cancer cells, is a promising source of biomarkers as the secreted proteins are most likely to enter the blood circulation. Moreover, since secreted proteins are responsible for signaling and communication with the tumor microenvironment, studying the cancer secretome would further the understanding of cancer biology. Latest developments in proteomics technologies have significantly advanced the study of the cancer secretome. In this review, we will present an overview of the secretome sample preparation process and summarize the data from recent secretome studies of six common cancers with high mortality (breast, colorectal, gastric, liver, lung and prostate cancers). In particular, we will focus on the various platforms that were employed and discuss the clinical applicability of the key findings in these studies. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Qifeng Lin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore
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35
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Rabilloud T, Triboulet S. Two-dimensional SDS-PAGE fractionation of biological samples for biomarker discovery. Methods Mol Biol 2013; 1002:151-165. [PMID: 23625402 DOI: 10.1007/978-1-62703-360-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two-dimensional electrophoresis is still a very valuable tool in proteomics, due to its reproducibility and its ability to analyze complete proteins. However, due to its sensitivity to dynamic range issues, its most suitable use in the frame of biomarker discovery is not on very complex fluids such as plasma, but rather on more proximal, simpler fluids such as CSF, urine, or secretome samples. Here, we describe the complete workflow for the analysis of such dilute samples by two-dimensional electrophoresis, starting from sample concentration, then the two-dimensional electrophoresis step per se, ending with the protein detection by fluorescence.
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Affiliation(s)
- Thierry Rabilloud
- Chemistry and Biology of Metals Grenoble, CEA Grenoble, Grenoble, France
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36
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Abstract
Most biological processes including growth, proliferation, differentiation, and apoptosis are coordinated by tightly regulated signaling pathways, which also involve secreted proteins acting in an autocrine and/or paracrine manner. In addition, extracellular signaling molecules affect local niche biology and influence the cross-talking with the surrounding tissues. The understanding of this molecular language may provide an integrated and broader view of cellular regulatory networks under physiological and pathological conditions. In this context, the profiling at a global level of cell secretomes (i.e., the subpopulations of a proteome secreted from the cell) has become an active area of research. The current interest in secretome research also deals with its high potential for the biomarker discovery and the identification of new targets for therapeutic strategies. Several proteomic and mass spectrometry platforms and methodologies have been applied to secretome profiling of conditioned media of cultured cell lines and primary cells. Nevertheless, the analysis of secreted proteins is still a very challenging task, because of the technical difficulties that may hamper the subsequent mass spectrometry analysis. This chapter describes a typical workflow for the analysis of proteins secreted by cultured cells. Crucial issues related to cell culture conditions for the collection of conditioned media, secretome preparation, and mass spectrometry analysis are discussed. Furthermore, an overview of quantitative LC-MS-based approaches, computational tools for data analysis, and strategies for validation of potential secretome biomarkers is also presented.
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Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nat Biotechnol 2012; 30:984-90. [PMID: 23000932 DOI: 10.1038/nbt.2356] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/08/2012] [Indexed: 02/02/2023]
Abstract
Secreted proteins constitute a large and biologically important subset of proteins that are involved in cellular communication, adhesion and migration. Yet secretomes are understudied because of technical limitations in the detection of low-abundance proteins against a background of serum-containing media. Here we introduce a method that combines click chemistry and pulsed stable isotope labeling with amino acids in cell culture to selectively enrich and quantify secreted proteins. The combination of these two labeling approaches allows cells to be studied irrespective of the complexity of the background proteins. We provide an in-depth and differential secretome analysis of various cell lines and primary cells, quantifying secreted factors, including cytokines, chemokines and growth factors. In addition, we reveal that serum starvation has a marked effect on secretome composition. We also analyze the kinetics of protein secretion by macrophages in response to lipopolysaccharides.
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Chen HL, Seol H, Brown KJ, Gordish-Dressman H, Hill A, Gallo V, Packer R, Hathout Y. Secretome survey of human plexiform neurofibroma derived Schwann Cells reveals a secreted form of the RARRES1 protein. Int J Mol Sci 2012; 13:9380-9399. [PMID: 22942771 PMCID: PMC3430302 DOI: 10.3390/ijms13079380] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/12/2012] [Accepted: 07/19/2012] [Indexed: 01/28/2023] Open
Abstract
To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified in the conditioned media of Schwann cell cultures combined. Label free proteome profiling revealed consistent release of high levels of 22 proteins by the four biological replicates of NF1 Schwann cell cultures relative to the two normal Schwann cell cultures. Inversely, 9 proteins displayed decreased levels in the conditioned media of NF1 relative to normal Schwann cells. The proteins with increased levels included proteins involved in cell growth, angiogenesis and complement pathway while proteins with decreased levels included those involved in cell adhesion, plasminogen pathway and extracellular matrix remodeling. Retinoic acid receptor responder protein-1 (RARRES1), previously described as an integral membrane tumor suppressor, was found exclusively secreted by NF1 Schwann cells but not by normal Schwann cells. All-trans retinoic acid modulated secretion of RARRES1 in a dose dependent manner. This study shows altered secretion of key proteins in NF1 derived Schwann cells. The potential implication of these proteins in neurofibroma biology is discussed.
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Affiliation(s)
| | | | | | | | | | | | | | - Yetrib Hathout
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-202-476-3136; Fax: +1-202-476-6014
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Jin L, Zhang Y, Li H, Yao L, Fu D, Yao X, Xu LX, Hu X, Hu G. Differential secretome analysis reveals CST6 as a suppressor of breast cancer bone metastasis. Cell Res 2012; 22:1356-73. [PMID: 22688893 DOI: 10.1038/cr.2012.90] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bone metastasis is a frequent complication of breast cancer and a common cause of morbidity and mortality from the disease. During metastasis secreted proteins play crucial roles in the interactions between cancer cells and host stroma. To characterize the secreted proteins that are associated with breast cancer bone metastasis, we preformed a label-free proteomic analysis to compare the secretomes of four MDA-MB-231 (MDA231) derivative cell lines with varied capacities of bone metastasis. A total of 128 proteins were found to be consistently up-/down-regulated in the conditioned medium of bone-tropic cancer cells. The enriched molecular functions of the altered proteins included receptor binding and peptidase inhibition. Through additional transcriptomic analyses of breast cancer cells, we selected cystatin E/M (CST6), a cysteine protease inhibitor down-regulated in bone-metastatic cells, for further functional studies. Our results showed that CST6 suppressed the proliferation, colony formation, migration and invasion of breast cancer cells. The suppressive function against cancer cell motility was carried out by cancer cell-derived soluble CST6. More importantly, ectopic expression of CST6 in cancer cells rescued mice from overt osteolytic metastasis and deaths in the animal study, while CST6 knockdown markedly enhanced cancer cell bone metastasis and shortened animal survival. Overall, our study provided a systemic secretome analysis of breast cancer bone tropism and established secreted CST6 as a bona fide suppressor of breast cancer osteolytic metastasis.
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Affiliation(s)
- Lei Jin
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, 225 South Chongqing Rd, Shanghai 200025, China
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Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics 2012; 11:202-14. [PMID: 22454539 PMCID: PMC3418851 DOI: 10.1074/mcp.m112.017707] [Citation(s) in RCA: 350] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models.
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Affiliation(s)
- Birgit Schilling
- Buck Institute for Research on Aging, Novato, California 94945, USA
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Krautzberger AM, Kosiol B, Scholze M, Schrewe H. Expression of vasorin (Vasn) during embryonic development of the mouse. Gene Expr Patterns 2012; 12:167-71. [PMID: 22426063 DOI: 10.1016/j.gep.2012.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 02/28/2012] [Indexed: 01/25/2023]
Abstract
The murine vasorin (Vasn) gene, initially known as Slit-like 2, encodes a transmembrane protein that shares structural similarities with the eponymous Slit proteins. However, whether it also shares functional similarities with these large secreted proteins remains to be elucidated. Here, we report expression of Vasn during embryonic and fetal development of the mouse using whole-mount in situ hybridization (WISH) and histochemical detection of β-galactosidase expressed from a targeted Vasn(lacZ) knock-in allele. Comparison of whole-mount staining patterns of both approaches showed identical expression domains, confirming that Vasn promoter-driven β-galactosidase expression faithfully reflects endogenous Vasn expression. Vasn is highly expressed in vascular smooth muscle cells (hence the name), a finding consistent with a previous report on its human homolog VASN, whose extracellular domain was shown to function as a TGF-β trap (Ikeda et al., 2004). Most striking, however, is Vasn's prominent expression in the developing skeletal system, starting as early as the first mesenchymal condensations appear. Moreover, distinct expression domains outside the bones, e.g., in the developing kidneys and lungs, suggest further roles for this gene in the mouse. Recently, it was shown that mitochondria-localized Vasn protects cells from TNFα- and hypoxia-induced apoptosis, and partial deletion of the Vasn coding sequence leads to increased sensitivity of hepatocytes to TNFα-induced apoptosis (Choksi et al., 2011). By providing a first comprehensive analysis of the Vasn expression pattern during mouse embryonic development, our study will help to further elucidate its biological functions.
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Affiliation(s)
- A Michaela Krautzberger
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics. J Proteomics 2011; 75:1043-54. [PMID: 22079246 DOI: 10.1016/j.jprot.2011.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/16/2011] [Accepted: 10/22/2011] [Indexed: 01/21/2023]
Abstract
Human cell line secretome represents a valuable source of therapeutic targets and candidate biomarkers. Secreted proteins found in biological fluids or culture media are by essence highly diluted. Secretome investigation with proteomic approaches is hardly compatible with the high content of proteins found in complete cell culture media. Therefore, many studies are currently done with media containing few or no protein. Such conditions may perturb cell metabolism and proliferation. Here, we compared seventeen different compositions of culture media for the human bronchial epithelial BEAS-2B cell line. Cell viability, proliferation rate and initial protein charge were systematically compared. We have shown that an important difficulty for the proteomic analysis is due to the presence of detergents such as Pluronic F-68 which hinders peptide mass spectrometry. The high glucose containing DMEM medium which is free of proteins was shown to preserve a good viability and proliferation of cells. With this conditioning medium, we identified 81 extracellular proteins in the secretome of BEAS-2B cells. Moreover, to illustrate this approach, we exposed BEAS-2B cells to a low toxic dose of CoCl(2,) and found 24 extracellular proteins modulated by cobalt. This study highlights the possible contribution of such proteomic approach in the field of toxicology.
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