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Yu H, Xiao H, Deng H, Frew A, Hossain MA, Tan W, Xi B. Upgrade from aerated static pile to agitated bed systems promotes lignocellulose degradation in large-scale composting through enhanced microbial functional diversity. J Environ Sci (China) 2024; 144:55-66. [PMID: 38802238 DOI: 10.1016/j.jes.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 05/29/2024]
Abstract
Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21%-32.54%, 10.21%-39.41%, and 6.21%-26.78%) than those (5.72%-23.15%, 7.01%-33.26%, and 4.79%-19.76%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and β-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.
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Affiliation(s)
- Hanxia Yu
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Haoyan Xiao
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Huiyu Deng
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Adam Frew
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Md Akhter Hossain
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Suárez-Martínez E, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR, Carnero A. Protein homeostasis maintained by HOOK1 levels promotes the tumorigenic and stemness properties of ovarian cancer cells through reticulum stress and autophagy. J Exp Clin Cancer Res 2024; 43:150. [PMID: 38807192 PMCID: PMC11134651 DOI: 10.1186/s13046-024-03071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/18/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Ovarian cancer has a high mortality rate mainly due to its resistance to currently used therapies. This resistance has been associated with the presence of cancer stem cells (CSCs), interactions with the microenvironment, and intratumoral heterogeneity. Therefore, the search for new therapeutic targets, particularly those targeting CSCs, is important for improving patient prognosis. HOOK1 has been found to be transcriptionally altered in a substantial percentage of ovarian tumors, but its role in tumor initiation and development is still not fully understood. METHODS The downregulation of HOOK1 was performed in ovarian cancer cell lines using CRISPR/Cas9 technology, followed by growth in vitro and in vivo assays. Subsequently, migration (Boyden chamber), cell death (Western-Blot and flow cytometry) and stemness properties (clonal heterogeneity analysis, tumorspheres assay and flow cytometry) of the downregulated cell lines were analysed. To gain insights into the specific mechanisms of action of HOOK1 in ovarian cancer, a proteomic analysis was performed, followed by Western-blot and cytotoxicity assays to confirm the results found within the mass spectrometry. Immunofluorescence staining, Western-blotting and flow cytometry were also employed to finish uncovering the role of HOOK1 in ovarian cancer. RESULTS In this study, we observed that reducing the levels of HOOK1 in ovarian cancer cells reduced in vitro growth and migration and prevented tumor formation in vivo. Furthermore, HOOK1 reduction led to a decrease in stem-like capabilities in these cells, which, however, did not seem related to the expression of genes traditionally associated with this phenotype. A proteome study, along with other analysis, showed that the downregulation of HOOK1 also induced an increase in endoplasmic reticulum stress levels in these cells. Finally, the decrease in stem-like properties observed in cells with downregulated HOOK1 could be explained by an increase in cell death in the CSC population within the culture due to endoplasmic reticulum stress by the unfolded protein response. CONCLUSION HOOK1 contributes to maintaining the tumorigenic and stemness properties of ovarian cancer cells by preserving protein homeostasis and could be considered an alternative therapeutic target, especially in combination with inducers of endoplasmic reticulum or proteotoxic stress such as proteasome inhibitors.
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Affiliation(s)
- Elisa Suárez-Martínez
- Instituto de Biomedicina de Sevilla (IBIS), HUVR/CSIC/Universidad de Sevilla, Avda. Manuel Siurot S/N; Campus HUVR, Ed. IBIS,, Seville, 41013, Spain
- CIBER de Cancer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Sander R Piersma
- OncoProteomics Laboratory, VUmc-Cancer Center Amsterdam, VU University Medical Center, CCA 1-60, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, VUmc-Cancer Center Amsterdam, VU University Medical Center, CCA 1-60, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Irene V Bijnsdorp
- OncoProteomics Laboratory, VUmc-Cancer Center Amsterdam, VU University Medical Center, CCA 1-60, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, VUmc-Cancer Center Amsterdam, VU University Medical Center, CCA 1-60, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla (IBIS), HUVR/CSIC/Universidad de Sevilla, Avda. Manuel Siurot S/N; Campus HUVR, Ed. IBIS,, Seville, 41013, Spain.
- CIBER de Cancer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
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Almeida-Marques C, Rolfs F, Piersma SR, Bijnsdorp IV, Pham TV, Knol JC, Jimenez CR. Secretome processing for proteomics: A methods comparison. Proteomics 2024; 24:e2300262. [PMID: 38221716 DOI: 10.1002/pmic.202300262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment with high detectability in biofluids. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: (1) Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); (2) Acetone protein precipitation coupled to IGD; (3) MWCO filter-based protein concentration followed by to in-solution digestion (ISD); (4) Acetone protein precipitation coupled to ISD; (5) Direct ISD; (6) Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines, and growth factors. Our findings revealed that acetone protein precipitation coupled to ISD outperformed the other methods in terms of the number of identified proteins (2246) and method reproducibility (correlation coefficient between replicates (r = 0.94, CV = 19%). Overall, especially small proteins such as those from the classes mentioned above were better identified using ISD workflows. Concluding, herein we report that secretome protein precipitation coupled to ISD is the method of choice for high-throughput secretome proteomics via single shot nanoLC-MS/MS.
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Affiliation(s)
- Catarina Almeida-Marques
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
| | - Frank Rolfs
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
| | - Sander R Piersma
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
| | - Irene V Bijnsdorp
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
- Department Urology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Thang V Pham
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
| | - Jaco C Knol
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
| | - Connie R Jimenez
- Department Laboratory Medical Oncology, Amsterdam University Medical Center, Amsterdam, Netherlands
- Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands
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Gali A, Bijnsdorp IV, Piersma SR, Pham TV, Gutiérrez-Galindo E, Kühnel F, Tsolakos N, Jimenez CR, Hausser A, Alexopoulos LG. Protein kinase D drives the secretion of invasion mediators in triple-negative breast cancer cell lines. iScience 2024; 27:108958. [PMID: 38323010 PMCID: PMC10844833 DOI: 10.1016/j.isci.2024.108958] [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: 05/02/2023] [Revised: 11/28/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Abstract
The protein kinase D (PKD) family members regulate the fission of cargo vesicles at the Golgi complex and play a pro-oncogenic role in triple-negative breast cancer (TNBC). Whether PKD facilitates the secretion of tumor-promoting factors in TNBC, however, is still unknown. Using the pharmacological inhibition of PKD activity and siRNA-mediated depletion of PKD2 and PKD3, we identified the PKD-dependent secretome of the TNBC cell lines MDA-MB-231 and MDA-MB-468. Mass spectrometry-based proteomics and antibody-based assays revealed a significant downregulation of extracellular matrix related proteins and pro-invasive factors such as LIF, MMP-1, MMP-13, IL-11, M-CSF and GM-CSF in PKD-perturbed cells. Notably, secretion of these proteins in MDA-MB-231 cells was predominantly controlled by PKD2 and enhanced spheroid invasion. Consistently, PKD-dependent secretion of pro-invasive factors was more pronounced in metastatic TNBC cell lines. Our study thus uncovers a novel role of PKD2 in releasing a pro-invasive secretome.
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Affiliation(s)
- Alexia Gali
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Irene V. Bijnsdorp
- Department of Urology, Cancer Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, Amsterdam 1081 HV, the Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | | | - Fiona Kühnel
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Nikos Tsolakos
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, OncoProteomics Laboratory, de Boelelaan 1117, , Amsterdam 1081 HV, the Netherlands
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Leonidas G. Alexopoulos
- Biomedical Systems Laboratory, National Technical University of Athens, 15780 Athens, Greece
- Protavio Ltd, Demokritos Science Park, 15341 Athens, Greece
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Meulendijks ER, Al-Shama RFM, Kawasaki M, Fabrizi B, Neefs J, Wesselink R, Ernault AC, Piersma S, Pham TV, Jimenez CR, Knol JC, van Boven WJP, Driessen AHG, de Vries TAC, van der Leeden B, Niessen HWM, de Boer OJ, Krul SPJ, de Groot JR. Atrial epicardial adipose tissue abundantly secretes myeloperoxidase and activates atrial fibroblasts in patients with atrial fibrillation. J Transl Med 2023; 21:366. [PMID: 37280612 DOI: 10.1186/s12967-023-04231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Epicardial adipose tissue (EAT) secretome induces fibrosis. Fibrosis, primarily extracellular matrix (ECM) produced by fibroblasts, creates a substrate for atrial fibrillation (AF). Whether the EAT secretome from patients with AF activates human atrial fibroblasts and through which components, remains unexplored. RESEARCH AIMS (a) To investigate if the EAT secretome from patients with versus without AF increases ECM production in atrial fibroblasts. (b) To identify profibrotic proteins and processes in the EAT secretome and EAT from patients with, who will develop (future onset), and without AF. METHODS Atrial EAT was obtainded during thoracoscopic ablation (AF, n = 20), or open-heart surgery (future onset and non-AF, n = 35). ECM gene expression of human atrial fibroblasts exposed to the EAT secretome and the proteomes of EAT secretome and EAT were assessed in patients with and without AF. Myeloperoxidase and neutrophil extracellular traps (NETs) were assessed immunohistochemically in patients with paroxysmal, persistent, future onset, and those who remain free of AF (non-AF). RESULTS The expression of COL1A1 and FN1 in fibroblasts exposed to secretome from patients with AF was 3.7 and 4.7 times higher than in patients without AF (p < 0.05). Myeloperoxidase was the most increased protein in the EAT secretome and EAT from patients with versus without AF (FC 18.07 and 21.57, p < 0.005), as was the gene-set neutrophil degranulation. Immunohistochemically, myeloperoxidase was highest in persistent (FC 13.3, p < 0.0001) and increased in future onset AF (FC 2.4, p = 0.02) versus non-AF. Myeloperoxidase aggregated subepicardially and around fibrofatty infiltrates. NETs were increased in patients with persistent versus non-AF (p = 0.03). CONCLUSION In AF, the EAT secretome induces ECM gene expression in atrial fibroblasts and contains abundant myeloperoxidase. EAT myeloperoxidase was increased prior to AF onset, and both myeloperoxidase and NETs were highest in persistent AF, highlighting the role of EAT neutrophils in the pathophysiology of AF.
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Affiliation(s)
- Eva R Meulendijks
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands.
| | - Rushd F M Al-Shama
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
| | - Makiri Kawasaki
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - Benedetta Fabrizi
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - Jolien Neefs
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin Wesselink
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
| | - Auriane C Ernault
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
| | - Sander Piersma
- Amsterdam UMC, VU Medical Center, Department of Medical Oncology, VU university, Amsterdam, The Netherlands
| | - Thang V Pham
- Amsterdam UMC, VU Medical Center, Department of Medical Oncology, VU university, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, VU Medical Center, Department of Medical Oncology, VU university, Amsterdam, The Netherlands
| | - Jaco C Knol
- Amsterdam UMC, VU Medical Center, Department of Medical Oncology, VU university, Amsterdam, The Netherlands
| | - Wim J P van Boven
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H G Driessen
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
| | - Tim A C de Vries
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Department of Cardiology, Rijnstate Hospital, Arnhem, The Netherlands
| | - Britt van der Leeden
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
- Amsterdam UMC, Department of Pathology, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC, Infection & Immunity, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans W M Niessen
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
- Amsterdam UMC, Department of Pathology, University of Amsterdam, Amsterdam, The Netherlands
| | - Onno J de Boer
- Amsterdam UMC, Department of Pathology, University of Amsterdam, Amsterdam, The Netherlands
| | - Sébastien P J Krul
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Department of Cardiology, Isala Heart Centre, Zwolle, The Netherlands
| | - Joris R de Groot
- Amsterdam UMC, Heart Center, Department of Clinical and Experimental Cardiology and Cardiothoracic Surgery, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure and Arrhythmias, Amsterdam, The Netherlands
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Mumtaz M, Bijnsdorp IV, Böttger F, Piersma SR, Pham TV, Mumtaz S, Brakenhoff RH, Akhtar MW, Jimenez CR. Secreted protein markers in oral squamous cell carcinoma (OSCC). Clin Proteomics 2022; 19:4. [PMID: 35130834 PMCID: PMC8903575 DOI: 10.1186/s12014-022-09341-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is a main cause of oral cancer mortality and morbidity in central south Asia. To improve the clinical outcome of OSCC patients, detection markers are needed, which are preferably non-invasive and thus independent of a tissue biopsy. Methods In the present study, we aimed to identify robust candidate protein biomarkers for non-invasive OSCC diagnosis. To this end, we measured the global protein profiles of OSCC tissue lysates to matched normal adjacent mucosa samples (n = 14) and the secretomes of nine HNSCC cell lines using LC–MS/MS-based proteomics. Results A total of 5123 tissue proteins were identified, of which 205 were robustly up- regulated (p-value < 0.01, fold change > + 2) in OSCC-tissues compared to normal adjacent tissues. The biological process “Secretion” was highly enriched in this set of proteins. Other upregulated biological pathways included “Unfolded Protein Response”, “Spliceosomal complex assembly”, “Protein localization to endosome” and “Interferon Gamma Response”. Transcription factor analysis implicated Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP as potential regulators. Of the 205 upregulated tissue proteins, 132 were identified in the cancer cell line secretomes, underscoring their potential use as non-invasive biofluid markers. To further prioritize our candidate markers for non-invasive OSCC detection, we integrated our data with public biofluid datasets including OSCC saliva, yielding 25 candidate markers for further study. Conclusions We identified several key proteins and processes that are associated with OSCC tissues, underscoring the importance of altered secretion. Cancer-associated OSCC secretome proteins present in saliva have potential to be used as novel non-invasive biomarkers for the diagnosis of OSCC. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09341-5.
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Affiliation(s)
- Madiha Mumtaz
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Irene V Bijnsdorp
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.,Department of Urology, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Franziska Böttger
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | | | - Ruud H Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M Waheed Akhtar
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam UMC, VU University Medical Center, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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Kumari M, Pradhan UK, Joshi R, Punia A, Shankar R, Kumar R. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC PLANT BIOLOGY 2021; 21:604. [PMID: 34937558 PMCID: PMC8693493 DOI: 10.1186/s12870-021-03394-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. RESULTS We were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. CONCLUSIONS This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.
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Affiliation(s)
- Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upendra Kumar Pradhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
- Present address: ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, 110012, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Erozenci LA, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR. Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. Sci Rep 2021; 11:15629. [PMID: 34341426 PMCID: PMC8329217 DOI: 10.1038/s41598-021-95082-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.
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Affiliation(s)
- Leyla A. Erozenci
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands ,grid.509540.d0000 0004 6880 3010Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Sander R. Piersma
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Thang V. Pham
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Irene V. Bijnsdorp
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands ,grid.509540.d0000 0004 6880 3010Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Connie R. Jimenez
- grid.509540.d0000 0004 6880 3010Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
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9
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Effects of Cancer Presence and Therapy on the Platelet Proteome. Int J Mol Sci 2021; 22:ijms22158236. [PMID: 34361002 PMCID: PMC8347210 DOI: 10.3390/ijms22158236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022] Open
Abstract
Platelets are involved in tumor angiogenesis and cancer progression. Previous studies indicated that cancer could affect platelet content. In the current study, we investigated whether cancer-associated proteins can be discerned in the platelets of cancer patients, and whether antitumor treatment may affect the platelet proteome. Platelets were isolated from nine patients with different cancer types and ten healthy volunteers. From three patients, platelets were isolated before and after the start of antitumor treatment. Mass spectrometry-based proteomics of gel-fractionated platelet proteins were used to compare patients versus controls and before and after treatment initiation. A total of 4059 proteins were detected, of which 50 were significantly more abundant in patients, and 36 more in healthy volunteers. Eight of these proteins overlapped with our previous cancer platelet proteomics study. From these data, we selected potential biomarkers of cancer including six upregulated proteins (RNF213, CTSG, PGLYRP1, RPL8, S100A8, S100A9) and two downregulated proteins (GPX1, TNS1). Antitumor treatment resulted in increased levels of 432 proteins and decreased levels of 189 proteins. In conclusion, the platelet proteome may be affected in cancer patients and platelets are a potential source of cancer biomarkers. In addition, we found in a small group of patients that anticancer treatment significantly changes the platelet proteome.
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10
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Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep 2021; 22:e51913. [PMID: 33890711 PMCID: PMC8183412 DOI: 10.15252/embr.202051913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/- ) CRC models and an indirect co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that the absence of Ndrg4 does not trigger any functional or morphological GI abnormalities. However, combining in vivo, in vitro, and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance migration capacities of CRC cells, and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
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Affiliation(s)
- Nathalie Vaes
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Simone L Schonkeren
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Glenn Rademakers
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Amy M Holland
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Marion J Gijbels
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Molecular GeneticsCardiovascular Research Institute Maastricht (CARIM)MaastrichtThe Netherlands
- Department of Medical BiochemistryAcademic Medical CenterAmsterdamThe Netherlands
| | - Tom G Keulers
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Meike de Wit
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Laura Moonen
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jaleesa R M Van der Meer
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Edith van den Boezem
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Tim G A M Wolfs
- Department of PediatricsGROW‐School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - David W Threadgill
- Department of Molecular and Cellular MedicineTexas A&M University Health Science CenterCollege StationTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Jeroen Demmers
- Proteomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS) and Translational Research Center for Gastrointestinal Disorders (TARGID)Department of Chronic Diseases, Metabolism and AgeingKU LeuvenLeuvenBelgium
| | - Kim M Smits
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Kasper M A Rouschop
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Werend Boesmans
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Biomedical Research Institute (BIOMED)Hasselt UniversityHasseltBelgium
| | - Robert M W Hofstra
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
| | - Veerle Melotte
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
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11
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Garcia de Durango CR, Monteiro MN, Bijnsdorp IV, Pham TV, De Wit M, Piersma SR, Knol JC, Pérez-Gordo M, Fijneman RJA, Vidal-Vanaclocha F, Jimenez CR. Lipopolysaccharide-regulated secretion of soluble and vesicle-based proteins from a panel of colorectal cancer cell lines. Proteomics Clin Appl 2021; 15:e1900119. [PMID: 33587312 DOI: 10.1002/prca.201900119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/15/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023]
Abstract
PURPOSE To mimic the perioperative microenvironment where bacterial products get in contact with colorectal cancer (CRC) cells and study its impact on protein release, we exposed six CRC cell lines to lipopolysaccharide (LPS) and investigated the effect on the secretome using in-depth mass spectrometry-based proteomics. EXPERIMENTAL DESIGN Cancer cell secretome was harvested in bio-duplicate after LPS treatment, and separated in EV and soluble secretome (SS) fractions. Gel-fractionated proteins were analysed by label-free nano-liquid chromatography coupled to tandem mass spectrometry. NF-κB activation, triggered upon LPS treatment, was evaluated. RESULTS We report a CRC secretome dataset of 5601 proteins. Comparison of all LPS-treated cells with controls revealed 37 proteins with altered abundance in the SS, including RPS25; and 13 in EVs, including HMGB1. Comparing controls and LPS-treated samples per cell line, revealed 564 significant differential proteins with fold-change >3. The LPS-induced release of RPS25 was validated by western blot. CONCLUSIONS AND CLINICAL RELEVANCE Bacterial endotoxin has minor impact on the global CRC cell line secretome, yet it may alter protein release in a cell line-specific manner. This modulation might play a role in orchestrating the development of a permissive environment for CRC liver metastasis, especially through EV-communication.
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Affiliation(s)
- Cira R Garcia de Durango
- Instituto de Medicina Molecular Aplicada, Universidad CEU San Pablo, Pathology Institute Munich, DKTK Partner Site, Madrid, Munich, Spain, Germany
| | - Madalena N Monteiro
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Irene V Bijnsdorp
- Department of Urology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Thang V Pham
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Meike De Wit
- Department of Urology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sander Rogier Piersma
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jaco C Knol
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marina Pérez-Gordo
- Instituto de Medicina Molecular Aplicada, Universidad CEU San Pablo, Pathology Institute Munich, DKTK Partner Site, Madrid, Munich, Spain, Germany
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fernando Vidal-Vanaclocha
- Valencia Institute of Pathology (IVP), Catholic University of Valencia School of Medicine and Odontology, Valencia, Spain
| | - Connie R Jimenez
- Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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12
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Bögels M, Braster R, Nijland PG, Gül N, van de Luijtgaarden W, Fijneman RJA, Meijer GA, Jimenez CR, Beelen RHJ, van Egmond M. Carcinoma origin dictates differential skewing of monocyte function. Oncoimmunology 2021; 1:798-809. [PMID: 23162747 PMCID: PMC3489735 DOI: 10.4161/onci.20427] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Macrophages are versatile cells, which phenotype is profoundly influenced by their environment. Pro-inflammatory classically activated or M1 macrophages, and anti-inflammatory alternatively-activated or M2 macrophages represent two extremes of a continuum of functional states. Consequently, macrophages that are present in tumors can exert tumor-promoting and tumor-suppressing activity, depending on the tumor milieu. In this study we investigated how human monocytes-the precursors of macrophages-are influenced by carcinoma cells of different origin. We demonstrate that monocytes, stimulated with breast cancer supernatant, showed increased expression of interleukin (IL)-10, IL-8 and chemokines CCL17 and CCL22, which are associated with an alternatively-activated phenotype. By contrast, monocytes that were cultured in supernatants of colon cancer cells produced more pro-inflammatory cytokines (e.g., IL-12 and TNFα) and reactive oxygen species. Secretome analysis revealed differential secretion of proteins by colon and breast cancer cell lines, of which the proteoglycan versican was exclusively secreted by colon carcinoma cell lines. Reducing active versican by blocking with monoclonal antibodies or shRNA diminished pro-inflammatory cytokine production by monocytes. Thus, colon carcinoma cells polarize monocytes toward a more classically-activated anti-tumorigenic phenotype, whereas breast carcinomas predispose monocytes toward an alternatively activated phenotype. Interestingly, presence of macrophages in breast or colon carcinomas correlates with poor or good prognosis in patients, respectively. The observed discrepancy in macrophage activation by either colon or breast carcinoma cells may therefore explain the dichotomy between patient prognosis and macrophage presence in these different tumors. Designing new therapies, directing development of monocytes toward M1 activated tumor macrophages in cancer patients, may have great clinical benefits.
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Affiliation(s)
- Marijn Bögels
- Department of Surgery; VU University Medical Center; Amsterdam, The Netherlands ; Department of Molecular Cell Biology and Immunology; VU University Medical Center; Amsterdam, The Netherlands
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13
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Ji X, Huang S, Zhang J, Bruce TF, Tan Z, Wang D, Zhu J, Marcus RK, Lubman DM. A novel method of high-purity extracellular vesicle enrichment from microliter-scale human serum for proteomic analysis. Electrophoresis 2021; 42:245-256. [PMID: 33169421 PMCID: PMC8018574 DOI: 10.1002/elps.202000223] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023]
Abstract
We have developed a rapid, low-cost, and simple separation strategy to separate extracellular vesicles (EVs) from a small amount of serum (i.e.,<100 μL) with minimal contamination by serum proteins and lipoprotein particles to meet the high purity requirement for EV proteome analysis. EVs were separated by a novel polyester capillary channel polymer (PET C-CP) fiber phase/hydrophobic interaction chromatography (HIC) method which is rapid and can process small size samples. The collected EV fractions were subjected to a post-column cleanup protocol using a centrifugal filter to perform buffer exchange and eliminate potential coeluting non-EV proteins while minimizing EV sample loss. Downstream characterization demonstrated that our current strategy can separate EVs with the anticipated exosome-like particle size distribution and high yield (∼1 × 1011 EV particles per mL of serum) in approximately 15 min. Proteome profiling of the EVs reveals that a group of genuine EV components were identified that have significantly less high-abundance blood proteins and lipoprotein particle contamination in comparison to traditional separation methods. The use of this methodology appears to address the major challenges facing EV separation for proteomics analysis. In addition, the EV post-column cleanup protocol proposed in the current work has the potential to be combined with other separation methods, such as ultracentrifugation (UC), to further purify the separated EV samples.
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Affiliation(s)
- Xiaohui Ji
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, P. R. China
| | - Sisi Huang
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Terri F. Bruce
- Department of Bioengineering, Life Sciences Facility, Clemson University, Clemson, SC, USA
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Donglin Wang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, P. R. China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - R. Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
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14
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Glykofridis IE, Knol JC, Balk JA, Westland D, Pham TV, Piersma SR, Lougheed SM, Derakhshan S, Veen P, Rooimans MA, van Mil SE, Böttger F, Poddighe PJ, van de Beek I, Drost J, Zwartkruis FJ, de Menezes RX, Meijers-Heijboer HE, Houweling AC, Jimenez CR, Wolthuis RM. Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells. eLife 2021; 10:61630. [PMID: 33459596 PMCID: PMC7899648 DOI: 10.7554/elife.61630] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Germline mutations in the Folliculin (FLCN) tumor suppressor gene cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing carriers to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanism by which FLCN prevents kidney cancer remains unknown. Here, we show that disrupting FLCN in human renal tubular epithelial cells (RPTEC/TERT1) activates TFE3, upregulating expression of its E-box targets, including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, the absence of FLCN or its binding partners FNIP1/FNIP2 induces interferon response genes independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence immune responses. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.
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Affiliation(s)
- Iris E Glykofridis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jaco C Knol
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jesper A Balk
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Denise Westland
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | - Thang V Pham
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sander R Piersma
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sinéad M Lougheed
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Sepide Derakhshan
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Puck Veen
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Martin A Rooimans
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Saskia E van Mil
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Franziska Böttger
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Pino J Poddighe
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Irma van de Beek
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, Heidelberglaan, Utrecht, Netherlands
| | - Fried Jt Zwartkruis
- University Medical Center Utrecht, Center for Molecular Medicine, Molecular Cancer Research, Universiteitsweg, Utrecht, Netherlands
| | | | - Hanne Ej Meijers-Heijboer
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Arjan C Houweling
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Amsterdam, Netherlands
| | - Connie R Jimenez
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Rob Mf Wolthuis
- Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands
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15
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Huang W, Liao CC, Han Y, Lv J, Lei M, Li Y, Lv Q, Dong D, Zhang S, Pan YH, Luo J. Co-activation of Akt, Nrf2, and NF-κB signals under UPR ER in torpid Myotis ricketti bats for survival. Commun Biol 2020; 3:658. [PMID: 33177645 PMCID: PMC7658203 DOI: 10.1038/s42003-020-01378-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022] Open
Abstract
Bats hibernate to survive stressful conditions. Examination of whole cell and mitochondrial proteomes of the liver of Myotis ricketti revealed that torpid bats had endoplasmic reticulum unfolded protein response (UPRER), global reduction in glycolysis, enhancement of lipolysis, and selective amino acid metabolism. Compared to active bats, torpid bats had higher amounts of phosphorylated serine/threonine kinase (p-Akt) and UPRER markers such as PKR-like endoplasmic reticulum kinase (PERK) and activating transcription factor 4 (ATF4). Torpid bats also had lower amounts of the complex of Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) (p65)/I-κBα. Cellular redistribution of 78 kDa glucose-regulated protein (GRP78) and reduced binding between PERK and GRP78 were also seen in torpid bats. Evidence of such was not observed in fasted, cold-treated, or normal mice. These data indicated that bats activate Akt, Nrf2, and NF-κB via the PERK-ATF4 regulatory axis against endoplasmic reticulum stresses during hibernation.
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Affiliation(s)
- Wenjie Huang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei, 11221, Taiwan
| | - Yijie Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junyan Lv
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Ming Lei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangyang Li
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Qingyun Lv
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yi-Husan Pan
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Jian Luo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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16
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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17
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Zubair H, Patel GK, Khan MA, Azim S, Zubair A, Singh S, Srivastava SK, Singh AP. Proteomic Analysis of MYB-Regulated Secretome Identifies Functional Pathways and Biomarkers: Potential Pathobiological and Clinical Implications. J Proteome Res 2020; 19:794-804. [PMID: 31928012 DOI: 10.1021/acs.jproteome.9b00641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Earlier we have shown important roles of MYB in pancreatic tumor pathobiology. To better understand the role of MYB in the tumor microenvironment and identify MYB-associated secreted biomarker proteins, we conducted mass spectrometry analysis of the secretome from MYB-modulated and control pancreatic cancer cell lines. We also performed in silico analyses to determine MYB-associated biofunctions, gene networks, and altered biological pathways. Our data demonstrated significant modulation (p < 0.05) of 337 secreted proteins in MYB-silenced MiaPaCa cells, whereas 282 proteins were differentially present in MYB-overexpressing BxPC3 cells, compared to their respective control cells. Alteration of several phenotypes such as cellular movement, cell death and survival, inflammatory response, protein synthesis, etc. was associated with MYB-induced differentially expressed proteins (DEPs) in secretomes. DEPs from MYB-silenced MiaPaCa PC cells were suggestive of the downregulation of genes primarily associated with glucose metabolism, PI3K/AKT signaling, and oxidative stress response, among others. DEPs from MYB-overexpressing BxPC3 cells suggested the enhanced release of proteins associated with glucose metabolism and cellular motility. We also observed that MYB positively regulated the expression of four proteins with potential biomarker properties, i.e., FLNB, ENO1, ITGB1, and INHBA. Mining of publicly available databases using Oncomine and UALCAN demonstrated that these genes are overexpressed in pancreatic tumors and associated with reduced patient survival. Altogether, these data provide novel avenues for future investigations on diverse biological functions of MYB, specifically in the tumor microenvironment, and could also be exploited for biomarker development.
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Affiliation(s)
- Haseeb Zubair
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Girijesh Kumar Patel
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Mohammad Aslam Khan
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Shafquat Azim
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Asif Zubair
- Molecular and Computational Biology, School of Biological Sciences, Dornsife College of Letters, Arts and Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Seema Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
| | - Sanjeev Kumar Srivastava
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
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18
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Le Large TY, Meijer LL, Paleckyte R, Boyd LN, Kok B, Wurdinger T, Schelfhorst T, Piersma SR, Pham TV, van Grieken NC, Zonderhuis BM, Daams F, van Laarhoven HW, Bijlsma MF, Jimenez CR, Giovannetti E, Kazemier G. Combined Expression of Plasma Thrombospondin-2 and CA19-9 for Diagnosis of Pancreatic Cancer and Distal Cholangiocarcinoma: A Proteome Approach. Oncologist 2020; 25:e634-e643. [PMID: 31943574 PMCID: PMC7160420 DOI: 10.1634/theoncologist.2019-0680] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background Minimally invasive diagnostic biomarkers for patients with pancreatic ductal adenocarcinoma (PDAC) and distal cholangiocarcinoma (dCCA) are warranted to facilitate accurate diagnosis. This study identified diagnostic plasma proteins based on proteomics of tumor secretome. Materials and Methods Secretome of tumor and normal tissue was collected after resection of PDAC and dCCA. Differentially expressed proteins were measured by mass spectrometry. Selected candidate biomarkers and carbohydrate antigen 19‐9 (CA19‐9) were validated by enzyme‐linked immunosorbent assay in plasma from patients with PDAC (n = 82), dCCA (n = 29), benign disease (BD; n = 30), and healthy donors (HDs; n = 50). Areas under the curve (AUCs) of receiver operator characteristic curves were calculated to determine the discriminative power. Results In tumor secretome, 696 discriminatory proteins were identified, including 21 candidate biomarkers. Thrombospondin‐2 (THBS2) emerged as promising biomarker. Abundance of THBS2 in plasma from patients with cancer was significantly higher compared to HDs (p < .001, AUC = 0.844). Combined expression of THBS2 and CA19‐9 yielded the optimal discriminatory capacity (AUC = 0.952), similarly for early‐ and late‐stage disease (AUC = 0.971 and AUC = 0.911). Remarkably, this combination demonstrated a power similar to CA19‐9 to discriminate cancer from BD (AUC = 0.764), and THBS2 provided an additive value in patients with high expression levels of bilirubin. Conclusion Our proteome approach identified a promising set of candidate biomarkers. The combined plasma expression of THBS2/CA19‐9 is able to accurately distinguish patients with PDAC or dCCA from HD and BD. Implications for Practice The combined plasma expression of thrombospondin‐2 and carbohydrate antigen 19‐9 is able to accurately diagnose patients with pancreatic cancer and distal cholangiocarcinoma. This will facilitate minimally invasive diagnosis for these patients by distinguishing them from healthy individuals and benign diseases. This article identifies diagnostic plasma proteins to distinguish patients with pancreatic ductal adenocarcinoma and distal cholangiocarcinoma from benign disease and health donors and evaluates these new markers for additive value with CA19‐9 at different disease stages.
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Affiliation(s)
- Tessa Y.S. Le Large
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Laura L. Meijer
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Rosita Paleckyte
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Lenka N.C. Boyd
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Bart Kok
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Tim Schelfhorst
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Nicole C.T. van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Barbara M. Zonderhuis
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Freek Daams
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Hanneke W.M. van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Maarten F. Bijlsma
- Laboratory of Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam University Medical Center, University of AmsterdamAmsterdamThe Netherlands
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
- Cancer Pharmacology Lab, Associazione Italiana per la Ricerca sul Cancro (AIRC) Start‐Up Unit, Fondazione Pisana per la Scienza, University of PisaPisaItaly
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU UniversityAmsterdamThe Netherlands
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19
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Poel D, Boyd LN, Beekhof R, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Jimenez CR, Verheul HM, Buffart TE. Proteomic Analysis of miR-195 and miR-497 Replacement Reveals Potential Candidates that Increase Sensitivity to Oxaliplatin in MSI/P53wt Colorectal Cancer Cells. Cells 2019; 8:cells8091111. [PMID: 31546954 PMCID: PMC6770888 DOI: 10.3390/cells8091111] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/17/2022] Open
Abstract
Most patients with advanced colorectal cancer (CRC) eventually develop resistance to systemic combination therapy. miR-195-5p and miR-497-5p are downregulated in CRC tissues and associated with drug resistance. Sensitization to 5-FU, oxaliplatin, and irinotecan by transfection with miR-195-5p and miR-497-5p mimics was studied using cell viability and clonogenic assays in cell lines HCT116, RKO, DLD-1, and SW480. In addition, proteomic analysis of transfected cells was implemented to identify potential targets. Significantly altered proteins were subjected to STRING (protein-protein interaction networks) database analysis to study the potential mechanisms of drug resistance. Cell viability analysis of transfected cells revealed increased sensitivity to oxaliplatin in microsatellite instable (MSI)/P53 wild-type HCT116 and RKO cells. HCT116 transfected cells formed significantly fewer colonies when treated with oxaliplatin. In sensitized cells, proteomic analysis showed 158 and 202 proteins with significantly altered expression after transfection with miR-195-5p and miR-497-5p mimics respectively, of which CHUK and LUZP1 proved to be coinciding downregulated proteins. Resistance mechanisms of these proteins may be associated with nuclear factor kappa-B signaling and G1 cell-cycle arrest. In conclusion, miR-195-5p and miR-497-5p replacement enhanced sensitivity to oxaliplatin in treatment naïve MSI/P53 wild-type CRC cells. Proteomic analysis revealed potential miRNA targets associated with the cell-cycle which possibly bare a relation with chemotherapy sensitivity.
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Affiliation(s)
- Dennis Poel
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Department of Medical Oncology, Radboud University medical center, 6525GA Nijmegen, The Netherlands
| | - Lenka N.C. Boyd
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Robin Beekhof
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Tim Schelfhorst
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Jaco C. Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
| | - Henk M.W. Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Department of Medical Oncology, Radboud University medical center, 6525GA Nijmegen, The Netherlands
| | - Tineke E. Buffart
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands; (D.P.); (R.B.); (T.S.); (T.V.P.); (S.R.P.); (J.C.K.); (C.R.J.)
- Antoni van Leeuwenhoek, Department of Gastrointestinal Oncology, 1066CX Amsterdam, The Netherlands
- Correspondence: ; Tel.: +20-5122-566
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20
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Böttger F, Schaaij-Visser TB, de Reus I, Piersma SR, Pham TV, Nagel R, Brakenhoff RH, Thunnissen E, Smit EF, Jimenez CR. Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction. J Proteomics 2019; 196:106-119. [DOI: 10.1016/j.jprot.2019.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
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21
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Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies. J Proteomics 2018; 192:27-36. [PMID: 30071318 DOI: 10.1016/j.jprot.2018.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/17/2018] [Accepted: 07/16/2018] [Indexed: 12/11/2022]
Abstract
Nephronophthisis is one of the leading genetic causes of end-stage renal disease in childhood. Early diagnostics and prognostics for nephronophthisis are currently limited. We aimed to identify non-invasive protein biomarkers for nephronophthisis in urinary extracellular vesicles. Extracellular vesicles were isolated from urine of 12 patients with a nephronophthisis-related ciliopathy and 12 age- and gender-matched controls, followed by in-depth label-free LC-MS/MS proteomics analysis of gel fractionated extracellular vesicle proteins. Supervised cluster analysis of proteomic profiles separated patients from controls. We identified 156 differentially expressed proteins with fold change ≥4 in patients compared to controls (P < .05). Importantly, expression levels of discriminating proteins were correlated with chronic kidney disease stage, suggesting possible applications for urinary extracellular vesicle biomarkers in prognostics for nephronophthisis. Enrichment analysis of gene ontology terms revealed GO terms including signaling, actin cytoskeleton and endocytosis among the downregulated proteins in patients, whereas terms related to response to wounding and extracellular matrix organization were enriched among upregulated proteins. Our findings represent the first step towards a non-invasive diagnostic test for nephronophthisis. Further research is needed to determine specificity of the candidate biomarkers. In conclusion, proteomic profiles of urinary extracellular vesicles differentiate nephronophthisis-related ciliopathy patients from healthy controls. SIGNIFICANCE: Nephronophthisis is an important cause of end-stage renal disease in children and is associated with an average diagnostic delay of 3.5 years. This is the first study investigating candidate biomarkers for nephronophthisis using global proteomics analysis of urinary extracellular vesicles in patients with nephronophthisis compared to control individuals. We show that measuring protein markers in urinary extracellular vesicles is a promising approach for non-invasive early diagnostics of nephronophthisis.
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22
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Warmoes M, Lam SW, van der Groep P, Jaspers JE, Smolders YHCM, de Boer L, Pham TV, Piersma SR, Rottenberg S, Boven E, Jonkers J, van Diest PJ, Jimenez CR. Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget 2018; 7:63537-63548. [PMID: 27566577 PMCID: PMC5325383 DOI: 10.18632/oncotarget.11535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/13/2016] [Indexed: 11/25/2022] Open
Abstract
Breast cancer arising in female BRCA1 mutation carriers is characterized by an aggressive phenotype and early age of onset. We performed tandem mass spectrometry-based proteomics of secretomes and exosome-like extracellular vesicles from BRCA1-deficient and BRCA1-proficient murine breast tumor models to identify extracellular protein biomarkers, which can be used as an adjunct to current diagnostic modalities in patients with BRCA1-deficient breast cancer. We identified 2,107 proteins, of which 215 were highly enriched in the BRCA1-deficient secretome. We demonstrated that BRCA1-deficient secretome proteins could cluster most human BRCA1- and BRCA2-related breast carcinomas at the transcriptome level. Topoisomerase I (TOP1) and P-cadherin (CDH3) expression was investigated by immunohistochemistry on tissue microarrays of a large panel of 253 human breast carcinomas with and without BRCA1/2 mutations. We showed that expression of TOP1 and CDH3 was significantly increased in human BRCA1-related breast carcinomas relative to sporadic cases (p = 0.002 and p < 0.001, respectively). Multiple logistic regression showed that TOP1 (adjusted odds ratio [OR] 3.75; 95% confidence interval [95% CI], 1.85 - 7.71, p < 0.001) as well as CDH3 positivity (adjusted OR 2.45; 95% CI, 1.08 - 5.49, p = 0.032) were associated with BRCA1/2-related breast carcinomas after adjustment for triple-negative phenotype and age. In conclusion, proteome profiling of secretome using murine breast tumor models is a powerful strategy to identify non-invasive candidate biomarkers of BRCA1-deficient breast cancer. We demonstrate that TOP1 and CDH3 are closely associated to BRCA1-deficient breast cancer. These data merit further investigation for early detection of tumors arising in BRCA1 mutation carriers.
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Affiliation(s)
- Marc Warmoes
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Siu W Lam
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Janneke E Jaspers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yvonne H C M Smolders
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leon de Boer
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Epie Boven
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Connie R Jimenez
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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23
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Sabrkhany S, Kuijpers MJE, Knol JC, Olde Damink SWM, Dingemans AMC, Verheul HM, Piersma SR, Pham TV, Griffioen AW, Oude Egbrink MGA, Jimenez CR. Exploration of the platelet proteome in patients with early-stage cancer. J Proteomics 2018; 177:65-74. [PMID: 29432918 DOI: 10.1016/j.jprot.2018.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/29/2017] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
Abstract
Platelets play an important role in tumor growth and, at the same time, platelet characteristics are affected by cancer presence. Therefore, we investigated whether the platelet proteome harbors differentially expressed proteins associated with early-stage cancer. For this proof-of-concept study, patients with early-stage lung (n = 8) or head of pancreas cancer (n = 4) were included, as were healthy sex- and age-matched controls for both subgroups. Blood samples were collected from controls and from patients before surgery. Furthermore, from six of the patients, a second sample was collected two months after surgery. NanoLC-MS/MS-based proteomics of gel-fractionated platelet proteins was used for comparative spectral count analyses of patients to controls and before to after surgery samples. The total platelet proteome dataset included 4384 unique proteins of which 85 were significantly (criteria Fc > 1.5 and p < 0.05) changed in early-stage cancer compared to controls. In addition, the levels of 81 platelet proteins normalized after tumor resection. When filtering for the most discriminatory proteins, we identified seven promising platelet proteins associated with early-stage cancer. In conclusion, this pioneering study on the platelet proteome in cancer patients clearly identifies platelets as a new source of candidate protein biomarkers of early-stage cancer. BIOLOGICAL SIGNIFICANCE Currently, most blood-based diagnostics/biomarker research is performed in serum or plasma, while the content of blood cells is usually neglected. It is known that especially blood platelets, which are the main circulating pool of many bioactive proteins, such as growth factors, chemokines, and cytokines, are a potentially rich source of biomarkers. The current study is the first to measure the effect of early-stage cancer on the platelet proteome of patients. Our study demonstrates that the platelet proteome of patients with early-stage lung or head of pancreas cancer differs considerably compared to that of healthy individuals of matched sex and age. In addition, the platelet proteome of cancer patients normalized after surgical resection of the tumor. Exploiting platelet proteome differences linked to both tumor presence and disease status, we were able to demonstrate that the platelet proteome can be mined for potential biomarkers of cancer.
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Affiliation(s)
- Siamack Sabrkhany
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marijke J E Kuijpers
- Cardiovascular Research Institute Maastricht, Department of Biochemistry, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Steven W M Olde Damink
- Cardiovascular Research Institute Maastricht, Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anne-Marie C Dingemans
- Cardiovascular Research Institute Maastricht, Department of Pulmonology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Henk M Verheul
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam G A Oude Egbrink
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands.
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24
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Jia X, Xi B, Li M, Liu D, Hou J, Hao Y, Meng F. Metaproteomic analysis of the relationship between microbial community phylogeny, function and metabolic activity during biohydrogen-methane coproduction under short-term hydrothermal pretreatment from food waste. BIORESOURCE TECHNOLOGY 2017; 245:1030-1039. [PMID: 28946205 DOI: 10.1016/j.biortech.2017.08.180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Short-term hydrothermal pretreatment (SHP) is an attractive method for food waste anaerobic digestion, which facilitates the solubilisation of recalcitrant particles. This study employed metaproteomic method to evaluate the relationships among microbial community phylogeny, function, and metabolic activity during two-stage anaerobic digestion under SHP (SHPT) from food waste. The presence of 651 bacterial proteins and 477 archaeal protein has been detected by liquid chromatography online linked to mass spectrometry, revealing a high metabolic heterogeneity during SHPT. The different stages of SHPT highlighted important roles for the bacterial proteins from Gammaproteobacteria, Bacilli, and Clostridia and the archaeal proteins from Methanosarcinales. The identified proteins related to biohydrogen production come from pyruvic acid decarboxylase and formic acid decomposition pathway in carbohydrate metabolism and methanogenesis from acetate, CO2 and a methylotrophic pathway during energy metabolism. This could provide functional evidence of the metabolic activities and biogas production during SHPT.
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Affiliation(s)
- Xuan Jia
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Mingxiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Dongming Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jiaqi Hou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yan Hao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fanhua Meng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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25
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Hsiao YC, Chu LJ, Chen JT, Yeh TS, Yu JS. Proteomic profiling of the cancer cell secretome: informing clinical research. Expert Rev Proteomics 2017; 14:737-756. [PMID: 28695748 DOI: 10.1080/14789450.2017.1353913] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Cancer represents one of the major causes of human deaths. Identification of proteins as biomarkers for early detection of cancer and therapeutic targets for cancer treatment are important issues in precision medicine. Secretome of cancer cells represents the collection of proteins secreted or shed from cancer cells. Proteomic profiling of the cancer cell secretome has been proven to be a convenient and efficient way to discover cancer biomarker and/or therapeutic targets. Areas covered: There have been numerous reviews describing the history and application of secretome analysis in cancer biomarker/therapeutic target research. The present review focuses on the technological advancement for profiling low-molecular-mass proteins in secretome, the latest information regarding the new candidate biomarkers and molecular mechanisms discovered on the basis of cancer cell secretome analysis, as well as the previously discovered candidate biomarkers that enter into clinical trials. Expert commentary: Current technologies for protein sample preparation/separation and MS-based protein identification have allowed in-depth analysis of cancer cell secretome. Future efforts should focus on the comprehensiveness of cancer cell secretome, meta-analysis of different secretome datasets and integrated analysis via combining other omics datasets, as well as the incorporation of MS-based biomarker verification pipeline into both preclinical studies and clinical trials.
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Affiliation(s)
- Yung-Chin Hsiao
- a Molecular Medicine Research Center , Chang Gung University , Taoyuan , Taiwan.,b Liver Research Center , Chang Gung Memorial Hospital at Linkou , Taoyuan , Taiwan
| | - Lichieh Julie Chu
- a Molecular Medicine Research Center , Chang Gung University , Taoyuan , Taiwan.,b Liver Research Center , Chang Gung Memorial Hospital at Linkou , Taoyuan , Taiwan
| | - Jeng-Ting Chen
- c Department of Surgery , Chang Gung Memorial Hospital at Linkou , Taoyuan , Taiwan
| | - Ta-Sen Yeh
- c Department of Surgery , Chang Gung Memorial Hospital at Linkou , Taoyuan , Taiwan
| | - Jau-Song Yu
- a Molecular Medicine Research Center , Chang Gung University , Taoyuan , Taiwan.,b Liver Research Center , Chang Gung Memorial Hospital at Linkou , Taoyuan , Taiwan.,d Department of Cell and Molecular Biology , College of Medicine, Chang Gung University , Taoyuan , Taiwan
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Bridel C, Koel-Simmelink MJA, Peferoen L, Derada Troletti C, Durieux S, Gorter R, Nutma E, Gami P, Iacobaeus E, Brundin L, Kuhle J, Vrenken H, Killestein J, Piersma SR, Pham TV, De Vries HE, Amor S, Jimenez CR, Teunissen CE. Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro. Neuropathol Appl Neurobiol 2017; 44:404-416. [PMID: 28543098 DOI: 10.1111/nan.12412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 02/05/2023]
Abstract
AIMS Cell matrix modulating protein SPARCL-1 is highly expressed by astrocytes during CNS development and following acute CNS damage. Applying NanoLC-MS/MS to CSF of RRMS and SPMS patients, we identified SPARCL-1 as differentially expressed between these two stages of MS, suggesting a potential as CSF biomarker to differentiate RRMS from SPMS and a role in MS pathogenesis. METHODS This study examines the potential of SPARCL-1 as CSF biomarker discriminating RRMS from SPMS in three independent cohorts (n = 249), analyses its expression pattern in MS lesions (n = 26), and studies its regulation in cultured human brain microvasculature endothelial cells (BEC) after exposure to MS-relevant inflammatory mediators. RESULTS SPARCL-1 expression in CSF was significantly higher in SPMS compared to RRMS in a Dutch cohort of 76 patients. This finding was not replicated in 2 additional cohorts of MS patients from Sweden (n = 81) and Switzerland (n = 92). In chronic MS lesions, but not active lesions or NAWM, a vessel expression pattern of SPARCL-1 was observed in addition to the expression by astrocytes. EC were found to express SPARCL-1 in chronic MS lesions, and SPARCL-1 expression was regulated by MS-relevant inflammatory mediators in cultured human BEC. CONCLUSIONS Conflicting results of SPARCL-1's differential expression in CSF of three independent cohorts of RRMS and SPMS patients precludes its use as biomarker for disease progression. The expression of SPARCL-1 by BEC in chronic MS lesions together with its regulation by inflammatory mediators in vitro suggest a role for SPARCL-1 in MS neuropathology, possibly at the brain vascular level.
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Affiliation(s)
- C Bridel
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - M J A Koel-Simmelink
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - L Peferoen
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - C Derada Troletti
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
| | - S Durieux
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
| | - R Gorter
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - E Nutma
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - P Gami
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands
| | - E Iacobaeus
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institute, Solna, Sweden.,Center for Molecular Medicine, Stockholm, Sweden
| | - L Brundin
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institute, Solna, Sweden.,Center for Molecular Medicine, Stockholm, Sweden
| | - J Kuhle
- Neurology, Department of Medicine, Biomedicine and Clinical Research, University Hospital Basel, Basel, Switzerland
| | - H Vrenken
- Department of Radiology and Nuclear Medicine and Department of Physics and Medical Technology, VU University Medical Center, Amsterdam, The Netherlands
| | - J Killestein
- Department of Neurology, MS Centre Amsterdam, VU Medical Centre, Amsterdam, The Netherlands
| | - S R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - T V Pham
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - H E De Vries
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Centre, Amsterdam, The Netherlands
| | - S Amor
- Department of Pathology, VU Medical Centre, Amsterdam, The Netherlands.,Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, UK
| | - C R Jimenez
- Department of Medical Oncology, OncoProteomics Laboratory, VU Medical Centre, Amsterdam, The Netherlands
| | - C E Teunissen
- Department of Clinical Chemistry, Neurochemistry Lab and Biobank, VU Medical Centre, Amsterdam, The Netherlands
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27
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Bijnsdorp IV, Maxouri O, Kardar A, Schelfhorst T, Piersma SR, Pham TV, Vis A, van Moorselaar RJ, Jimenez CR. Feasibility of urinary extracellular vesicle proteome profiling using a robust and simple, clinically applicable isolation method. J Extracell Vesicles 2017; 6:1313091. [PMID: 28717416 PMCID: PMC5505003 DOI: 10.1080/20013078.2017.1313091] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/26/2017] [Indexed: 12/31/2022] Open
Abstract
Extracellular vesicles (EVs) secreted by prostate cancer (PCa) cells contain specific biomarkers and can be isolated from urine. Collection of urine is not invasive, and therefore urinary EVs represent a liquid biopsy for diagnostic and prognostic testing for PCa. In this study, we optimised urinary EV isolation using a method based on heat shock proteins and compared it to gold-standard ultracentrifugation. The urinary EV isolation protocol using the Vn96-peptide is easier, time convenient (≈1.5 h) and no special equipment is needed, in contrast to ultracentrifugation protocol (>3.5 h), making this protocol clinically feasible. We compared the isolated vesicles of both ultracentrifugation and Vn96-peptide by proteome profiling using mass spectrometry-based proteomics (n = 4 per method). We reached a depth of >3000 proteins, with 2400 proteins that were commonly detected in urinary EVs from different donors. We show a large overlap (>85%) between proteins identified in EVs isolated by ultracentrifugation and Vn96-peptide. Addition of the detergent NP40 to Vn96-peptide EV isolations reduced levels of background proteins and highly increased the levels of the EV-markers TSG101 and PDCD6IP, indicative of an increased EV yield. Thus, the Vn96-peptide-based EV isolation procedure is clinically feasibly and allows large-scale protein profiling of urinary EV biomarkers.
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Affiliation(s)
- Irene V Bijnsdorp
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Olga Maxouri
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands.,Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Aarzo Kardar
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands.,Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Tim Schelfhorst
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Andre Vis
- Department of Urology, VU University Medical Centre, Amsterdam, The Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, The Netherlands
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Boyatzis AE, Bringans SD, Piggott MJ, Duong MN, Lipscombe RJ, Arthur PG. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation. J Proteome Res 2017; 16:2004-2015. [DOI: 10.1021/acs.jproteome.6b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amber E. Boyatzis
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Matthew J. Piggott
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Marisa N. Duong
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Peter G. Arthur
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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29
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Barton JS, Schomacker R. Comparative protein profiles of the Ambrosia plants. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:633-639. [PMID: 28315734 DOI: 10.1016/j.bbapap.2017.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/22/2017] [Accepted: 03/14/2017] [Indexed: 12/17/2022]
Abstract
Ragweed pollen is primarily responsible for the hay fever allergies of sufferers throughout the world. A proteome study of three ragweed plants (Ambrosia artemisiifolia, Ambrosia trifida, and Ambrosia psilostachya) was undertaken to document and compare their protein profiles. Proteins extracted from the pollen of the three plants were subjected to one dimensional electrophoresis followed by tandem liquid chromatography-mass spectroscopy. Peptide sequence mapping permitted discovery of proteins not previously reported for all three plants and 45% of the identified proteins were shared by all three of them. Application of stringent criteria revealed not only a majority of known allergens for short ragweed but also allergens not previously reported for the other two plants. Additionally, potentially allergy inducing enolases are reported for the three plants. These results suggest that all three ragweed plants could contribute to the allergy malady.
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Affiliation(s)
- Janice S Barton
- Department of Chemistry, Washburn University, 1700 S College Avenue, Topeka, KS 66621, United States.
| | - Rachel Schomacker
- Department of Chemistry, Washburn University, 1700 S College Avenue, Topeka, KS 66621, United States
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30
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Multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus. Sci Data 2016; 3:160068. [PMID: 27529540 PMCID: PMC4986542 DOI: 10.1038/sdata.2016.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/11/2016] [Indexed: 11/29/2022] Open
Abstract
Temporal lobe epilepsy (TLE) can develop from alterations in hippocampal structure and circuit characteristics, and can be modeled in mice by administration of kainic acid (KA). Adult neurogenesis in the dentate gyrus (DG) contributes to hippocampal functions and has been reported to contribute to the development of TLE. Some of the phenotypical changes include neural stem and precursor cells (NPSC) apoptosis, shortly after their birth, before they produce hippocampal neurons. Here we explored these early phenotypical changes in the DG 3 days after a systemic injection of KA inducing status epilepticus (KA-SE), in mice. We performed a multi-omics experimental setup and analyzed DG tissue samples using proteomics, transcriptomics and microRNA profiling techniques, detecting the expression of 2327 proteins, 13401 mRNAs and 311 microRNAs. We here present a description of how these data were obtained and make them available for further analysis and validation. Our data may help to further identify and characterize molecular mechanisms involved in the alterations induced shortly after KA-SE in the mouse DG.
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31
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Manfredi M, Martinotti S, Gosetti F, Ranzato E, Marengo E. The secretome signature of malignant mesothelioma cell lines. J Proteomics 2016; 145:3-10. [DOI: 10.1016/j.jprot.2016.02.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/18/2016] [Accepted: 02/21/2016] [Indexed: 12/17/2022]
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Comparative analysis of novel autoantibody isotypes against citrullinated-inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3)542–556 peptide in serum from Taiwanese females with rheumatoid arthritis, primary Sjögren's syndrome and secondary Sjögren's syndrome in rheumatoid arthritis. J Proteomics 2016; 141:1-11. [DOI: 10.1016/j.jprot.2016.03.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/10/2016] [Accepted: 03/16/2016] [Indexed: 12/29/2022]
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33
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Knol JC, de Reus I, Schelfhorst T, Beekhof R, de Wit M, Piersma SR, Pham TV, Smit EF, Verheul HM, Jiménez CR. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics. EUPA OPEN PROTEOMICS 2016; 11:11-15. [PMID: 29900106 PMCID: PMC5988555 DOI: 10.1016/j.euprot.2016.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 01/14/2023]
Abstract
Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since EVs are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, they represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation are laborious, time-consuming, and require high inputs. Ghosh and co-workers recently described an isolation method utilizing Heat Shock Protein (HSP)-binding peptide Vn96 to aggregate HSP-decorated EVs, which can be performed at small 'miniprep' scale. Based on microscopic, immunoblot, and RNA sequencing analyses this method compared well with ultracentrifugation-mediated EV isolation, but a detailed proteomic comparison was lacking. Therefore, we compared both methods using label-free proteomics of replicate EV isolations from HT-29 cell-conditioned medium. Despite a 30-fold different scale (ultracentrifugation: 60 ml/Vn96-mediated aggregation: 2 ml) both methods yielded comparable numbers of identified proteins (3115/3085), with similar reproducibility of identification (72.5%/75.5%) and spectral count-based quantification (average CV: 31%/27%). EV fractions obtained with either method contained established EV markers and proteins linked to vesicle-related gene ontologies. Thus, Vn96 peptide-mediated aggregation is an advantageous, simple and rapid approach for EV isolation from small biological samples, enabling high-throughput analysis in a biomarker discovery setting.
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Affiliation(s)
- Jaco C. Knol
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Inge de Reus
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Tim Schelfhorst
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Robin Beekhof
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Egbert F. Smit
- Department of Pulmonary Diseases, VU University Medical Center, The Netherlands
| | - Henk M.W. Verheul
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
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34
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Barkla BJ, Vera-Estrella R, Raymond C. Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins. BMC PLANT BIOLOGY 2016; 16:110. [PMID: 27160145 PMCID: PMC4862212 DOI: 10.1186/s12870-016-0797-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/02/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Epidermal bladder cells (EBC) are large single-celled, specialized, and modified trichomes found on the aerial parts of the halophyte Mesembryanthemum crystallinum. Recent development of a simple but high throughput technique to extract the contents from these cells has provided an opportunity to conduct detailed single-cell-type analyses of their molecular characteristics at high resolution to gain insight into the role of these cells in the salt tolerance of the plant. RESULTS In this study, we carry out large-scale complementary quantitative proteomic studies using both a label (DIGE) and label-free (GeLC-MS) approach to identify salt-responsive proteins in the EBC extract. Additionally we perform an ionomics analysis (ICP-MS) to follow changes in the amounts of 27 different elements. Using these methods, we were able to identify 54 proteins and nine elements that showed statistically significant changes in the EBC from salt-treated plants. GO enrichment analysis identified a large number of transport proteins but also proteins involved in photosynthesis, primary metabolism and Crassulacean acid metabolism (CAM). Validation of results by western blot, confocal microscopy and enzyme analysis helped to strengthen findings and further our understanding into the role of these specialized cells. As expected EBC accumulated large quantities of sodium, however, the most abundant element was chloride suggesting the sequestration of this ion into the EBC vacuole is just as important for salt tolerance. CONCLUSIONS This single-cell type omics approach shows that epidermal bladder cells of M. crystallinum are metabolically active modified trichomes, with primary metabolism supporting cell growth, ion accumulation, compatible solute synthesis and CAM. Data are available via ProteomeXchange with identifier PXD004045.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, MOR, México
| | - Carolyn Raymond
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
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Schmudlach A, Felton J, Cipolla C, Sun L, Kennedy RT, Dovichi NJ. Sample preparation protocol for bottom-up proteomic analysis of the secretome of the islets of Langerhans. Analyst 2016; 141:1700-6. [PMID: 26863548 PMCID: PMC4764456 DOI: 10.1039/c5an02265g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We evaluate a set of protocols for preparation of the secretome from murine islets of Langerhans for bottom-up proteomic analysis. Of the protocols evaluated, a filter-aided sample preparation based approach using sodium dodecyl sulfate as a detergent to solubilize proteins generated the most protein identifications. A total of 362 protein groups (average of 3.7 peptides/protein) were identified from the secretome using the SDS-FASP protocol; a combination of data from three protocols generated 413 protein group identifications. As expected, the identified proteins included insulin 1 and 2, somatostatin, and glucagon, the four main secreted components from islets. STRING network analysis classified the other proteins as being associated with extracellular exosomes, membrane-bounded vesicles, vesicles, and the extracellular region.
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Affiliation(s)
- Andrew Schmudlach
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeremy Felton
- Departments of Chemistry and Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cynthia Cipolla
- Departments of Chemistry and Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Robert T Kennedy
- Departments of Chemistry and Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJP, van Meerloo J, Assaraf YG, Kaspers GJL, Zweegman S, Cloos J, Jimenez CR. Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis. Mol Cell Proteomics 2016; 15:1281-98. [PMID: 26801919 DOI: 10.1074/mcp.m115.052944] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/28/2022] Open
Abstract
Expression of apoptosis-regulating proteins (B-cell CLL/lymphoma 2 - BCL-2, Myeloid Cell Leukemia 1 - MCL-1, BCL-2 like 1 - BCL-X and BCL-2-associated X protein - BAX) in acute myeloid leukemia (AML) blasts at diagnosis is associated with disease-free survival. We previously found that the initially high apoptosis-resistance of AML cells decreased after therapy, while regaining high levels at relapse. Herein, we further explored this aspect of dynamic apoptosis regulation in AML. First, we showed that the intraindividualex vivoapoptosis-related profiles of normal lymphocytes and AML blasts within the bone marrow of AML patients were highly correlated. The expression values of apoptosis-regulating proteins were far beyond healthy control lymphocytes, which implicates the influence of microenvironmental factors. Second, we demonstrated that apoptosis-resistant primary AML blasts, as opposed to apoptosis-sensitive cells, were able to up-regulate BCL-2 expression in sensitive AML blasts in contact cultures (p= 0.0067 andp= 1.0, respectively). Using secretome proteomics, we identified novel proteins possibly engaged in apoptosis regulation. Intriguingly, this analysis revealed that major functional protein clusters engaged in global gene regulation, including mRNA splicing, protein translation, and chromatin remodeling, were more abundant (p= 4.01E-06) in secretomes of apoptosis-resistant AML. These findings were confirmed by subsequent extracellular vesicle proteomics. Finally, confocal-microscopy-based colocalization studies show that splicing factors-containing vesicles secreted by high AAI cells are taken up by low AAI cells. The current results constitute the first comprehensive analysis of proteins released by apoptosis-resistant and sensitive primary AML cells. Together, the data point to vesicle-mediated release of global gene regulatory protein clusters as a plausible novel mechanism of induction of apoptosis resistance. Deciphering the modes of communication between apoptosis-resistant blasts may in perspective lead to the discovery of prognostic tools and development of novel therapeutic interventions, aimed at limiting or overcoming therapy resistance.
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Affiliation(s)
| | | | | | | | - Jaco C Knol
- ¶OncoProteomics Laboratory, Dept. of Medical Oncology
| | - Thang V Pham
- ¶OncoProteomics Laboratory, Dept. of Medical Oncology
| | - Gerrit Jansen
- ‖Dept. of Rheumatology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - René J P Musters
- **Dept. of Physiology, ICaR-VU, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | | | - Yehuda G Assaraf
- ‡‡Dept. of Biology, Fred Wyszkowski Cancer Research Laboratory, Faculty of Biology, Technion-Israel, Institute of Technology, Haifa 3200003, Israel
| | | | | | - Jacqueline Cloos
- From the ‡Dept. of Pediatric Oncology/Hematology, §Dept. of Hematology
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Novel diagnostic cerebrospinal fluid biomarkers for pathologic subtypes of frontotemporal dementia identified by proteomics. ALZHEIMER'S & DEMENTIA: DIAGNOSIS, ASSESSMENT & DISEASE MONITORING 2016; 2:86-94. [PMID: 27239539 PMCID: PMC4879654 DOI: 10.1016/j.dadm.2015.12.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction Reliable cerebrospinal fluid (CSF) biomarkers enabling identification of frontotemporal dementia (FTD) and its pathologic subtypes are lacking. Methods Unbiased high-resolution mass spectrometry–based proteomics was applied on CSF of FTD patients with TAR DNA-binding protein 43 (TDP-43, FTD-TDP, n = 12) or tau pathology (FTD-tau, n = 8), and individuals with subjective memory complaints (SMC, n = 10). Validation was performed by applying enzyme-linked immunosorbent assay (ELISA) or enzymatic assays, when available, in a larger cohort (FTLD-TDP, n = 21, FTLD-tau, n = 10, SMC, n = 23) and in Alzheimer's disease (n = 20), dementia with Lewy bodies (DLB, n = 20), and vascular dementia (VaD, n = 18). Results Of 1914 identified CSF proteins, 56 proteins were differentially regulated (fold change >1.2, P < .05) between the different patient groups: either between the two pathologic subtypes (10 proteins), or between at least one of these FTD subtypes and SMC (47 proteins). We confirmed the differential expression of YKL-40 by ELISA in a partly independent cohort. Furthermore, enzyme activity of catalase was decreased in FTD subtypes compared with SMC. Further validation in a larger cohort showed that the level of YKL-40 was twofold increased in both FTD pathologic subtypes compared with SMC and that the levels in FTLD-tau were higher compared to Alzheimer's dementia (AD), DLB, and VaD patients. Clinical validation furthermore showed that the catalase enzyme activity was decreased in the FTD subtypes compared to SMC, AD and DLB. Discussion We identified promising CSF biomarkers for both FTD differential diagnosis and pathologic subtyping. YKL-40 and catalase enzyme activity should be validated further in similar pathology defined patient cohorts for their use for FTD diagnosis or treatment development.
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Sensing of latent EBV infection through exosomal transfer of 5'pppRNA. Proc Natl Acad Sci U S A 2016; 113:E587-96. [PMID: 26768848 DOI: 10.1073/pnas.1518130113] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Complex interactions between DNA herpesviruses and host factors determine the establishment of a life-long asymptomatic latent infection. The lymphotropic Epstein-Barr virus (EBV) seems to avoid recognition by innate sensors despite massive transcription of immunostimulatory small RNAs (EBV-EBERs). Here we demonstrate that in latently infected B cells, EBER1 transcripts interact with the lupus antigen (La) ribonucleoprotein, avoiding cytoplasmic RNA sensors. However, in coculture experiments we observed that latent-infected cells trigger antiviral immunity in dendritic cells (DCs) through selective release and transfer of RNA via exosomes. In ex vivo tonsillar cultures, we observed that EBER1-loaded exosomes are preferentially captured and internalized by human plasmacytoid DCs (pDCs) that express the TIM1 phosphatidylserine receptor, a known viral- and exosomal target. Using an EBER-deficient EBV strain, enzymatic removal of 5'ppp, in vitro transcripts, and coculture experiments, we established that 5'pppEBER1 transfer via exosomes drives antiviral immunity in nonpermissive DCs. Lupus erythematosus patients suffer from elevated EBV load and activated antiviral immunity, in particular in skin lesions that are infiltrated with pDCs. We detected high levels of EBER1 RNA in such skin lesions, as well as EBV-microRNAs, but no intact EBV-DNA, linking non-cell-autonomous EBER1 presence with skin inflammation in predisposed individuals. Collectively, our studies indicate that virus-modified exosomes have a physiological role in the host-pathogen stand-off and may promote inflammatory disease.
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Liu D, Li M, Xi B, Zhao Y, Wei Z, Song C, Zhu C. Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microb Biotechnol 2015; 8:950-60. [PMID: 25989417 PMCID: PMC4621448 DOI: 10.1111/1751-7915.12290] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 01/14/2023] Open
Abstract
Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase.
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Affiliation(s)
- Dongming Liu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Mingxiao Li
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Beidou Xi
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Yue Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Caihong Song
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Chaowei Zhu
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
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40
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Nynca J, Arnold GJ, Fröhlich T, Ciereszko A. Cryopreservation-induced alterations in protein composition of rainbow trout semen. Proteomics 2015; 15:2643-54. [PMID: 25780999 DOI: 10.1002/pmic.201400525] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/30/2015] [Accepted: 03/13/2015] [Indexed: 11/06/2022]
Abstract
The aim of this study was to detect cryopreservation-induced alterations in the protein composition of rainbow trout semen using two independent methods 1DE SDS-PAGE prefractionation combined with LC-MS/MS and 2D difference gel electrophoresis followed by MALDI-TOF/TOF identification. Here, we show the first comprehensive dataset of changes in rainbow trout semen proteome after cryopreservation, with a total of 73 identified proteins released from sperm to extracellular fluid, including mitochondrial, cytoskeletal, nuclear, and cytosolic proteins. Our study provides new information about proteins released from sperm, their relation to sperm structure and function, and changes of metabolism of sperm cells as a result of cryopreservation. The identified proteins represent potential markers of cryoinjures of sperm structures and markers of the disturbances of particular sperm metabolic pathways. Further studies will allow to decipher the precise function of the proteins altered during rainbow trout cryopreservation and are useful for the development of extensive diagnostic tests of sperm cryoinjures and for the successful improvement of sperm cryopreservation of this economically important species.
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Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima, Olsztyn, Poland
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima, Olsztyn, Poland
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41
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Verweij FJ, de Heus C, Kroeze S, Cai H, Kieff E, Piersma SR, Jimenez CR, Middeldorp JM, Pegtel DM. Exosomal sorting of the viral oncoprotein LMP1 is restrained by TRAF2 association at signalling endosomes. J Extracell Vesicles 2015; 4:26334. [PMID: 25865256 PMCID: PMC4394166 DOI: 10.3402/jev.v4.26334] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/28/2015] [Accepted: 03/02/2015] [Indexed: 11/20/2022] Open
Abstract
The Epstein–Barr virus (EBV)-encoded oncoprotein latent membrane protein 1 (LMP1) constitutively activates nuclear factor κB (NFκB) from intracellular membranes to promote cell growth and survival. LMP1 associates with CD63 in intracellular membranes and is released via exosomes. Whether tumour necrosis factor (TNF) receptor-associated factors (TRAFs) mediate LMP1 NFκB signalling from endosomes and modulate exosomal sorting is unknown. In this article, we show that LMP1–TRAF2 signalling complexes accumulate at endosomes in a palmitoylation-dependent manner, thereby driving LMP1-dependent oncogenicity. Palmitoylation is a reversible post-translational modification and is considered to function as a membrane anchor for proteins. Mutagenesis studies showed that LMP1–TRAF2 trafficking to endosomes is dependent on one single cysteine residue (C78), a known palmitoylation site of LMP1. Notably, growth assays in soft agar revealed that oncogenic properties of the palmitoylation-deficient LMP1 mutant C78A were diminished compared to wild-type LMP1. Since LMP1 recruitment of TRAF2 and downstream NFκB signalling were not affected by a disturbance in palmitoylation, the specific localization of LMP1 at endosomal membranes appears crucial for its transforming potential. The importance of palmitoylation for trafficking to and signalling from endosomal membranes was not restricted to LMP1, as similar observations were made for the cellular oncoproteins Src and Fyn. Despite abundant LMP1–TRAF2 association at endosomal membranes TRAF2 could not be detected in exosomes by Western blotting or proteomics. Interestingly, point mutations that prevented TRAF binding strongly promoted the sorting and release of LMP1 via exosomes. These observations reveal that LMP1–TRAF2 complexes at endosomes support oncogenic NFκB activation and suggest that LMP1 dissociates from the activated signalling complexes upon sorting into intraluminal vesicles. We propose that “signalling endosomes” in EBV-infected tumour cells can fuse with the plasma membrane, explaining LMP1 release via exosomes.
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Affiliation(s)
- Frederik J Verweij
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Cecilia de Heus
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Stefanie Kroeze
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Houjian Cai
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Elliott Kieff
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Jaap M Middeldorp
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Dirk Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands;
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42
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Ramchandani D, Weber GF. Interactions between osteopontin and vascular endothelial growth factor: Implications for cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:202-22. [PMID: 25732057 DOI: 10.1016/j.bbcan.2015.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/10/2015] [Accepted: 02/22/2015] [Indexed: 12/12/2022]
Abstract
For this comprehensive review, 257 publications with the keywords "osteopontin" or "OPN" and "vascular endothelial growth factor" or "VEGF" in PubMed were screened (time frame from year 1996 to year 2014). 37 articles were excluded because they were not focused on the interactions between these molecules, and papers relevant for transformation-related phenomena were selected. Osteopontin (OPN) and vascular endothelial growth factor (VEGF) are characterized by a convergence in function for regulating cell motility and angiogenesis, the response to hypoxia, and apoptosis. Often, they are co-expressed or one molecule induces the other, however, in some settings OPN-associated pathways and VEGF-associated pathways are distinct. Their relationships affect the pathogenesis in cancer, where they contribute to progression and angiogenesis and serve as markers for poor prognosis. The inhibition of OPN may reduce VEGF levels and suppress tumor progression. In vascular pathologies, these two cytokines mediate remodeling, but may also perpetuate inflammation and narrowing of the arteries. OPN and VEGF are elevated and contribute to vascularization in inflammatory diseases.
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Affiliation(s)
| | - Georg F Weber
- James L. Winkle College of Pharmacy, University of Cincinnati, USA.
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43
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Secretion of one adipokine Nampt/Visfatin suppresses the inflammatory stress-induced NF-κB activity and affects Nampt-dependent cell viability in Huh-7 cells. Mediators Inflamm 2015; 2015:392471. [PMID: 25814788 PMCID: PMC4357042 DOI: 10.1155/2015/392471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 01/21/2023] Open
Abstract
Nampt/visfatin acts in both intracellular and extracellular compartments to regulate multiple biological roles, including NAD metabolism, cancer, inflammation, and senescence. However, its function in chronic inflammation and carcinogenesis in hepatocellular carcinoma (HCC) has not been well-defined. Here we use Huh-7 hepatoma cells as a model to determine how Nampt/visfatin affects cellular survival under oxidative stress. We found that the transition of Nampt/visfatin from intracellular into extracellular form was induced by H2O2 treatment in 293T cells and confirmed that this phenomenon was not due to cell death but through the secretion of Nampt/visfatin. In addition, Nampt/visfatin suppressed cell viability in oxidative treatment in Huh-7 cells and acted on the inhibition of hepatoma cell growth. Oxidative stress also reduced the Nampt-mediated activation of NF-κB gene expression. In this study, we identify a novel feature of Nampt/visfatin which functions as an adipokine that can be secreted upon cellular stress. Our results provide an example to understand how adipokine interacts with chemotherapeutic treatment by oxidative stress in HCC.
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44
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Liao CC, Lin YL, Kuo CF. Effect of high-fat diet on hepatic proteomics of hamsters. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:1869-1881. [PMID: 25634685 DOI: 10.1021/jf506118j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A high-fat diet contributes to the etiology of metabolic diseases. As the liver plays a crucial role in metabolism, an insight into the hepatic proteomics will help to illustrate the physiological effect of a high-fat diet. Fourteen nine-week old male Syrian hamsters were maintained on either control (C) or high-fat (HF) diets (0.2% cholesterol +22% fat) for 8 weeks. Hamsters were chosen because they show close similarity to human lipid metabolism. At the end of study, blood and livers were collected for analysis. Liver proteins were fractionated by electrophoresis, digested by trypsin, and then separated by label-free nano-LC/MS/MS. The TurboSequest algorithm was used to identify the peptide sequences against the hamster database in Universal Proteins Resource Knowledgebase (UniProt). The results indicate that 1191 hepatic proteins were identified and 135 of them were expressed differentially in the high-fat group (p < 0.05). Some of these 135 proteins that involve in metabolic diseases were further validated by Western blotting. The animals maintained on the high-fat diet had significantly (p < 0.05) higher serum triglyceride, cholesterol, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and uric acid. Animals consuming a high-fat diet also had significantly (p < 0.05) more accumulation of triglyceride and cholesterol in livers. Xanthine dehydrogenase (XDH), which plays an important role in uric acid synthesis, was up-regulated by the high-fat diet (p < 0.05). The α-subunit of hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (HADHA), which catalyzes the second and third reactions of β-oxidation, was down-regulated by the high-fat diet (p < 0.05). Aconitate hydratase 2 (ACO2), which catalyzes the conversion of citrate to isocitrate in TCA cycle, was down-regulated in animals of the high-fat group (p < 0.05). Inflammatory markers annexin A3 (ANXA3) and annexin A5 (ANXA5) were up-regulated by the high-fat diet (p < 0.05). Moreover, enzymes involved in the urea cycle were suppressed by high-fat diet, including carbamoyl phosphate synthase 1 (CPS1), ornithine transcarbamoylase (OTC), argininosuccinate synthase (ASS), argininosuccinate lyase (ASL), and arginase 1 (ARG 1). Post-translational modifications (PTM) of ANXA3, ANXA5, and XDH were also analyzed. A set of differentially expressed proteins were identified as molecular markers for elucidating the pathological mechanism of high-fat diet.
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Affiliation(s)
- Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University , Taipei 112, Taiwan
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45
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Méndez O, Villanueva J. Challenges and opportunities for cell line secretomes in cancer proteomics. Proteomics Clin Appl 2015; 9:348-57. [DOI: 10.1002/prca.201400131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 11/19/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Olga Méndez
- Vall d'Hebron Institute of Oncology (VHIO); Barcelona Spain
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46
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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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47
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Shin J, Kim HJ, Kim G, Song M, Woo SJ, Lee ST, Kim H, Lee C. Discovery of melanotransferrin as a serological marker of colorectal cancer by secretome analysis and quantitative proteomics. J Proteome Res 2014; 13:4919-31. [PMID: 25216327 DOI: 10.1021/pr500790f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To discover serological colorectal cancer (CRC) markers, we analyzed cell line secretome to gather proteins of higher potential to be secreted from tissues into circulation. A total of 898 human proteins were identified, of which 62.2% were predicted to be released or shed from cells. The identified proteins were compared with tissue proteomes to find candidate proteins whose expressions were elevated in tumor tissues compared with normal tissues as revealed by (i) quantitative proteomic analysis based on cICAT and mTRAQ or (ii) data mining of immunohistochemical images piled in Human Protein Atlas database. By applying various stringent criteria, 11 candidate proteins were selected. Among these, we validated an significant increase (p = 0.0018) of melanotransferrin (TRFM) at the plasma level of CRC patients through Western blotting, using 130 plasma samples containing 30 healthy controls, 80 CRC patients, and 20 patients of other diseases. Finally, we measured the expression level of TRFM in 325 plasma samples containing 77 healthy controls and 228 CRC patients (34.6 ± 4.2 ng/mL and 67.0 ± 6.4 ng/mL, p < 0.0001) through ELISA and demonstrated the area under the receiver operating characteristic curve of 0.723 (p < 0.0001) with a 92.5% specificity, 48.2% sensitivity, and 95.7% positive predictive value. Furthermore, unlike CEA and PAI-1, up-regulation of TRFM in pathological stages I & II groups compared with stages III & IV groups lead us to expect the use TRFM for early-stage diagnosis of CRC. In this study, we suggest TRFM as a potential serological marker for CRC and expect our discovery strategy to help identify highly cancer-specific and body-fluid-accessible biomarkers.
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Affiliation(s)
- Jihye Shin
- Center for Theragnosis, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk, Seoul 136-791, Korea
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Martinez-Pinna R, Burillo E, Madrigal-Matute J, Lopez JA, Camafeita E, Torres-Fonseca MM, Llamas-Granda P, Egido J, Michel JB, Blanco-Colio LM, Martin-Ventura JL. Label-free proteomic analysis of red blood cell membrane fractions from abdominal aortic aneurysm patients. Proteomics Clin Appl 2014; 8:626-30. [DOI: 10.1002/prca.201400035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/02/2014] [Accepted: 06/24/2014] [Indexed: 11/07/2022]
Affiliation(s)
| | - Elena Burillo
- Vascular Research Lab, IIS-Fundación Jiménez Díaz; Universidad Autónoma de Madrid
| | | | | | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares; Madrid Spain
| | | | | | - Jesus Egido
- Vascular Research Lab, IIS-Fundación Jiménez Díaz; Universidad Autónoma de Madrid
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Sayers KT, Brooks AD, Sayers TJ, Chertov O. Increased secretory leukocyte protease inhibitor (SLPI) production by highly metastatic mouse breast cancer cells. PLoS One 2014; 9:e104223. [PMID: 25110884 PMCID: PMC4128660 DOI: 10.1371/journal.pone.0104223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/11/2014] [Indexed: 02/04/2023] Open
Abstract
The precise molecular mechanisms enabling cancer cells to metastasize from the primary tumor to different tissue locations are still largely unknown. Secretion of some proteins by metastatic cells could facilitate metastasis formation. The comparison of secreted proteins from cancer cells with different metastatic capabilities in vivo might provide insight into proteins involved in the metastatic process. Comparison of the secreted proteins from the mouse breast cancer cell line 4T1 and its highly metastatic 4T1.2 clone revealed a prominent differentially secreted protein which was identified as SLPI (secretory leukocyte protease inhibitor). Western blotting indicated higher levels of the protein in both conditioned media and whole cell lysates of 4T1.2 cells. Additionally higher levels of SLPI were also observed in 4T1.2 breast tumors in vivo following immunohistochemical staining. A comparison of SLPI mRNA levels by gene profiling using microarrays and RT-PCR did not detect major differences in SLPI gene expression between the 4T1 and 4T1.2 cells indicating that SLPI secretion is regulated at the protein level. Our results demonstrate that secretion of SLPI is drastically increased in highly metastatic cells, suggesting a possible role for SLPI in enhancing the metastatic behavior of breast cancer cell line 4T1.
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Affiliation(s)
- Kevin T Sayers
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Alan D Brooks
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Thomas J Sayers
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Oleg Chertov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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50
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Rajcevic U, Knol JC, Piersma S, Bougnaud S, Fack F, Sundlisaeter E, Søndenaa K, Myklebust R, Pham TV, Niclou SP, Jiménez CR. Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture. Proteome Sci 2014; 12:39. [PMID: 25075203 PMCID: PMC4114130 DOI: 10.1186/1477-5956-12-39] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 06/09/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Organotypic tumor spheroids, a 3D in vitro model derived from patient tumor material, preserve tissue heterogeneity and retain structural tissue elements, thus replicating the in vivo tumor more closely than commonly used 2D and 3D cell line models. Such structures harbour tumorigenic cells, as revealed by xenograft implantation studies in animal models and maintain the genetic makeup of the original tumor material. The aim of our work was a morphological and proteomic characterization of organotypic spheroids derived from colorectal cancer tissue in order to get insight into their composition and associated biology. RESULTS Morphological analysis showed that spheroids were of about 250 μm in size and varied in structure, while the spheroid cells differed in shape and size and were tightly packed together by desmosomes and tight junctions. Our proteomic data revealed significant alterations in protein expression in organotypic tumor spheroids cultured as primary explants compared to primary colorectal cancer tissue. Components underlying cellular and tissue architecture were changed; nuclear DNA/ chromatin maintenance systems were up-regulated, whereas various mitochondrial components were down-regulated in spheroids. Most interestingly, the mesenchymal cells appear to be substantial component in such cellular assemblies. Thus the observed changes may partly occur in this cellular compartment. Finally, in the proteomics analysis stem cell-like characteristics were observed within the spheroid cellular assembly, reflected by accumulation of Alcam, Ctnnb1, Aldh1, Gpx2, and CD166. These findings were underlined by IHC analysis of Ctnnb1, CD24 and CD44, therefore warranting closer investigation of the tumorigenic compartment in this 3D culture model for tumor tissue. CONCLUSIONS Our analysis of organotypic CRC tumor spheroids has identified biological processes associated with a mixture of cell types and states, including protein markers for mesenchymal and stem-like cells. This 3D tumor model in which tumor heterogeneity is preserved may represent an advantageous model system to investigate novel therapeutic approaches.
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Affiliation(s)
- Uros Rajcevic
- NorLux Neuro-Oncology Laboratory, Department of Oncology, CRP-Santé, Luxembourg, Luxembourg ; Department of Research and Development, Blood Transfusion Center of Slovenia, Ljubljana, Slovenia ; Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Sander Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Sébastien Bougnaud
- NorLux Neuro-Oncology Laboratory, Department of Oncology, CRP-Santé, Luxembourg, Luxembourg
| | - Fred Fack
- NorLux Neuro-Oncology Laboratory, Department of Oncology, CRP-Santé, Luxembourg, Luxembourg
| | | | - Karl Søndenaa
- Department of Surgery, Haraldsplass Deaconal Hospital, University of Bergen, Bergen, Norway
| | | | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, CRP-Santé, Luxembourg, Luxembourg
| | - Connie R Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
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