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Navarro-Carrasco E, Monte-Serrano E, Campos-Díaz A, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, González-Alonso P, Jiménez CR, Lazo PA. VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells. Int J Mol Sci 2024; 25:4874. [PMID: 38732093 PMCID: PMC11084957 DOI: 10.3390/ijms25094874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to oxidative stress. which alters the nuclear pattern of histone epigenetic modifications and phosphoproteome pathways. The early effect of oxidative stress on chromatin was studied by determining the levels of 8-oxoG lesions and the alteration of the epigenetic modification of histones. Oxidative stress caused an accumulation of 8-oxoG DNA lesions that were increased by VRK1 depletion, causing a significant accumulation of DNA strand breaks detected by labeling free 3'-DNA ends. In addition, oxidative stress altered the pattern of chromatin epigenetic marks and the nuclear phosphoproteome pathways that were impaired by VRK1 depletion. Oxidative stress induced the acetylation of H4K16ac and H3K9 and the loss of H3K4me3. The depletion of VRK1 altered all these modifications induced by oxidative stress and resulted in losses of H4K16ac and H3K9ac and increases in the H3K9me3 and H3K4me3 levels. All these changes were induced by the oxidative stress in the epigenetic pattern of histones and impaired by VRK1 depletion, indicating that VRK1 plays a major role in the functional reorganization of chromatin in the response to oxidative stress. The analysis of the nuclear phosphoproteome in response to oxidative stress detected an enrichment of the phosphorylated proteins associated with the chromosome organization and chromatin remodeling pathways, which were significantly decreased by VRK1 depletion. VRK1 depletion alters the histone epigenetic pattern and nuclear phosphoproteome pathways in response to oxidative stress. The enzymes performing post-translational epigenetic modifications are potential targets in synthetic lethality strategies for cancer therapies.
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Affiliation(s)
- Elena Navarro-Carrasco
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Eva Monte-Serrano
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Aurora Campos-Díaz
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Frank Rolfs
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Thang V. Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Paula González-Alonso
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Pedro A. Lazo
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
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Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024. [PMID: 38650175 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés-Martí
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Italy
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
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3
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Navarro-Carrasco E, Campos-Díaz A, Monte-Serrano E, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, Jiménez CR, Lazo PA. Loss of VRK1 alters the nuclear phosphoproteome in the DNA damage response to doxorubicin. Chem Biol Interact 2024; 391:110908. [PMID: 38367682 DOI: 10.1016/j.cbi.2024.110908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024]
Abstract
Dynamic chromatin remodeling requires regulatory mechanisms for its adaptation to different nuclear function, which are likely to be mediated by signaling proteins. In this context, VRK1 is a nuclear Ser-Thr kinase that regulates pathways associated with transcription, replication, recombination, and DNA repair. Therefore, VRK1 is a potential regulatory, or coordinator, molecule in these processes. In this work we studied the effect that VRK1 depletion has on the basal nuclear and chromatin phosphoproteome, and their associated pathways. VRK1 depletion caused an alteration in the pattern of the nuclear phosphoproteome, which is mainly associated with nucleoproteins, ribonucleoproteins, RNA splicing and processing. Next, it was determined the changes in proteins associated with DNA damage that was induced by doxorubicin treatment. Doxorubicin alters the nuclear phosphoproteome affecting proteins implicated in DDR, including DSB repair proteins NBN and 53BP1, cellular response to stress and chromatin organization proteins. In VRK1-depleted cells, the effect of doxorubicin on protein phosphorylation was reverted to basal levels. The nuclear phosphoproteome patterns induced by doxorubicin are altered by VRK1 depletion, and is enriched in histone modification proteins and chromatin associated proteins. These results indicate that VRK1 plays a major role in processes requiring chromatin remodeling in its adaptation to different biological contexts.
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Affiliation(s)
- Elena Navarro-Carrasco
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007, Salamanca, Spain.
| | - Aurora Campos-Díaz
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007, Salamanca, Spain.
| | - Eva Monte-Serrano
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007, Salamanca, Spain.
| | - Frank Rolfs
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands.
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands.
| | - Thang V Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands.
| | - Sander R Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands.
| | - Connie R Jiménez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands.
| | - Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - Universidad de Salamanca, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007, Salamanca, Spain.
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4
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Vallés-Martí A, Mantini G, Manoukian P, Waasdorp C, Sarasqueta AF, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Giovannetti E, Bijlsma MF, Jiménez CR. Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma. Cell Rep 2023; 42:112581. [PMID: 37269289 DOI: 10.1016/j.celrep.2023.112581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited set of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a readout of aberrant signaling and has the potential to identify new targets and guide treatment decisions. Using two-step sequential phosphopeptide enrichment, we generate a comprehensive phosphoproteome and proteome of nine PDAC cell lines, encompassing more than 20,000 phosphosites on 5,763 phospho-proteins, including 316 protein kinases. By using integrative inferred kinase activity (INKA) scoring, we identify multiple (parallel) activated kinases that are subsequently matched to kinase inhibitors. Compared with high-dose single-drug treatments, INKA-tailored low-dose 3-drug combinations against multiple targets demonstrate superior efficacy against PDAC cell lines, organoid cultures, and patient-derived xenografts. Overall, this approach is particularly more effective against the aggressive mesenchymal PDAC model compared with the epithelial model in both preclinical settings and may contribute to improved treatment outcomes in PDAC patients.
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Affiliation(s)
- Andrea Vallés-Martí
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands
| | - Giulia Mantini
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Paul Manoukian
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | | | - Richard R de Goeij-de Haas
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Alex A Henneman
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Sander R Piersma
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Thang V Pham
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Jaco C Knol
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Elisa Giovannetti
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Connie R Jiménez
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands.
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5
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van der Wijngaart H, Jagga S, Dekker H, de Goeij R, Piersma SR, Pham TV, Knol JC, Zonderhuis BM, Holland HJ, Jiménez CR, Verheul HMW, Vanapalli S, Labots M. Advancing wide implementation of precision oncology: A liquid nitrogen-free snap freezer preserves molecular profiles of biological samples. Cancer Med 2023; 12:10979-10989. [PMID: 36916528 DOI: 10.1002/cam4.5781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE In precision oncology, tumor molecular profiles guide selection of therapy. Standardized snap freezing of tissue biospecimens is necessary to ensure reproducible, high-quality samples that preserve tumor biology for adequate molecular profiling. Quenching in liquid nitrogen (LN2 ) is the golden standard method, but LN2 has several limitations. We developed a LN2 -independent snap freezer with adjustable cold sink temperature. To benchmark this device against the golden standard, we compared molecular profiles of biospecimens. METHODS Cancer cell lines and core needle normal tissue biopsies from five patients' liver resection specimens were used to compare mass spectrometry (MS)-based global phosphoproteomic and RNA sequencing profiles and RNA integrity obtained by both freezing methods. RESULTS Unsupervised cluster analysis of phosphoproteomic and transcriptomic profiles of snap freezer versus LN2 -frozen K562 samples and liver biopsies showed no separation based on freezing method (with Pearson's r 0.96 (range 0.92-0.98) and >0.99 for K562 profiles, respectively), while samples with +2 h bench-time formed a separate cluster. RNA integrity was also similar for both snap freezing methods. Molecular profiles of liver biopsies were clearly identified per individual patient regardless of the applied freezing method. Two to 25 s freezing time variations did not induce profiling differences in HCT116 samples. CONCLUSION The novel snap freezer preserves high-quality biospecimen and allows identification of individual patients' molecular profiles, while overcoming important limitations of the use of LN2 . This snap freezer may provide a useful tool in clinical cancer research and practice, enabling a wider implementation of (multi-)omics analyses for precision oncology.
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Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sahil Jagga
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Richard de Goeij
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Babs M Zonderhuis
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry J Holland
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Srinivas Vanapalli
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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6
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Piersma SR, Valles-Marti A, Rolfs F, Pham TV, Henneman AA, Jiménez CR. Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications. Mass Spectrom Rev 2022:e21808. [PMID: 36156810 DOI: 10.1002/mas.21808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry-based phosphoproteomic experiments nowadays routinely allow identification and quantitation of >10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM-SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase-substrate databases, and user-friendliness is presented. The most widely-used tools are compared in-depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM-SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.
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Affiliation(s)
- Sander R Piersma
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Andrea Valles-Marti
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frank Rolfs
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex A Henneman
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
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7
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van Linde ME, Labots M, Brahm CG, Hovinga KE, De Witt Hamer PC, Honeywell RJ, de Goeij-de Haas R, Henneman AA, Knol JC, Peters GJ, Dekker H, Piersma SR, Pham TV, Vandertop WP, Jiménez CR, Verheul HM. Tumor Drug Concentration and Phosphoproteomic Profiles After Two Weeks of Treatment With Sunitinib in Patients with Newly Diagnosed Glioblastoma. Clin Cancer Res 2022; 28:1595-1602. [PMID: 35165100 PMCID: PMC9365363 DOI: 10.1158/1078-0432.ccr-21-1933] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/14/2021] [Accepted: 02/09/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Tyrosine kinase inhibitors (TKI) have poor efficacy in patients with glioblastoma (GBM). Here, we studied whether this is predominantly due to restricted blood-brain barrier penetration or more to biological characteristics of GBM. PATIENTS AND METHODS Tumor drug concentrations of the TKI sunitinib after 2 weeks of preoperative treatment was determined in 5 patients with GBM and compared with its in vitro inhibitory concentration (IC50) in GBM cell lines. In addition, phosphotyrosine (pTyr)-directed mass spectrometry (MS)-based proteomics was performed to evaluate sunitinib-treated versus control GBM tumors. RESULTS The median tumor sunitinib concentration of 1.9 μmol/L (range 1.0-3.4) was 10-fold higher than in concurrent plasma, but three times lower than sunitinib IC50s in GBM cell lines (median 5.4 μmol/L, 3.0-8.5; P = 0.01). pTyr-phosphoproteomic profiles of tumor samples from 4 sunitinib-treated versus 7 control patients revealed 108 significantly up- and 23 downregulated (P < 0.05) phosphopeptides for sunitinib treatment, resulting in an EGFR-centered signaling network. Outlier analysis of kinase activities as a potential strategy to identify drug targets in individual tumors identified nine kinases, including MAPK10 and INSR/IGF1R. CONCLUSIONS Achieved tumor sunitinib concentrations in patients with GBM are higher than in plasma, but lower than reported for other tumor types and insufficient to significantly inhibit tumor cell growth in vitro. Therefore, alternative TKI dosing to increase intratumoral sunitinib concentrations might improve clinical benefit for patients with GBM. In parallel, a complex profile of kinase activity in GBM was found, supporting the potential of (phospho)proteomic analysis for the identification of targets for (combination) treatment.
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Affiliation(s)
- Myra E. van Linde
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cyrillo G. Brahm
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Koos E. Hovinga
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Philip C. De Witt Hamer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Richard J. Honeywell
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Pharmacy, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Richard de Goeij-de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Alex A. Henneman
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jaco C. Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Godefridus J. Peters
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Henk Dekker
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - William P. Vandertop
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Medical Oncology, Radboud UMC, Nijmegen, the Netherlands
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8
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Buffart TE, van den Oord RAHM, van den Berg A, Hilhorst R, Bastiaensen N, Pruijt HFM, van den Brule A, Nooijen P, Labots M, de Goeij-de Haas RR, Dekker H, Piersma SR, Pham TV, van der Leij T, de Wijn R, Ruijtenbeek R, Jiménez CR, Verheul HMW. Time dependent effect of cold ischemia on the phosphoproteome and protein kinase activity in fresh-frozen colorectal cancer tissue obtained from patients. Clin Proteomics 2021; 18:8. [PMID: 33602116 PMCID: PMC7893972 DOI: 10.1186/s12014-020-09306-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Based on their potential to analyze aberrant cellular signaling in relation to biological function, kinase activity profiling in tumor biopsies by peptide microarrays and mass spectrometry-based phosphoproteomics may guide selection of protein kinase inhibitors in patients with cancer. Variable tissue handling procedures in clinical practice may influence protein phosphorylation status and kinase activity and therewith may hamper biomarker discovery. Here, the effect of cold ischemia time (CIT) on the stability of kinase activity and protein phosphorylation status in fresh-frozen clinical tissue samples was studied using peptide microarrays and mass spectrometry-based phosphoproteomics. Methods Biopsies of colorectal cancer resection specimens from five patients were collected and snap frozen immediately after surgery and at 6 additional time points between 0 and 180 min of CIT. Kinase activity profiling was performed for all samples using a peptide microarray. MS-based global phosphoproteomics was performed in tumors from 3 patients at 4 time points. Statistical and cluster analyses were performed to analyze changes in kinase activity and phosphoproteome resulting from CIT. Results Unsupervised cluster analysis of kinase activity and phosphoproteome data revealed that samples from the same patients cluster together. Continuous ANOVA analysis of all 7 time points for 5 patient samples resulted in 4 peptides out of 210 (2%) with significantly (p < 0.01 and fold change > 2) altered signal intensity in time. In 4 out of 5 patients tumor kinase activity was stable with CIT. MS-based phosphoproteomics resulted in the detection of 10,488 different phosphopeptides with on average 6044 phosphopeptides per tumor sample. 2715 phosphopeptides were detected in all samples at time point 0, of which 90 (3.3%) phosphopeptides showed significant changes in intensity with CIT (p < 0.01). Only two phosphopeptides were significantly changed in all time points, including one peptide (PKP3) with a fold change > 2. Conclusions The vast majority of the phosphoproteome as well as the activity of protein kinases in colorectal cancer resection tissue is stable up to 180 min of CIT and reflects tumor characteristics. However, specific changes in kinase activity with increasing CIT were observed. Therefore, stringent tissue collection procedures are advised to minimize changes in kinase activity during CIT.
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Affiliation(s)
- Tineke E Buffart
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rosanne A H M van den Oord
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | | | - Riet Hilhorst
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | | | - Hans F M Pruijt
- Department of Medical Oncology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Adriaan van den Brule
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Peet Nooijen
- Department of Pathology, Jeroen Bosch Hospital, 'S-Hertogenbosch, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Rik de Wijn
- PamGene International BV, 'S-Hertogenbosch, The Netherlands
| | - Rob Ruijtenbeek
- PamGene International BV, 'S-Hertogenbosch, The Netherlands.,GenMab BV, Utrecht, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands. .,Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein 10, 6525GA, Nijmegen, The Netherlands.
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9
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Labots M, Pham TV, Honeywell RJ, Knol JC, Beekhof R, de Goeij-de Haas R, Dekker H, Neerincx M, Piersma SR, van der Mijn JC, van der Peet DL, Meijerink MR, Peters GJ, van Grieken NC, Jiménez CR, Verheul HM. Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome. Cancers (Basel) 2020; 12:cancers12020330. [PMID: 32024067 PMCID: PMC7072422 DOI: 10.3390/cancers12020330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 12/22/2022] Open
Abstract
Identification of predictive biomarkers for targeted therapies requires information on drug exposure at the target site as well as its effect on the signaling context of a tumor. To obtain more insight in the clinical mechanism of action of protein kinase inhibitors (PKIs), we studied tumor drug concentrations of protein kinase inhibitors (PKIs) and their effect on the tyrosine-(pTyr)-phosphoproteome in patients with advanced cancer. Tumor biopsies were obtained from 31 patients with advanced cancer before and after 2 weeks of treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). Tumor concentrations were determined by LC-MS/MS. pTyr-phosphoproteomics was performed by pTyr-immunoprecipitation followed by LC-MS/MS. Median tumor concentrations were 2–10 µM for SOR, ERL, DAS, SUN, EVE and >1 mM for VEM. These were 2–178 × higher than median plasma concentrations. Unsupervised hierarchical clustering of pTyr-phosphopeptide intensities revealed patient-specific clustering of pre- and on-treatment profiles. Drug-specific alterations of peptide phosphorylation was demonstrated by marginal overlap of robustly up- and downregulated phosphopeptides. These findings demonstrate that tumor drug concentrations are higher than anticipated and result in drug specific alterations of the phosphoproteome. Further development of phosphoproteomics-based personalized medicine is warranted.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Richard J. Honeywell
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Jaco C. Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Robin Beekhof
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Richard de Goeij-de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Henk Dekker
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Maarten Neerincx
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Johannes C. van der Mijn
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Donald L. van der Peet
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Martijn R. Meijerink
- Department of Radiology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Godefridus J. Peters
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Nicole C.T. van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Connie R. Jiménez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
- Correspondence: or (C.R.J.); (H.M.W.V.)
| | - Henk M.W. Verheul
- Department of Medical Oncology, RadboudUMC, Radboud University, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
- Correspondence: or (C.R.J.); (H.M.W.V.)
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10
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López González M, Oosterhoff D, Lindenberg JJ, Milenova I, Lougheed SM, Martiáñez T, Dekker H, Quixabeira DCA, Hangalapura B, Joore J, Piersma SR, Cervera-Carrascon V, Santos JM, Scheper RJ, Verheul HMW, Jiménez CR, Van De Ven R, Hemminki A, Van Beusechem VW, De Gruijl TD. Constitutively active GSK3β as a means to bolster dendritic cell functionality in the face of tumour-mediated immune suppression. Oncoimmunology 2019; 8:e1631119. [PMID: 31646076 PMCID: PMC6791458 DOI: 10.1080/2162402x.2019.1631119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/31/2019] [Accepted: 06/08/2019] [Indexed: 01/05/2023] Open
Abstract
In patients with cancer, the functionality of Dendritic Cells (DC) is hampered by high levels of tumor-derived suppressive cytokines, which interfere with DC development and maturation. Poor DC development can limit the efficacy of immune checkpoint blockade and in vivo vaccination approaches. Interference in intracellular signaling cascades downstream from the receptors of major tumor-associated suppressive cytokines like IL-10 and IL-6, might improve DC development and activation, and thus enhance immunotherapy efficacy. We performed exploratory functional screens on arrays consisting of >1000 human kinase peptide substrates to identify pathways involved in DC development and its inhibition by IL-10 or IL-6. The resulting alterations in phosphorylation of the kinome substrate profile pointed to glycogen-synthase kinase-3β (GSK3β) as a pivotal kinase in both DC development and suppression. GSK3β inhibition blocked human DC differentiation in vitro, which was accompanied by decreased levels of IL-12p70 secretion, and a reduced capacity for T cell priming. More importantly, adenoviral transduction of monocytes with a constitutively active form of GSK3β induced resistance to the suppressive effects of IL-10 and melanoma-derived supernatants alike, resulting in improved DC development, accompanied by up-regulation of co-stimulatory markers, an increase in CD83 expression levels in mature DC, and diminished release of IL-10. Moreover, adenovirus-mediated intratumoral manipulation of this pathway in an in vivo melanoma model resulted in DC activation and recruitment, and in improved immune surveillance and tumor control. We propose the induction of constitutive GSK3β activity as a novel therapeutic means to bolster DC functionality in the tumor microenvironment.
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Affiliation(s)
- Marta López González
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Dinja Oosterhoff
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Jelle J Lindenberg
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Ioanna Milenova
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Sinead M Lougheed
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Tania Martiáñez
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Dafne Carolina Alves Quixabeira
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Basav Hangalapura
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Jos Joore
- PepScope B.V., VB Utrecht, Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Victor Cervera-Carrascon
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Joao Manuel Santos
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,TILT Biotherapeutics Ltd, Helsinki, Finland
| | - Rik J Scheper
- Department of Pathology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Rieneke Van De Ven
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,TILT Biotherapeutics Ltd, Helsinki, Finland.,Department Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Victor W Van Beusechem
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
| | - Tanja D De Gruijl
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, HV Amsterdam, The Netherlands
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11
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Buffart T, Beekhof R, van den Oord R, de Haas RR, Pham TV, Dekker H, van Grieken NC, Piersma SR, van den Brule A, Nooijen P, Pruijt H, Jiménez CR, Verheul HM. Comparison of phosphoproteomic profiles in left- and right-sided colorectal cancers. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
582 Background: Left- and right-sided colorectal cancers (CRCs) are different in terms of prognosis, treatment response and underlying molecular mechanisms. The aim of this study was to unravel the phosphoproteomic profiles of left- and right-sided primary CRCs and to identify potential drug targets for both primary tumor sites. Methods: In total phosphoproteomic profiles of 69 fresh-frozen biopsies, including 34 left-sided and 35 right-sided primary CRCs, were obtained by LC-MS/MS after cell lysis, digestion and phosphopeptide enrichment using anti-phosphotyrosine antibodies. MS/MS spectra were searched against a UniProt human reference proteome FASTA file using MaxQuant software. Fold changes between normalized intensities were calculated. Group comparison was performed using the R package Limma. P values below 0.01 and fold changes > two were considered significant and biologically relevant. Results: In total 2,840 phosphopeptides were detected in at least 5% of the samples. Of these, 36 phosphopeptides were significantly upregulated and 14 were significantly downregulated in right-sided compared to left-sided CRCs using our stringent selection criteria. Since BRAF mutations and deficient DNA mismatch repair (dMMR) were more frequently observed in right-sided CRC (p < 0.01), group comparison was repeated with MMR proficient CRCs only, resulting in 21 phosphopeptides up- and one downregulated in left- versus right-sided CRC. The identified phosphoproteins from the phosphopeptides included three FDA approved drug targets. Conclusions: Differences in phosphoproteomic profiles were detected between left- and right-sided CRCs, besides molecular differences such as BRAF mutation and MMR status. These results indicate that the molecular biology of left-and right-sided CRCs may explain their differences in clinical behavior and response to treatment.
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Affiliation(s)
- Tineke Buffart
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Robin Beekhof
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Richard R. de Haas
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Sander R. Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Peet Nooijen
- Jeroen Bosch Hospital, 's-Hertogenbosch, Netherlands
| | - Hans Pruijt
- Jeroen Bosch Hospital, Den Bosch, Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk M.W. Verheul
- VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
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12
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Phan TH, van Leeuwen LM, Kuijl C, Ummels R, van Stempvoort G, Rubio-Canalejas A, Piersma SR, Jiménez CR, van der Sar AM, Houben ENG, Bitter W. EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF. PLoS Pathog 2018; 14:e1007247. [PMID: 30102741 PMCID: PMC6107294 DOI: 10.1371/journal.ppat.1007247] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/23/2018] [Accepted: 07/26/2018] [Indexed: 12/31/2022] Open
Abstract
The pathogen Mycobacterium tuberculosis employs a range of ESX-1 substrates to manipulate the host and build a successful infection. Although the importance of ESX-1 secretion in virulence is well established, the characterization of its individual components and the role of individual substrates is far from complete. Here, we describe the functional characterization of the Mycobacterium marinum accessory ESX-1 proteins EccA1, EspG1 and EspH, i.e. proteins that are neither substrates nor structural components. Proteomic analysis revealed that EspG1 is crucial for ESX-1 secretion, since all detectable ESX-1 substrates were absent from the cell surface and culture supernatant in an espG1 mutant. Deletion of eccA1 resulted in minor secretion defects, but interestingly, the severity of these secretion defects was dependent on the culture conditions. Finally, espH deletion showed a partial secretion defect; whereas several ESX-1 substrates were secreted in normal amounts, secretion of EsxA and EsxB was diminished and secretion of EspE and EspF was fully blocked. Interaction studies showed that EspH binds EspE and therefore could function as a specific chaperone for this substrate. Despite the observed differences in secretion, hemolytic activity was lost in all M. marinum mutants, implying that hemolytic activity is not strictly correlated with EsxA secretion. Surprisingly, while EspH is essential for successful infection of phagocytic host cells, deletion of espH resulted in a significantly increased virulence phenotype in zebrafish larvae, linked to poor granuloma formation and extracellular outgrowth. Together, these data show that different sets of ESX-1 substrates play different roles at various steps of the infection cycle of M. marinum. M. tuberculosis is a facultative intracellular pathogen that has an intimate relationship with host macrophages. Proteins secreted by the ESX-1 secretion system play an important role in this interaction, for instance by orchestrating the escape from the phagosome into the cytosol of the macrophage. However, the exact role of the ESX-1 substrates is unknown, due to their complicated interdependency for secretion. Here, we study the function of ESX-1 accessory proteins EccA1, EspG1 and EspH in ESX-1 secretion in Mycobacterium marium, the causative agent of fish tuberculosis. We found that these proteins affect the secretion of different substrate classes, which offers an approach to study the roles of these substrate groups. An espG1 deletion broadly aborts ESX-1 secretion and thus resulted in severe attenuation in a zebrafish model for tuberculosis, whereas EccA1 is only crucial under specific growth conditions. The most surprising results were obtained for EspH. This protein seems to function as a molecular chaperone for EspE and is as such involved in the secretion of a small subset of ESX-1 substrates. Disruption of espH showed a dual character: whereas this gene is essential for the successful infection of macrophages, deletion of espH resulted in significantly increased virulence in zebrafish larvae. These data convincingly show that different subsets of ESX-1 substrates play different roles at various steps in the mycobacterial infection cycle.
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Affiliation(s)
- Trang H. Phan
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lisanne M. van Leeuwen
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Coen Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Gunny van Stempvoort
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Alba Rubio-Canalejas
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, OncoProteomics Laboratory, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Astrid M. van der Sar
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Edith N. G. Houben
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- * E-mail:
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Ates LS, Dippenaar A, Ummels R, Piersma SR, van der Woude AD, van der Kuij K, Le Chevalier F, Mata-Espinosa D, Barrios-Payán J, Marquina-Castillo B, Guapillo C, Jiménez CR, Pain A, Houben ENG, Warren RM, Brosch R, Hernández-Pando R, Bitter W. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis. Nat Microbiol 2018; 3:181-188. [DOI: 10.1038/s41564-017-0090-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/29/2017] [Indexed: 12/30/2022]
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14
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Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NC, Verheul HM, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics 2017; 162:99-107. [DOI: 10.1016/j.jprot.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
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15
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Labots M, Gotink KJ, Dekker H, Azijli K, van der Mijn JC, Huijts CM, Piersma SR, Jiménez CR, Verheul HMW. Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer. Exp Mol Med 2016; 48:e279. [PMID: 27980342 PMCID: PMC5192072 DOI: 10.1038/emm.2016.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/19/2016] [Accepted: 06/11/2016] [Indexed: 01/05/2023] Open
Abstract
Personalized cancer medicine aims to accurately predict the response of individual patients to targeted therapies, including tyrosine kinase inhibitors (TKIs). Clinical implementation of this concept requires a robust selection tool. Here, using both cancer cell lines and tumor tissue from patients, we evaluated a high-throughput tyrosine kinase peptide substrate array to determine its readiness as a selection tool for TKI therapy. We found linearly increasing phosphorylation signal intensities of peptides representing kinase activity along the kinetic curve of the assay with 7.5–10 μg of lysate protein and up to 400 μM adenosine triphosphate (ATP). Basal kinase activity profiles were reproducible with intra- and inter-experiment coefficients of variation of <15% and <20%, respectively. Evaluation of 14 tumor cell lines and tissues showed similar consistently high phosphorylated peptides in their basal profiles. Incubation of four patient-derived tumor lysates with the TKIs dasatinib, sunitinib, sorafenib and erlotinib primarily caused inhibition of substrates that were highly phosphorylated in the basal profile analyses. Using recombinant Src and Axl kinase, relative substrate specificity was demonstrated for a subset of peptides, as their phosphorylation was reverted by co-incubation with a specific inhibitor. In conclusion, we demonstrated robust technical specifications of this high-throughput tyrosine kinase peptide microarray. These features required as little as 5–7 μg of protein per sample, facilitating clinical implementation as a TKI selection tool. However, currently available peptide substrates can benefit from an enhancement of the differential potential for complex samples such as tumor lysates. We propose that mass spectrometry-based phosphoproteomics may provide such an enhancement by identifying more discriminative peptides.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Kristy J Gotink
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Kaamar Azijli
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Charlotte M Huijts
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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Beekhof R, Labots M, Knol JC, Schelfhorst TR, van Grieken N, Piersma SR, Pham TV, Bertotti A, Trusolino L, Verheul HM, Jiménez CR. Abstract 880: Mapping the metastatic colorectal cancer phospho-proteome for predicting response to cetuximab. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The discovery of the key role of the epidermal growth factor receptor (EGFR) and its downstream signaling effectors in the pathophysiology of colorectal cancer (CRC) has resulted in the clinical use of targeted therapies in the treatment of metastatic CRC (mCRC). However, clinical benefit to EGFR blockade is observed in only a subgroup of CRC patients wild type for KRAS andNRAS. Genomic characterization of patient derived xenograft (PDX) models of mCRC have revealed additional resistance mechanisms to the EGFR MAb cetuximab including amplification of MET, HER2 and mutations in ERBB2, EGFR, FGFR1, PDGFRA, and MAP2K1 (Bertotti et al. 2011, 2015). However, not all resistance is understood and the biochemical signaling correlates of sensitivity and resistance remain incompletely understood. Phosphoproteomics allows for comprehensive protein phosphorylation profiling, and thereby may shed new insights into the biology of CRC and the molecular basis of cetuximab response.
Aim: To identify aberrant signaling pathways, predictive biomarkers, and alternative drug targets in genomically-annotated CRC PDX models by mass spectrometry-based phosphoproteomics.
Methods: We performed LC-MS/MS based phosphoproteome profiling (van der Mijn et al. 2015; Piersma et al. 2015) on untreated CRC PDX models lacking KRAS, NRAS or BRAF mutation (n = 20). For comparison, KRAS, BRAF or NRAS-mutant and MET or HER2 amplified models (n = 21) were analyzed. Phosphopeptides were captured by phosphotyrosine antibodies and titanium dioxide. MS/MS data was searched using MaxQuant. Phosphoproteome data (ion intensities and spectral counts) were correlated with drug sensitivity. Dedicated bioinformatics was used to identify hyperactive kinases and signaling pathways in individual tumors.
Results: The dataset contained 13.418 tyrosine-, serine- and threonine-phosphorylated peptides derived from 4588 proteins, including 237 phosphorylated kinases. Unsupervised hierarchical clustering of phosphopeptide intensities revealed subclusters enriched for sensitive and resistant models. Among cetuximab-resistant models, HER2 and MET were identified as hyperphosphorylated and hyperactive driver kinases, confirming the genomic annotation. Sensitivity to combination treatment of both EGFR and driver kinases was observed previously, providing proof-of-principle of the use of phosphoproteomics for the identification of driver kinases.
Conclusion/Future: This project is uncovering the phosphoproteomic landscape of colorectal tumors and will yield a better understanding of signaling pathways involved, with an emphasis on identifying activated drug targets and predictive biomarkers in this disease, in relation to KRAS/NRAS/BRAF status and response to anti-EGFR therapy.
Citation Format: Robin Beekhof, Mariette Labots, Jaco C. Knol, Tim R.A. Schelfhorst, Nicole van Grieken, Sander R. Piersma, Thang V. Pham, Andrea Bertotti, Livio Trusolino, Henk M.W. Verheul, Connie R. Jiménez. Mapping the metastatic colorectal cancer phospho-proteome for predicting response to cetuximab. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 880.
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Affiliation(s)
- Robin Beekhof
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
| | - Mariette Labots
- 2VUmc - Department of Medical Oncology, Amsterdam, Netherlands
| | - Jaco C. Knol
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
| | - Tim R.A. Schelfhorst
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
| | | | - Sander R. Piersma
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
| | - Thang V. Pham
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
| | - Andrea Bertotti
- 4University of Torino Medical School, Candiolo, Torino, Italy
| | - Livio Trusolino
- 4University of Torino Medical School, Candiolo, Torino, Italy
| | | | - Connie R. Jiménez
- 1VUmc - OncoProteomics Laboratory, Department of Medical Oncology, Amsterdam, Netherlands
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van der Mijn JC, Broxterman HJ, Knol JC, Piersma SR, De Haas RR, Dekker H, Pham TV, Van Beusechem VW, Halmos B, Mier JW, Jiménez CR, Verheul HMW. Sunitinib activates Axl signaling in renal cell cancer. Int J Cancer 2016; 138:3002-10. [PMID: 26815723 DOI: 10.1002/ijc.30022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/01/2015] [Accepted: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Mass spectrometry-based phosphoproteomics provides a unique unbiased approach to evaluate signaling network in cancer cells. The tyrosine kinase inhibitor sunitinib is registered as treatment for patients with renal cell cancer (RCC). We investigated the effect of sunitinib on tyrosine phosphorylation in RCC tumor cells to get more insight in its mechanism of action and thereby to find potential leads for combination treatment strategies. Sunitinib inhibitory concentrations of proliferation (IC50) of 786-O, 769-p and A498 RCC cells were determined by MTT-assays. Global tyrosine phosphorylation was measured by LC-MS/MS after immunoprecipitation with the antiphosphotyrosine antibody p-TYR-100. Phosphoproteomic profiling of 786-O cells yielded 1519 phosphopeptides, corresponding to 675 unique proteins including 57 different phosphorylated protein kinases. Compared to control, incubation with sunitinib at its IC50 of 2 µM resulted in downregulation of 86 phosphopeptides including CDK5, DYRK3, DYRK4, G6PD, PKM and LDH-A, while 94 phosphopeptides including Axl, FAK, EPHA2 and p38α were upregulated. Axl- (y702), FAK- (y576) and p38α (y182) upregulation was confirmed by Western Blot in 786-O and A498 cells. Subsequent proliferation assays revealed that inhibition of Axl with a small molecule inhibitor (R428) sensitized 786-O RCC cells and immortalized endothelial cells to sunitinib up to 3 fold. In conclusion, incubation with sunitinib of RCC cells causes significant upregulation of multiple phosphopeptides including Axl. Simultaneous inhibition of Axl improves the antitumor activity of sunitinib. We envision that evaluation of phosphoproteomic changes by TKI treatment enables identification of new targets for combination treatment strategies.
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Affiliation(s)
- Johannes C van der Mijn
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Henk J Broxterman
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Richard R De Haas
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Victor W Van Beusechem
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Balazs Halmos
- Department of Hematology/Oncology, Columbia University Medical Center, New York, NY
| | - James W Mier
- Department of Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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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 Proteom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Labots M, Beekhof R, Knol JC, Neerincx M, de Haas RR, Dekker H, Pham TV, Piersma SR, Henneberry E, Van der Mijn JC, Rovithi M, Van der Peet DL, Meijerink MR, van Grieken NC, Jiménez CR, Verheul HM. Mass spectrometry-based phosphoproteomics of tumor needle biopsies from patients (pts) with advanced solid tumors during treatment with protein kinase inhibitors. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.11609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Robin Beekhof
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Jaco C. Knol
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Maarten Neerincx
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Richard R. de Haas
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Thang V. Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Evan Henneberry
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Maria Rovithi
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | | | | | - Connie R. Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
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20
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Ates LS, Ummels R, Commandeur S, van der Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria. PLoS Genet 2015; 11:e1005190. [PMID: 25938982 PMCID: PMC4418733 DOI: 10.1371/journal.pgen.1005190] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/02/2015] [Indexed: 12/03/2022] Open
Abstract
Mycobacteria possess different type VII secretion (T7S) systems to secrete proteins across their unusual cell envelope. One of these systems, ESX-5, is only present in slow-growing mycobacteria and responsible for the secretion of multiple substrates. However, the role of ESX-5 substrates in growth and/or virulence is largely unknown. In this study, we show that esx-5 is essential for growth of both Mycobacterium marinum and Mycobacterium bovis. Remarkably, this essentiality can be rescued by increasing the permeability of the outer membrane, either by altering its lipid composition or by the introduction of the heterologous porin MspA. Mutagenesis of the first nucleotide-binding domain of the membrane ATPase EccC5 prevented both ESX-5-dependent secretion and bacterial growth, but did not affect ESX-5 complex assembly. This suggests that the rescuing effect is not due to pores formed by the ESX-5 membrane complex, but caused by ESX-5 activity. Subsequent proteomic analysis to identify crucial ESX-5 substrates confirmed that all detectable PE and PPE proteins in the cell surface and cell envelope fractions were routed through ESX-5. Additionally, saturated transposon-directed insertion-site sequencing (TraDIS) was applied to both wild-type M. marinum cells and cells expressing mspA to identify genes that are not essential anymore in the presence of MspA. This analysis confirmed the importance of esx-5, but we could not identify essential ESX-5 substrates, indicating that multiple of these substrates are together responsible for the essentiality. Finally, examination of phenotypes on defined carbon sources revealed that an esx-5 mutant is strongly impaired in the uptake and utilization of hydrophobic carbon sources. Based on these data, we propose a model in which the ESX-5 system is responsible for the transport of cell envelope proteins that are required for nutrient uptake. These proteins might in this way compensate for the lack of MspA-like porins in slow-growing mycobacteria.
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Affiliation(s)
- Louis S. Ates
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Susanna Commandeur
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Robert van der Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marion Sparrius
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Eveline Weerdenburg
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sander R. Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Abdallah M. Abdallah
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Moataz Abd El Ghany
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Alyaa M. Abdel-Haleem
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Connie R. Jiménez
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Edith N.G. Houben
- Section Molecular Microbiology, Amsterdam Institute of Molecules, Medicine & Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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21
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van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR. Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics. J Proteomics 2015; 127:259-63. [PMID: 25890253 DOI: 10.1016/j.jprot.2015.04.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/06/2015] [Accepted: 04/08/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Mass spectrometry based phosphoproteomics emerged as advantageous approach for the analysis of tyrosine phosphorylation on proteins and tyrosine kinase signaling. Immunoaffinity purification is required for comprehensive analysis. Here we compared the performance of two antibodies for label-free phosphotyrosine-based phosphoproteomics. METHODS Phosphopeptide immunoprecipitation of six technical replicates corresponding to 10mg protein from HCT116 cells was performed using agarose bead-coupled phosphotyrosine antibodies P-Tyr-1000 (N=3) and 4G10 (N=3). NanoLC-MS/MS was performed using a Q Exactive mass spectrometer. For relative quantitation of protein phosphorylation, spectral counts of phosphoproteins and ion intensities of phosphopeptides were determined using MaxQuant. RESULTS From the 3 samples incubated with P-Tyr-1000 a total of 689 phosphopeptides were identified with 60% ID reproducibility. The phosphopeptide capture using 4G10 resulted in a total of 421 at 46% ID reproducibility. The P-Tyr-1000 was applied to EGFR mutated U87 cells. Erlotinib reduced EGFR phosphorylation with 59% at y978, y1125, y1138, y1172, and y1197. EGFR inhibition was accompanied by enhanced phosphorylation of FYN, MET, PTK2, DYRK1A, MAPK1 and EPHA2. CONCLUSION The P-Tyr-1000 phosphotyrosine antibody performs superiorly when compared to 4G10 antibody for label-free phosphotyrosine-based phosphoproteomics. This workflow allows evaluation of drug target phosphorylation and may give insights in the pharmacodynamic effects of tyrosine kinase inhibitors. CLINICAL SIGNIFICANCE In the past decade multiple tyrosine kinase inhibitors (TKIs) have been implemented in standard treatment regimens for patients with cancer. Unfortunately the majority of patients develops resistance to these drugs. Reliable tools for analysis of pharmacodynamic effects and drug resistance mechanisms are therefore warranted. Phosphoproteomic analyses have meanwhile emerged as a sophisticated approach for the determination of protein phosphorylation. These analyses rely on antibodies for enrichment of tyrosine-phosphorylated peptides. Here we compared two commercially available phosphotyrosine antibodies and show that P-Tyr-1000 yields 64% more phosphopeptides than 4G10 antibody, while including almost all 4G10 captured phosphopeptides. The workflow can be reproducibly performed at intermediate protein input levels of 10mg. Furthermore, application of the P-Tyr-1000 antibody in a standardized phosphoproteomics workflow allows relative quantitation of drug target inhibition and provides insights in alternative signaling pathways in cancer cells. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
| | - Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk J Broxterman
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
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Nagel R, Stigter-van Walsum M, Buijze M, van den Berg J, van der Meulen IH, Hodzic J, Piersma SR, Pham TV, Jiménez CR, van Beusechem VW, Brakenhoff RH. Genome-wide siRNA Screen Identifies the Radiosensitizing Effect of Downregulation of MASTL and FOXM1 in NSCLC. Mol Cancer Ther 2015; 14:1434-44. [PMID: 25808837 DOI: 10.1158/1535-7163.mct-14-0846] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/11/2015] [Indexed: 11/16/2022]
Abstract
Lung cancer is the most common cancer worldwide and on top of that has a very poor prognosis, which is reflected by a 5-year survival rate of 5% to 15%. Radiotherapy is an integral part of most treatment regimens for this type of tumor, often combined with radiosensitizing cytotoxic drugs. In this study, we identified many genes that could potentially be exploited for targeted radiosensitization using a genome-wide siRNA screen in non-small cell lung cancer (NSCLC) cells. The screen identified 433 siRNAs that potentially sensitize lung cancer cells to radiation. Validation experiments showed that knockdown of expression of Forkhead box M1 (FOXM1) or microtubule-associated serine/threonine kinase-like (MASTL) indeed causes radiosensitization in a panel of NSCLC cells. Strikingly, this effect was not observed in primary human fibroblasts, suggesting that the observed radiosensitization is specific for cancer cells. Phosphoproteomics analyses with and without irradiation showed that a number of cell-cycle-related proteins were significantly less phosphorylated after MASTL knockdown in comparison to the control, while there were no changes in the levels of phosphorylation of DNA damage response proteins. Subsequent analyses showed that MASTL knockdown cells respond differently to radiation, with a significantly shortened G2-M phase arrest and defects in cytokinesis, which are followed by a cell-cycle arrest. In summary, we have identified many potential therapeutic targets that could be used for radiosensitization of NSCLC cells, with MASTL being a very promising and druggable target to combine with radiotherapy.
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Affiliation(s)
- Remco Nagel
- Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands
| | - Marijke Stigter-van Walsum
- Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands
| | - Marijke Buijze
- Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands
| | - Jaap van den Berg
- Department of Radiation Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ida H van der Meulen
- RNA Interference Functional Oncogenomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands. Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Jasmina Hodzic
- 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
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Victor W van Beusechem
- RNA Interference Functional Oncogenomics Laboratory, VU University Medical Center, Amsterdam, the Netherlands. Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands.
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Labots M, Schütte LM, van der Mijn JC, Pham TV, Jiménez CR, Verheul HMW. Mass spectrometry-based serum and plasma peptidome profiling for prediction of treatment outcome in patients with solid malignancies. Oncologist 2014; 19:1028-39. [PMID: 25187478 DOI: 10.1634/theoncologist.2014-0101] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Treatment selection tools are needed to enhance the efficacy of targeted treatment in patients with solid malignancies. Providing a readout of aberrant signaling pathways and proteolytic events, mass spectrometry-based (MS-based) peptidomics enables identification of predictive biomarkers, whereas the serum or plasma peptidome may provide easily accessible signatures associated with response to treatment. In this systematic review, we evaluate MS-based peptide profiling in blood for prompt clinical implementation. METHODS PubMed and Embase were searched for studies using a syntax based on the following hierarchy: (a) blood-based matrix-assisted or surface-enhanced laser desorption/ionization time-of-flight MS peptide profiling (b) in patients with solid malignancies (c) prior to initiation of any treatment modality, (d) with availability of outcome data. RESULTS Thirty-eight studies were eligible for review; the majority were performed in patients with non-small cell lung cancer (NSCLC). Median classification prediction accuracy was 80% (range: 66%-93%) in 11 models from 14 studies reporting an MS-based classification model. A pooled analysis of 9 NSCLC studies revealed clinically significant median progression-free survival in patients classified as "poor outcome" and "good outcome" of 2.0 ± 1.06 months and 4.6 ± 1.60 months, respectively; median overall survival was also clinically significant at 4.01 ± 1.60 months and 10.52 ± 3.49 months, respectively. CONCLUSION Pretreatment MS-based serum and plasma peptidomics have shown promising results for prediction of treatment outcome in patients with solid tumors. Limited sample sizes and absence of signature validation in many studies have prohibited clinical implementation thus far. Our pooled analysis and recent results from the PROSE study indicate that this profiling approach enables treatment selection, but additional prospective studies are warranted.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Lisette M Schütte
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Thang V Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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Hassan C, Kester MGD, Oudgenoeg G, de Ru AH, Janssen GMC, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MHM, Falkenburg JHF, van Veelen PA. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J Proteomics 2014; 109:240-4. [PMID: 25050860 DOI: 10.1016/j.jprot.2014.07.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 11/30/2022]
Abstract
Knowledge of the accurate copy number of HLA class I presented ligands is important in fundamental and clinical immunology. Currently, the best copy number determinations are based on mass spectrometry, employing single reaction monitoring (SRM) in combination with a known amount of isotopically labeled peptide. The major drawback of this approach is that the losses during sample pretreatment, i.e. immunopurification and filtration steps, are not well defined and must, therefore, be estimated. In addition, such losses can vary for individual peptides. Therefore, we developed a new approach in which isotopically labeled peptide-MHC monomers (hpMHC) are prepared and added directly after cell lysis, i.e. before the usual sample processing. Using this approach, all losses during sample processing can be accounted for and allows accurate determination of specific MHC class I-presented ligands. Our study pinpoints the immunopurification step as the origin of the rather extreme losses during sample pretreatment and offers a solution to account for these losses. Obviously, this has important implications for accurate HLA-ligand quantitation. The strategy presented here can be used to obtain a reliable view of epitope copy number and thus allows improvement of vaccine design and strategies for immunotherapy.
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Affiliation(s)
- Chopie Hassan
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gideon Oudgenoeg
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Robbert M Spaapen
- Department of Cell Biology II, The Netherlands Cancer Institute (NKI-AVL), Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - J H Frederik Falkenburg
- Department of Hematology, Laboratory of Experimental hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Labots M, Schutte LM, Van der Mijn JC, Pham TV, Jiménez CR, Verheul HM. Mass spectrometry-based serum and plasma peptide profiling for prediction of treatment outcome in patients with cancer. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e22221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Lisette M. Schutte
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Thang V. Pham
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
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Chiasserini D, van Weering JRT, Piersma SR, Pham TV, Malekzadeh A, Teunissen CE, de Wit H, Jiménez CR. Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset. J Proteomics 2014; 106:191-204. [PMID: 24769233 DOI: 10.1016/j.jprot.2014.04.028] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/03/2014] [Accepted: 04/14/2014] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are present in human cerebrospinal fluid (CSF), yet little is known about their protein composition. The aim of this study is to provide a comprehensive analysis of the proteome of CSF EVs by electron microscopy and high resolution tandem mass spectrometry (MS/MS) in conjunction with bioinformatics. We report an extensive catalog of 1315 proteins identified in EVs isolated from two different CSF pools by ultracentrifugation, including 230 novel EV proteins. Out of 1315 proteins, 760 were identified in both CSF pools and about 30% of those were also quantitatively enriched in the EV fraction versus the soluble CSF fraction. The proteome of CSF EVs was enriched in exosomal markers such as alix and syntenin-1, heat shock proteins and tetraspanins and contained a high proportion of brain-derived proteins (n=373). Interestingly, several known biomarkers for neurodegenerative diseases such as the amyloid precursor protein, the prion protein and DJ-1 were identified in the EV fractions. Our dataset represents the first comprehensive inventory of the EV proteome in CSF, underscoring the biomarker potential of this organelle. Further comparative studies on CSF EVs isolated from patients diagnosed with neurological disorders are warranted. Data are available via ProteomeXchange with identifier PXD000608. Biological significance In this study we analyzed the protein composition of extracellular vesicles isolated from pooled samples of human cerebrospinal fluid (CSF). CSF is a colorless fluid surrounding the brain and the spinal cord, important for the physiology of the central nervous system, ensuing mechanical protection, regulation of brain blood flow and elimination of byproducts of the brain. Since brain (patho)physiology is reflected in CSF, this biological fluid represents an ideal source of soluble and vesicle-based biomarkers for neurological diseases. Here we confirm the presence of exosome-like extracellular vesicles in CSF, underscoring a potential role in the physiology of the brain. These extracellular vesicles provide a rich source of candidate biomarkers, representing a brain "fluid biopsy". Most interestingly, the involvement of extracellular vesicles in transferring toxic proteins such as α-synuclein and β-amyloid has been postulated as one of the mechanisms involved in the spreading of neurodegeneration to different brain areas. In line with this, we show that human CSF extracellular vesicles contain prionogenic proteins such as the amyloid precursor protein and the prion protein. Delineating the protein composition of extracellular vesicles in CSF is a first and crucial step to comprehend their origin and their function in the central nervous system and to establish their biomarker potential.
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Affiliation(s)
- Davide Chiasserini
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jan R T van Weering
- Department of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, VU University Medical Center, The Netherlands
| | - Sander R Piersma
- 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
| | - Arjan Malekzadeh
- Department of Clinical Chemistry, Neurochemistry Laboratory and Biobank, VU University Medical Center, Amsterdam, the Netherlands
| | - Charlotte E Teunissen
- Department of Clinical Chemistry, Neurochemistry Laboratory and Biobank, VU University Medical Center, Amsterdam, the Netherlands
| | - Heidi de Wit
- Department of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, VU University Medical Center, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
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Knol JC, de Wit M, Albrethsen J, Piersma SR, Pham TV, Mongera S, Carvalho B, Fijneman RJA, Meijer GA, Jiménez CR. Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues. Biochim Biophys Acta 2013; 1844:1034-43. [PMID: 24361553 DOI: 10.1016/j.bbapap.2013.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/28/2013] [Accepted: 12/10/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Altered nuclear and genomic structure and function are hallmarks of cancer cells. Research into nuclear proteins in human tissues could uncover novel molecular processes in cancer. Here, we examine biochemical tissue fractions containing chromatin-binding (CB) proteins in the context of colorectal cancer (CRC) progression. METHODS CB protein-containing fractions were biochemically extracted from human colorectal tissues, including carcinomas with chromosomal instability (CIN), carcinomas with microsatellite instability (MIN), and adenomas. The CB proteins were subjected to label-free LC-MS/MS and the data were analyzed by bioinformatics. RESULTS Over 1700 proteins were identified in the CB fraction from colonic tissues, including 938 proteins associated with nuclear annotation. Of the latter, 169 proteins were differential between adenomas and carcinomas. In this adenoma-versus-carcinoma comparison, apart from specific changes in components of the splicing and protein translational machineries, we also identified significant changes in several proteins associated with chromatin-directed functions. Furthermore, several key cell cycle proteins as well as those involved in cellular stress were increased, whereas specific components of chromosome segregation and DNA recombination/repair systems were decreased. CONCLUSIONS Our study identifies proteomic changes at the subnuclear level that are associated with CRC and may be further investigated. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Jaco C Knol
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Jakob Albrethsen
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands; Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Sander R Piersma
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands.
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van der Woude AD, Stoop EJM, Stiess M, Wang S, Ummels R, van Stempvoort G, Piersma SR, Cascioferro A, Jiménez CR, Houben ENG, Luirink J, Pieters J, van der Sar AM, Bitter W. Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector. Cell Microbiol 2013; 16:280-95. [PMID: 24119166 DOI: 10.1111/cmi.12221] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 09/14/2013] [Accepted: 09/24/2013] [Indexed: 02/03/2023]
Abstract
The pathogenicity of mycobacteria is closely associated with their ability to export virulence factors. For this purpose, mycobacteria possess different protein secretion systems, including the accessory Sec translocation pathway, SecA2. Although this pathway is associated with intracellular survival and virulence, the SecA2-dependent effector proteins remain largely undefined. In this work, we studied a Mycobacterium marinum secA2 mutant with an impaired capacity to initiate granuloma formation in zebrafish embryos. By comparing the proteomic profile of cell envelope fractions from the secA2 mutant with wild type M. marinum, we identified putative SecA2-dependent substrates. Immunoblotting procedures confirmed SecA2-dependent membrane localization for several of these proteins, including the virulence factor protein kinase G (PknG). Interestingly, phenotypical defects of the secA2 mutant are similar to those described for ΔpknG, including phagosomal maturation. Overexpression of PknG in the secA2 mutant restored its localization to the cell envelope. Importantly, PknG-overexpression also partially restored the virulence of the secA2 mutant, as indicated by enhanced infectivity in zebrafish embryos and restored inhibition of phagosomal maturation. These results suggest that SecA2-dependent membrane localization of PknG is an important determinant for M. marinum virulence.
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Affiliation(s)
- Aniek D van der Woude
- Department of Medical Microbiology and Infection Control, VU University Medical Center, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands; Department of Molecular Microbiology, Institute of Molecular Cell Biology, VU University, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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Kooij V, Zhang P, Piersma SR, Sequeira V, Boontje NM, Wijnker PJM, Jiménez CR, Jaquet KE, dos Remedios C, Murphy AM, Van Eyk JE, van der Velden J, Stienen GJM. PKCα-specific phosphorylation of the troponin complex in human myocardium: a functional and proteomics analysis. PLoS One 2013; 8:e74847. [PMID: 24116014 PMCID: PMC3792062 DOI: 10.1371/journal.pone.0074847] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/07/2013] [Indexed: 11/18/2022] Open
Abstract
Aims Protein kinase Cα (PKCα) is one of the predominant PKC isoforms that phosphorylate cardiac troponin. PKCα is implicated in heart failure and serves as a potential therapeutic target, however, the exact consequences for contractile function in human myocardium are unclear. This study aimed to investigate the effects of PKCα phosphorylation of cardiac troponin (cTn) on myofilament function in human failing cardiomyocytes and to resolve the potential targets involved. Methods and Results Endogenous cTn from permeabilized cardiomyocytes from patients with end-stage idiopathic dilated cardiomyopathy was exchanged (∼69%) with PKCα-treated recombinant human cTn (cTn (DD+PKCα)). This complex has Ser23/24 on cTnI mutated into aspartic acids (D) to rule out in vitro cross-phosphorylation of the PKA sites by PKCα. Isometric force was measured at various [Ca2+] after exchange. The maximal force (Fmax) in the cTn (DD+PKCα) group (17.1±1.9 kN/m2) was significantly reduced compared to the cTn (DD) group (26.1±1.9 kN/m2). Exchange of endogenous cTn with cTn (DD+PKCα) increased Ca2+-sensitivity of force (pCa50 = 5.59±0.02) compared to cTn (DD) (pCa50 = 5.51±0.02). In contrast, subsequent PKCα treatment of the cells exchanged with cTn (DD+PKCα) reduced pCa50 to 5.45±0.02. Two PKCα-phosphorylated residues were identified with mass spectrometry: Ser198 on cTnI and Ser179 on cTnT, although phosphorylation of Ser198 is very low. Using mass spectrometry based-multiple reaction monitoring, the extent of phosphorylation of the cTnI sites was quantified before and after treatment with PKCα and showed the highest phosphorylation increase on Thr143. Conclusion PKCα-mediated phosphorylation of the cTn complex decreases Fmax and increases myofilament Ca2+-sensitivity, while subsequent treatment with PKCα in situ decreased myofilament Ca2+-sensitivity. The known PKC sites as well as two sites which have not been previously linked to PKCα are phosphorylated in human cTn complex treated with PKCα with a high degree of specificity for Thr143.
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Affiliation(s)
- Viola Kooij
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| | - Pingbo Zhang
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Sander R. Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Vasco Sequeira
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
| | - Nicky M. Boontje
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
| | - Paul J. M. Wijnker
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Kornelia E. Jaquet
- St Josef-Hospital/Bergmannsheil, Clinic of the Ruhr-University of Bochum, Bochum, Germany
| | - Cris dos Remedios
- Muscle Research Unit, Institute for Biomedical Research, The University of Sydney, Sydney, Australia
| | - Anne M. Murphy
- Institute of Molecular Cardiobiology, Department of Pediatrics, School of Medical, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jennifer E. Van Eyk
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jolanda van der Velden
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
| | - Ger JM. Stienen
- Laboratory for Physiology, Institute for Cardiovascular Research, VU Medical Center, Amsterdam, The Netherlands
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
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Posthumadeboer J, Piersma SR, Pham TV, van Egmond PW, Knol JC, Cleton-Jansen AM, van Geer MA, van Beusechem VW, Kaspers GJL, van Royen BJ, Jiménez CR, Helder MN. Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery. Br J Cancer 2013; 109:2142-54. [PMID: 24064975 PMCID: PMC3798973 DOI: 10.1038/bjc.2013.578] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/23/2013] [Accepted: 08/28/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Osteosarcoma (OS) is the most common bone tumour in children and adolescents. Despite aggressive therapy regimens, treatment outcomes are unsatisfactory. Targeted delivery of drugs can provide higher effective doses at the site of the tumour, ultimately improving the efficacy of existing therapy. Identification of suitable receptors for drug targeting is an essential step in the design of targeted therapy for OS. METHODS We conducted a comparative analysis of the surface proteome of human OS cells and osteoblasts using cell surface biotinylation combined with nano-liquid chromatography - tandem mass spectrometry-based proteomics to identify surface proteins specifically upregulated on OS cells. This approach generated an extensive data set from which we selected a candidate to study for its suitability as receptor for targeted treatment delivery to OS. First, surface expression of the ephrin type-A receptor 2 (EPHA2) receptor was confirmed using FACS analysis. Ephrin type-A receptor 2 expression in human tumour tissue was tested using immunohistochemistry. Receptor targeting and internalisation studies were conducted to assess intracellular uptake of targeted modalities via EPHA2. Finally, tissue micro arrays containing cores of human OS tissue were stained using immunohistochemistry and EPHA2 staining was correlated to clinical outcome measures. RESULTS Using mass spectrometry, a total of 2841 proteins were identified of which 156 were surface proteins significantly upregulated on OS cells compared with human primary osteoblasts. Ephrin type-A receptor 2 was highly upregulated and the most abundant surface protein on OS cells. In addition, EPHA2 was expressed in a vast majority of human OS samples. Ephrin type-A receptor 2 effectively mediates internalisation of targeted adenoviral vectors into OS cells. Patients with EPHA2-positive tumours showed a trend toward inferior overall survival. CONCLUSION The results presented here suggest that the EPHA2 receptor can be considered an attractive candidate receptor for targeted delivery of therapeutics to OS.
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Affiliation(s)
- J Posthumadeboer
- Department of Orthopaedic Surgery, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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Labots M, Neerincx M, Van der Mijn JC, Dekker H, Honeywell R, Rovithi M, Gotink K, Voebel-De Jong M, Van der Peet DL, Meijerink MR, Meijer GA, Jiménez CR, Peters GJ, Verheul HM. Tumor, skin, and plasma concentrations of protein kinase inhibitors (PKIs) in patients with advanced cancer. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.11087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11087 Background: PKIs are selective for target receptors at low concentrations, but they act promiscuously at higher concentrations (PMID 18183025). This lack of selectivity may be relevant for their antitumor activity and for the development of PKI treatment selection tools. To obtain more insight in their clinical mechanism of action, we designed a pilot study to determine PKI tumor, skin and plasma concentrations in patients (pts) after 2 weeks of treatment. Results are related to cell line sensitivity data. Methods: Prior to standard palliative systemic treatment, pts were allocated to standard-dose PKI treatment (N=5 per PKI) for 10-14 days. Plasma, tumor and skin biopsies were collected within 24 hours of last dose. Sample PKI concentrations were determined by liquid chromatography – tandem mass spectrometry (LC-MS/MS); tissue concentrations in pg/mg were converted to molarity for comparison with preclinical sensitivity data (PMID 21980135). Concentrations of sunitinib (SUN), sorafenib (SOR), erlotinib (ERL), dasatinib (DAS) and everolimus (EVE) that inhibit 50% of cell proliferation (IC50) were determined by MTT assay in 1 RCC (786-O) and 8 CRC cell lines (HCT 116, HT-29, RKO, SW480, SW1398, DLD-1, COLO 205, CaCo-2). Results: Since August 2011 samples were obtained from 27 pts; 5 received SUN, 4 SOR, 4 ERL, 5 DAS and 5 EVE. After 12 ± 1 days of treatment, median tumor concentration (TC) was 9.0 µM (2.3-50.0) (range) for SUN, 8.5 µM (3.7-22.0) for SOR, 5.3 µM (0.9-10.8) for ERL and 2.1 µM (0.2-64.0) for DAS. EVE was measurable in 2 of 5 tumors: 3.5 µM (3.4-3.6). On average, PKI skin concentrations were 2.4-fold lower than TCs. SOR and ERL plasma concentrations (PCs) were in the range of TCs while SUN and DAS PCs were at least 14-fold lower than in tumors. Mean IC50 of the cell line panel was 1.3 µM (0.8-1.4) for SUN, 2.2 µM (1.4-3) for SOR, 8.2 µM (4-11.5) for ERL, 0.06 µM (0.02-1.8) for DAS and 1.2 µM (0.05-11) for EVE. Conclusions: PKI tumor concentrations may vary considerably from plasma concentrations, but are in the IC50 range of cancer cells in vitro. These results are indicative for the inhibitory concentrations of PKIs in patient tumors and should be considered for the development of individualized treatment strategies. Clinical trial information: NCT01636908.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Maarten Neerincx
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Henk Dekker
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Richard Honeywell
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Maria Rovithi
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Kristy Gotink
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | | | | | | | - Gerrit A. Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
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Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jiménez CR. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013; 11:17. [PMID: 23617947 PMCID: PMC3656797 DOI: 10.1186/1477-5956-11-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 04/11/2013] [Indexed: 12/24/2022] Open
Abstract
Background SDS-PAGE followed by in-gel digestion (IGD) is a popular workflow in mass spectrometry-based proteomics. In GeLC-MS/MS, a protein lysate of a biological sample is separated by SDS-PAGE and each gel lane is sliced in 5–20 slices which, after IGD, are analyzed by LC-MS/MS. The database search results for all slices of a biological sample are combined yielding global protein identification and quantification for each sample. In large scale GeLC-MS/MS experiments the manual processing steps including washing, reduction and alkylation become a bottleneck. Here we introduce the whole gel (WG) procedure where, prior to gel slice cutting, the processing steps are carried out on the whole gel. Results In two independent experiments human HCT116 cell lysate and mouse tumor tissue lysate were separated by 1D SDS PAGE. In a back to back comparison of the IGD procedure and the WG procedure, both protein identification (>80% overlap) and label-free protein quantitation (R2=0.94) are highly similar between procedures. Triplicate analysis of the WG procedure of both HCT116 cell lysate and formalin-fixed paraffin embedded (FFPE) tumor tissue showed identification reproducibility of >88% with a CV<20% on protein quantitation. Conclusions The whole gel procedure allows for reproducible large-scale differential GeLC-MS/MS experiments, without a prohibitive amount of manual processing and with similar performance as conventional in-gel digestion. This procedure will especially enable clinical proteomics for which GeLC-MS/MS is a popular workflow and sample numbers are relatively high.
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Affiliation(s)
- Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
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Schaaij-Visser TBM, de Wit M, Lam SW, Jiménez CR. The cancer secretome, current status and opportunities in the lung, breast and colorectal cancer context. Biochim Biophys Acta 2013; 1834:2242-58. [PMID: 23376433 DOI: 10.1016/j.bbapap.2013.01.029] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/18/2013] [Accepted: 01/23/2013] [Indexed: 12/20/2022]
Abstract
Despite major improvements on the knowledge and clinical management, cancer is still a deadly disease. Novel biomarkers for better cancer detection, diagnosis and treatment prediction are urgently needed. Proteins secreted, shed or leaking from the cancer cell, collectively termed the cancer secretome, are promising biomarkers since they might be detectable in blood or other biofluids. Furthermore, the cancer secretome in part represents the tumor microenvironment that plays a key role in tumor promoting processes such as angiogenesis and invasion. The cancer secretome, sampled as conditioned medium from cell lines, tumor/tissue interstitial fluid or tumor proximal body fluids, can be studied comprehensively by nanoLC-MS/MS-based approaches. Here, we outline the importance of current cancer secretome research and describe the mass spectrometry-based analysis of the secretome. Further, we provide an overview of cancer secretome research with a focus on the three most common cancer types: lung, breast and colorectal cancer. We conclude that the cancer secretome research field is a young, but rapidly evolving research field. Up to now, the focus has mainly been on the discovery of novel promising secreted cancer biomarker proteins. An interesting finding that merits attention is that in cancer unconventional secretion, e.g. via vesicles, seems increased. Refinement of current approaches and methods and progress in clinical validation of the current findings are vital in order to move towards applications in cancer management. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Tieneke B M Schaaij-Visser
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Division of Molecular Genetics and Centre for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Houben ENG, Bestebroer J, Ummels R, Wilson L, Piersma SR, Jiménez CR, Ottenhoff THM, Luirink J, Bitter W. Composition of the type VII secretion system membrane complex. Mol Microbiol 2012; 86:472-84. [DOI: 10.1111/j.1365-2958.2012.08206.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2012] [Indexed: 01/04/2023]
Affiliation(s)
| | - Jovanka Bestebroer
- Department of Medical Microbiology and Infection Control; VU University Medical Center; Amsterdam; The Netherlands
| | - Roy Ummels
- Department of Medical Microbiology and Infection Control; VU University Medical Center; Amsterdam; The Netherlands
| | - Louis Wilson
- Department of Infectious Diseases; Leiden University Medical Center; Leiden; The Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology; OncoProteomics Laboratory; VU University Medical Center; Amsterdam; The Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology; OncoProteomics Laboratory; VU University Medical Center; Amsterdam; The Netherlands
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases; Leiden University Medical Center; Leiden; The Netherlands
| | - Joen Luirink
- Department of Molecular Microbiology; Institute of Molecular Cell Biology; VU University Amsterdam; Amsterdam; The Netherlands
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Daleke MH, van der Woude AD, Parret AHA, Ummels R, de Groot AM, Watson D, Piersma SR, Jiménez CR, Luirink J, Bitter W, Houben ENG. Specific chaperones for the type VII protein secretion pathway. J Biol Chem 2012; 287:31939-47. [PMID: 22843727 DOI: 10.1074/jbc.m112.397596] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacteria use the dedicated type VII protein secretion systems ESX-1 and ESX-5 to secrete virulence factors across their highly hydrophobic cell envelope. The substrates of these systems include the large mycobacterial PE and PPE protein families, which are named after their characteristic Pro-Glu and Pro-Pro-Glu motifs. Pathogenic mycobacteria secrete large numbers of PE/PPE proteins via the major export pathway, ESX-5. In addition, a few PE/PPE proteins have been shown to be exported by ESX-1. It is not known how ESX-1 and ESX-5 recognize their cognate PE/PPE substrates. In this work, we investigated the function of the cytosolic protein EspG(5), which is essential for ESX-5-mediated secretion in Mycobacterium marinum, but for which the role in secretion is not known. By performing protein co-purifications, we show that EspG(5) interacts with several PPE proteins and a PE/PPE complex that is secreted by ESX-5, but not with the unrelated ESX-5 substrate EsxN or with PE/PPE proteins secreted by ESX-1. Conversely, the ESX-1 paralogue EspG(1) interacted with a PE/PPE couple secreted by ESX-1, but not with PE/PPE substrates of ESX-5. Furthermore, structural analysis of the complex formed by EspG(5) and PE/PPE indicates that these proteins interact in a 1:1:1 ratio. In conclusion, our study shows that EspG(5) and EspG(1) interact specifically with PE/PPE proteins that are secreted via their own ESX systems and suggests that EspG proteins are specific chaperones for the type VII pathway.
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Affiliation(s)
- Maria H Daleke
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 BT Amsterdam, The Netherlands
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Ginel PJ, Blanco B, Lucena R, Jiménez CR, Peinado-Guitart C, Mozos E. Steroid-sparing effect of mycophenolate mofetil in the treatment of a subepidermal blistering autoimmune disease in a dog. J S Afr Vet Assoc 2011; 81:253-7. [PMID: 21526742 DOI: 10.4102/jsava.v81i4.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
A 7-year-old female Cocker spaniel-cross was referred with an 8-month history of mucocutaneous erosive dermatitis. On physical examination, skin lesions affected the eyelids and periocular area, lips and vulva. Lesions were symmetrical with small diffuse superficial ulcers, haemorrhagic crusts, adherent purulent exudation in haired skin, and alopecia with hyperpigmentation and scarring. Histopathologic evaluation showed multiple, non-intact dermoepidermal junction vesicles and ulceration associated with a dermal lichenoid infiltrate. Immunohistochemistry showed strong to moderate reactivity in the dermoepidermal junction for the antibodies directed against canine IgG, human IgG lambda light chains and C3, respectively. A diagnosis of autoimmune subepidermal blistering dermatosis was made. Treatment with oral prednisone at 2 mg/kg and mycophenolate mofetil (MMF) at 20 mg/kg twice daily was initiated and after 4 weeks the ulcers and erosions were cured. During the rest of treatment, MMF was maintained at 10 mg/kg twice daily and prednisone could be tapered to 0.25 mg/kg once every other day without recurrences. In conclusion, this case report shows that MMF was well tolerated and might be effective as steroid-sparing agent in the long-term treatment of this autoimmune subepidermal blistering disease.
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Affiliation(s)
- P J Ginel
- Departamento de Medicina y Cirugía Animal, Universidad de Córdoba, Campus de Rabanales, 14014 Córdoba, Spain.
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Kooij V, Piersma SR, Zhang P, Boontje NM, Jiménez CR, Jaquet K, dos Remedios C, Murphy A, van Eyk J, van der Velden J, Stienen GJ. Protein Kinase Cα Mediated Phosphorylation of Cardiac Troponin Reduces Maximal Force and Exerts Dual Effects on Ca2+-Sensitivity in Human Cardiomyocytes. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.2210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Piersma SR, Fiedler U, Span S, Lingnau A, Pham TV, Hoffmann S, Kubbutat MHG, Jiménez CR. Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. J Proteome Res 2010; 9:1913-22. [PMID: 20085282 DOI: 10.1021/pr901072h] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cancer cell secretome has emerged as an attractive subproteome for discovery of candidate blood-based biomarkers. To choose the best performing workflow, we assessed the performance of three first-dimension separation strategies prior to nanoLC-MS/MS analysis: (1) 1D gel electrophoresis (1DGE), (2) peptide SCX chromatography, and (3) tC2 protein reversed phase chromatography. 1DGE using 4-12% gradient gels outperformed the SCX and tC2 methods with respect to number of identified proteins (1092 vs 979 and 580, respectively), reproducibility of protein identification (80% vs 70% and 72%, respectively, assessed in biological N = 3). Reproducibility of protein quantitation based on spectral counting was similar for all 3 methods (CV: 26% vs 24% and 24%, respectively). As a proof-of-concept of secretome proteomics for blood-based biomarker discovery, the gradient 1DGE workflow was subsequently applied to identify IGF1R-signaling related proteins in the secretome of mouse embryonic fibroblasts transformed with human IGF1R (MEF/Toff/IGF1R). VEGF and osteopontin were differentially detected by LC-MS/MS and verified in secretomes by ELISA. Follow-up in serum of mice bearing MEF/Toff/IGF1R-induced tumors showed an increase of osteopontin levels paralleling tumor growth, and reduction in the serum of mice in which IGF1R expression was shut off and tumor regressed.
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Affiliation(s)
- Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.
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Piersma SR, Labots M, Verheul HMW, Jiménez CR. Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods. Anal Bioanal Chem 2010; 397:3163-71. [PMID: 20526883 DOI: 10.1007/s00216-010-3784-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/06/2010] [Accepted: 04/24/2010] [Indexed: 11/30/2022]
Abstract
Kinases are key enzymes involved in deregulated signal transduction associated with cancer development and progression. The advent of personalized medicine drives the development of new diagnostic tools for patient stratification and therapy selection Ginsburg and Willard (Transl Res 154:277-287, 2009). Since deregulation of kinase-mediated signal transduction is implied in tumorigenesis, the analysis of all kinases (the kinome) active in a particular tumor may yield tumor-specific information on aberrant cell signalling pathways. Tumor tissue kinase activity profiles may correlate with response to therapy and therefore may be used for future therapy selection. In this Trend paper we describe peptide array and mass spectrometry-based technologies and new developments for kinome profiling, and we present an outlook towards future implementation of therapy selection based on kinome profiling in clinical practice.
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Affiliation(s)
- Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
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Sani M, Houben ENG, Geurtsen J, Pierson J, de Punder K, van Zon M, Wever B, Piersma SR, Jiménez CR, Daffé M, Appelmelk BJ, Bitter W, van der Wel N, Peters PJ. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS Pathog 2010; 6:e1000794. [PMID: 20221442 PMCID: PMC2832766 DOI: 10.1371/journal.ppat.1000794] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 01/26/2010] [Indexed: 11/19/2022] Open
Abstract
The cell envelope of mycobacteria, a group of Gram positive bacteria, is composed of a plasma membrane and a Gram-negative-like outer membrane containing mycolic acids. In addition, the surface of the mycobacteria is coated with an ill-characterized layer of extractable, non-covalently linked glycans, lipids and proteins, collectively known as the capsule, whose occurrence is a matter of debate. By using plunge freezing cryo-electron microscopy technique, we were able to show that pathogenic mycobacteria produce a thick capsule, only present when the cells were grown under unperturbed conditions and easily removed by mild detergents. This detergent-labile capsule layer contains arabinomannan, α-glucan and oligomannosyl-capped glycolipids. Further immunogenic and proteomic analyses revealed that Mycobacterium marinum capsule contains high amounts of proteins that are secreted via the ESX-1 pathway. Finally, cell infection experiments demonstrated the importance of the capsule for binding to cells and dampening of pro-inflammatory cytokine response. Together, these results show a direct visualization of the mycobacterial capsular layer as a labile structure that contains ESX-1-secreted proteins. The genus Mycobacterium contains a number of important pathogens, such as Mycobacterium tuberculosis. The highly characteristic cell envelope of these bacteria plays a crucial role in the infection process. The most apparent difference with other bacteria is the recently described outer membrane composed of unique (glyco)lipids. However, on top of this membrane mycobacteria also have an ill-defined capsular layer. In this paper, we studied this capsular layer using different electron microscopy techniques and mass spectrometry. Using close to native state preparation method, we show that both pathogenic and non-pathogenic mycobacteria have a labile capsular layer that covers the outer membrane. This capsular layer, in addition to containing arabinogalactan, glycan and mannose-containing glyco-lipids, also surprisingly contains a large amount of ESX-1-secreted proteins in Mycobacterium marinum. Furthermore, we also show that the capsule plays a role in the binding of macrophages and the induction of cytokines. Collectively, these results show for the first time that the capsule can be visualized on both pathogenic and non-pathogenic mycobacteria. In addition, growing mycobacteria under standard laboratory conditions in the presence of detergent with agitation promotes capsular shedding and influences the biological characteristics of the bacteria.
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Affiliation(s)
- Musa Sani
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
| | - Edith N. G. Houben
- Department of Medical Microbiology and Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Jeroen Geurtsen
- Department of Medical Microbiology and Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Jason Pierson
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
| | - Karin de Punder
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
| | - Maaike van Zon
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
| | - Brigitte Wever
- Department of Medical Microbiology and Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Sander R. Piersma
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, the Netherlands
| | - Connie R. Jiménez
- Department of Medical Oncology, VU University Medical Centre, Amsterdam, the Netherlands
| | - Mamadou Daffé
- CNRS, Institut de Pharmacologie et de Biologie Structurale, Département Mécanismes Moléculaires des Infections Mycobactériennes, Toulouse, France
| | - Ben J. Appelmelk
- Department of Medical Microbiology and Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Nicole van der Wel
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
- * E-mail: (NvdW); (PJP)
| | - Peter J. Peters
- Division of Cell Biology-B6, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital (NKI-AVL), Amsterdam, the Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
- * E-mail: (NvdW); (PJP)
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Abstract
Mass spectrometry (MS) has emerged as a sensitive, versatile, and rapid method for protein identification, following the advent of electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The advantages of MALDI-MS over ESI-MS include its relatively high tolerance to contamination from biological matrices, its high sensitivity, the relative ease of interpreting spectra from mixtures, and the formation of singly protonated molecular ions for tandem analysis. Peptide fingerprint mass mapping and partial peptide sequencing using post-source decay and ladder sequencing by MALDI-MS in combination with algorithms for sequence database interrogation have the potential for identification and structural investigation of proteins. This unit describes in-gel digestion for peptide mass mapping of picomole to subpicomole quantities of protein derived from Coomassie- or silver-stained polyacrylamide gels. After digestion, the peptides are extracted from the gel and mass analyzed.
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Affiliation(s)
- C R Jiménez
- University of California, San Francisco, San Francisco, California, USA
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Jiménez CR, Huang L, Qiu Y, Burlingame AL. Enzymatic approaches for obtaining amino acid sequence: on-target ladder sequencing. Curr Protoc Protein Sci 2008; Chapter 16:Unit 16.7. [PMID: 18429134 DOI: 10.1002/0471140864.ps1607s15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Peptide sequencing by mass spectrometry (MS) is usually based on detecting mass differences associated with various amino acids in the polymer chain. Post-source decay (PSD) and MS/MS spectra may yield internal peptide sequences. However, determination of the order of the first two, and sometimes the last few, amino acids in the peptide is often problematic without additional experiments. Several enzymatic approaches have proven useful for identifying the N- and C-terminal residues. They involve the use of carboxypeptidases and aminopeptidases to produce peptide ladders for rapid analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This unit describes the ladder sequence method to generate amino acid sequence information from low- to subpicomole quantities of peptides. It can be performed directly on the sample stage, thus minimizing potential sample losses to vials and through sample transfer.
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Affiliation(s)
- C R Jiménez
- University of California, San Francisco, San Francisco, California, USA
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Llamas MA, Sparrius M, Kloet R, Jiménez CR, Vandenbroucke-Grauls C, Bitter W. The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J Bacteriol 2006; 188:1882-91. [PMID: 16484199 PMCID: PMC1426570 DOI: 10.1128/jb.188.5.1882-1891.2006] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa secretes two siderophores, pyoverdine and pyochelin, under iron-limiting conditions. These siderophores are recognized at the cell surface by specific outer membrane receptors, also known as TonB-dependent receptors. In addition, this bacterium is also able to incorporate many heterologous siderophores of bacterial or fungal origin, which is reflected by the presence of 32 additional genes encoding putative TonB-dependent receptors. In this work, we have used a proteomic approach to identify the inducing conditions for P. aeruginosa TonB-dependent receptors. In total, 11 of these receptors could be discerned under various conditions. Two of them are only produced in the presence of the hydroxamate siderophores ferrioxamine B and ferrichrome. Regulation of their synthesis is affected by both iron and the presence of a cognate siderophore. Analysis of the P. aeruginosa genome showed that both receptor genes are located next to a regulatory locus encoding an extracytoplasmic function sigma factor and a transmembrane sensor. The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated. These results show that P. aeruginosa has evolved multiple specific regulatory systems to allow the regulation of TonB-dependent receptors.
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Affiliation(s)
- María A Llamas
- VU Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.
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Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse CK, Geraerts WPM, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li K. Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability. J Neurosci 2006; 26:518-29. [PMID: 16407549 PMCID: PMC6674408 DOI: 10.1523/jneurosci.2566-05.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In contrast to classical transmitters, the detailed structures and cellular and synaptic actions of neuropeptides are less well described. Peptide mass profiling of single identified neurons of the mollusc Lymnaea stagnalis indicated the presence of 17 abundant neuropeptides in the cardiorespiratory neuron, visceral dorsal 1 (VD1), and a subset of 14 peptides in its electrically coupled counterpart, right parietal dorsal 2. Altogether, based on this and previous work, we showed that the high number of peptides arises from the expression and processing of four distinct peptide precursor proteins, including a novel one. Second, we established a variety of posttranslational modifications of the generated peptides, including phosphorylation, disulphide linkage, glycosylation, hydroxylation, N-terminal pyroglutamylation, and C-terminal amidation. Specific synapses between VD1 and its muscle targets were formed, and their synaptic physiology was investigated. Whole-cell voltage-clamp analysis of dissociated heart muscle cells revealed, as tested for a selection of representative family members and their modifications, that the peptides of VD1 exhibit convergent activation of a high-voltage-activated Ca current. Moreover, the differentially glycosylated and hydroxylated alpha2 peptides were more potent than the unmodified alpha2 peptide in enhancing these currents. Together, this study is the first to demonstrate that single neurons exhibit such a complex pattern of peptide gene expression, precursor processing, and differential peptide modifications along with a remarkable degree of convergence of neuromodulatory actions. This study thus underscores the importance of a detailed mass spectrometric analysis of neuronal peptide content and peptide modifications related to neuromodulatory function.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Base Sequence
- Calcium Channels/physiology
- Calcium Channels, L-Type/metabolism
- Cells, Cultured/physiology
- Chromatography, High Pressure Liquid
- Coculture Techniques
- Ganglia, Invertebrate/cytology
- Gene Expression
- Glycosylation
- Hydroxylation
- Ion Transport/drug effects
- Lymnaea/chemistry
- Lymnaea/cytology
- Molecular Sequence Data
- Molecular Weight
- Myocytes, Cardiac/physiology
- Neurons/chemistry
- Neurons/physiology
- Neuropeptides/analysis
- Neuropeptides/genetics
- Neuropeptides/metabolism
- Neuropeptides/pharmacology
- Neuropeptides/physiology
- Patch-Clamp Techniques
- Peptide Fragments/analysis
- Phosphoproteins/metabolism
- Phosphoproteins/pharmacology
- Phosphorylation
- Protein Precursors/analysis
- Protein Processing, Post-Translational
- Proteomics
- RNA, Messenger/analysis
- Sequence Analysis, Protein
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Connie R Jiménez
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
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Van den Oever MC, Spijker S, Li KW, Jiménez CR, Koya E, Van der Schors RC, Gouwenberg Y, Binnekade R, De Vries TJ, Schoffelmeer ANM, Smit AB. A Proteomics Approach to Identify Long-Term Molecular Changes in Rat Medial Prefrontal Cortex Resulting from Sucrose Self-Administration. J Proteome Res 2005; 5:147-54. [PMID: 16396505 DOI: 10.1021/pr050303y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The medial prefrontal cortex (mPFC) is involved in the processing and retrieval of reward-related information. Here, we investigated long-lasting changes in protein composition of the mPFC in rats with a history of sucrose self-administration. Protein levels were analyzed using 2-D PAGE and MALDI-TOF sequencing. From approximately 1500 spots, 28 regulated proteins were unambiguously identified and were involved in cytoskeleton organization, energy metabolism, oxidative stress, neurotransmission, and neuronal outgrowth and differentiation. For several proteins, this change was also found as a long-lasting alteration in gene expression. We show that self-administration of sucrose produces long-lasting molecular neuroadaptations in the mPFC that may be involved in reward-related information processing.
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Affiliation(s)
- Michel C Van den Oever
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics & Cognitive Research, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Jiménez CR, Li KW, Smit AB, Janse C. Auto-inhibitory control of peptidergic molluscan neurons and reproductive senescence. Neurobiol Aging 2005; 27:763-9. [PMID: 15951060 DOI: 10.1016/j.neurobiolaging.2005.03.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 03/25/2005] [Accepted: 03/30/2005] [Indexed: 11/15/2022]
Abstract
We recently, characterized a novel peptide of the egg-laying controlling caudodorsal cells (CDC) of Lymnaea stagnalis. Here, we show that the novel peptide has autoinhibitory actions and its expression is significantly up-regulated in reproductively senescent animals. Intracellular recordings show that when bath-applied to the central nervous system in vitro, the peptide reduces the depolarizing after potential (DAP) in CDCs without affecting the action potential-threshold and -amplitude and the resting membrane potential. Moreover, peptide application can terminate an ongoing after discharge in the CDCs or, when electrical stimulation fails to induce an after discharge, can terminate the long-lasting depolarization. Semiquantitative peptide profiling by mass spectrometry demonstrated correct processing and targeting of peptides in the CDC somata and axon terminals of reproductively senescent animals. Interestingly, the level of the autoinhibitory peptide was selectively increased in the CDCs of reproductively senescent animals. Our results indicate that a shift in balance between excitatory and inhibitory auto-transmitter peptides in the CDC system of old non-egg-laying animals, plays a role in after discharge failure in CDCs of reproductively senescent Lymnaea.
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Affiliation(s)
- C R Jiménez
- Department of Molecular and Cellular Neurobiology, Faculty of Earth and Life Sciences, Research Institute Neurosciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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Altelaar AFM, van Minnen J, Jiménez CR, Heeren RMA, Piersma SR. Direct Molecular Imaging ofLymnaea stagnalisNervous Tissue at Subcellular Spatial Resolution by Mass Spectrometry. Anal Chem 2005; 77:735-41. [PMID: 15679338 DOI: 10.1021/ac048329g] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) and MALDI-MS sample preparation methods were combined. We used this method, named matrix-enhanced (ME) SIMS, for direct molecular imaging of nervous tissue at micrometer spatial resolution. Cryosections of the cerebral ganglia of the freshwater snail Lymnaea stagnalis were placed on indium-tin-oxide (ITO)-coated conductive glass slides and covered with a thin layer of 2,5-dihydroxybenzoic acid by electrospray deposition. High-resolution molecular ion maps of cholesterol and the neuropeptide APGWamide were constructed. APGWamide was predominantly localized in the cluster of neurons that regulate male copulation behavior of Lymnaea. ME-SIMS imaging allows direct molecule-specific imaging from tissue sections without labeling and opens a complementary mass window (<2500 Da) to MALDI imaging mass spectrometry at an order of magnitude higher spatial resolution (<3 microm).
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Affiliation(s)
- A F Maarten Altelaar
- FOM-Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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Abstract
Mass spectrometry (MS) is widely used as a rapid tool for peptide profiling and protein identification. However, the success of the method is compromised by dirty and contaminated samples. Moreover, analysis from a small sample volume with a relative high concentration is usually required. In this chapter, different microscale sample preparation methods are discussed for off-line, matrix-assisted laser desorption/ionization (MALDI) and nanoelectrospray ionization (nanoESI) MS analysis.
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Affiliation(s)
- Connie R Jiménez
- Mass Spectrometry Resource, Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
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