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Research Output 2009 2019

  • 73 Article
  • 3 Meeting Abstract
  • 3 Comment/Letter to the editor
  • 1 Erratum
2019

Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies

Stokman, M. F., Bijnsdorp, I. V., Schelfhorst, T., Pham, T. V., Piersma, S. R., Knol, J. C., Giles, R. H., Bongers, E. M. H. F., Knoers, N. V. A. M., Lilien, M. R., Jiménez, C. R. & Renkema, K. Y., 10 Feb 2019, In : Journal of Proteomics. 192, p. 27-36 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Chronic Ly49H Receptor Engagement in vivo Decreases NK Cell Response to Stimulation Through ITAM-Dependent and Independent Pathways Both in vitro and in vivo

Key, P. N., Germino, J., Yang, L., Piersma, S. J. & Tripathy, S. K., 1 Jan 2019, In : Frontiers in Immunology. 10, p. 1692

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Constitutively active GSK3β as a means to bolster dendritic cell functionality in the face of tumour-mediated immune suppression

Gonzalez, M. L., Oosterhoff, D., Lindenberg, J. J., Milenova, I., Lougheed, S. M., Martianez, T., Dekker, H., Quixabeira, D. C. A., Hangalapura, B., Joore, J., Piersma, S. R., Cervera-Carrascon, V., Santos, J. M., Scheper, R. J., Verheul, H. M. W., Jimenez, C. R., Van De Ven, R., Hemminki, A., Van Beusechem, V. W. & De Gruijl, T. D., 1 Jan 2019, In : OncoImmunology. 8, 10

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access

Human testis phosphoproteome reveals kinases as potential targets in spermatogenesis and testicular cancer

Castillo, J., Knol, J. C., Korver, C. M., Piersma, S. R., Pham, T. V., de Goeij-de Haas, R. R., van Pelt, A. M. M., Jimenez, C. R. & Jansen, B. J. H., 1 Mar 2019, In : Molecular and Cellular Proteomics. 18, p. S132-S144

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases

Beekhof, R., van Alphen, C., Henneman, A. A., Knol, J. C., Pham, T. V., Rolfs, F., Labots, M., Henneberry, E., le Large, T. Y., de Haas, R. R., Piersma, S. R., Vurchio, V., Bertotti, A., Trusolino, L., Verheul, H. M. & Jimenez, C. R., 1 Apr 2019, In : Molecular Systems Biology. 15, 4, p. e8250 e8250.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression

Komor, M. A., de Wit, M., van den Berg, J., Martens de Kemp, S. R., Delis-van Diemen, P. M., Bolijn, A. S., Tijssen, M., Schelfhorst, T., Piersma, S. R., Chiasserini, D., Sanders, J., Rausch, C., Hoogstrate, Y., Stubbs, A. P., de Jong, M., Jenster, G., Carvalho, B., Meijer, G. A., Jimenez, C. R., Fijneman, R. J. A. & 1 othersIn collaboration with the NGS-ProToCol Consortium, 14 Aug 2019, In : International Journal of Cancer.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression

Komor, M. A., Bosch, L. J. W., Coupé, V. M. H., Rausch, C., Pham, T. V., Piersma, S. R., Mongera, S., Mulder, C. J. J., Dekker, E., Kuipers, E. J., van de Wiel, M. A., Carvalho, B., Fijneman, R. J. A., Jimenez, C. R., Meijer, G. A. & de Wit, M., Nov 2019, In : Journal of Pathology.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction

Böttger, F., Schaaij-Visser, T. B., de Reus, I., Piersma, S. R., Pham, T. V., Nagel, R., Brakenhoff, R. H., Thunnissen, E., Smit, E. F. & Jimenez, C. R., 30 Mar 2019, In : Journal of Proteomics. 196, p. 106-119

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer

Böttger, F., Semenova, E. A., Song, J-Y., Ferone, G., van der Vliet, J., Cozijnsen, M., Bhaskaran, R., Bombardelli, L., Piersma, S. R., Pham, T. V., Jimenez, C. R. & Berns, A., 11 Jun 2019, In : Cell Reports. 27, 11, p. 3345-3358.e4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2018

Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro

Bridel, C., Koel-Simmelink, M. J. A., Peferoen, L., Derada Troletti, C., Durieux, S., Gorter, R., Nutma, E., Gami, P., Iacobaeus, E., Brundin, L., Kuhle, J., Vrenken, H., Killestein, J., Piersma, S. R., Pham, T. V., De Vries, H. E., Amor, S., Jimenez, C. R. & Teunissen, C. E., Jun 2018, In : Neuropathology and Applied Neurobiology. 44, 4, p. 404-416 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles

Steenbeek, S. C., Pham, T. V., de Ligt, J., Zomer, A., Knol, J. C., Piersma, S. R., Schelfhorst, T., Huisjes, R., Schiffelers, R. M., Cuppen, E., Jimenez, C. R. & van Rheenen, J., 2018, In : EMBO Journal. 37, 15, e98357.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Correction: Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

Verweij, F. J., Bebelman, M. P., Jimenez, C. R., Garcia-Vallejo, J. J., Janssen, H., Neefjes, J., Knol, J. C., de Goeij-de Haas, R., Piersma, S. R., Baglio, S. R., Verhage, M., Middeldorp, J. M., Zomer, A., van Rheenen, J., Coppolino, M. G., Hurbain, I., Raposo, G., Smit, M. J., Toonen, R. F. G., van Niel, G. & 1 othersPegtel, D. M., 5 Mar 2018, In : Journal of Cell Biology. 217, 3, p. 1157

Research output: Contribution to journalErratumAcademicpeer-review

EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF

Phan, T. H., van Leeuwen, L. M., Kuijl, C., Ummels, R., van Stempvoort, G., Rubio-Canalejas, A., Piersma, S. R., Jiménez, C. R., van der Sar, A. M., Houben, E. N. G. & Bitter, W., Aug 2018, In : PLoS Pathogens. 14, 8, p. e1007247

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Exploration of the platelet proteome in patients with early-stage cancer

Sabrkhany, S., Kuijpers, M. J. E., Knol, J. C., Olde Damink, S. W. M., Dingemans, A-M. C., Verheul, H. M., Piersma, S. R., Pham, T. V., Griffioen, A. W., oude Egbrink, M. G. A. & Jimenez, C. R., 2018, In : Journal of Proteomics. 177, p. 65-74

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Multidrug-resistant transporter expression does not always result in drug resistance

le Large, T. Y. S., el Hassouni, B., Kazemier, G., Piersma, S. R., van Laarhoven, H. W. M., Bijlsma, M. F., Jimenez, C. R. & Giovannetti, E., 2018, In : Cancer Science. 109, 10, p. 3360-3362 3 p.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access

Mutations in ppe38 block PE-PGRS secretion and increase virulence of Mycobacterium tuberculosis

Ates, L. S., Dippenaar, A., Ummels, R., Piersma, S. R., van der Woude, A. D., van der Kuij, K., le Chevalier, F., Mata-Espinosa, D., Barrios-Payán, J., Marquina-Castillo, B., Guapillo, C., Jiménez, C. R., Pain, A., Houben, E. N. G., Warren, R. M., Brosch, R., Hernández-Pando, R. & Bitter, W., 2018, In : Nature Microbiology. 3, 2, p. 181-188

Research output: Contribution to journalArticleAcademicpeer-review

Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

Verweij, F. J., Bebelman, M. P., Jimenez, C. R., Garcia-Vallejo, J. J., Janssen, H., Neefjes, J., Knol, J. C., de Goeij-de Haas, R., Piersma, S. R., Baglio, S. R., Verhage, M., Middeldorp, J. M., Zomer, A., van Rheenen, J., Coppolino, M. G., Hurbain, I., Raposo, G., Smit, M. J., Toonen, R. F. G., van Niel, G. & 1 othersPegtel, D. M., 5 Mar 2018, In : Journal of Cell Biology. 217, 3, p. 1129-1142 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

Identification of differentially expressed splice variants by the proteogenomic pipeline splicify

Komor, M. A., Pham, T. V., Hiemstra, A. C., Piersma, S. R., Bolijn, A. S., Schelfhorst, T., Delis-Van Diemen, P. M., Tijssen, M., Sebra, R. P., Ashby, M., Meijer, G. A., Jimenez, C. R. & Fijneman, R. J. A., 1 Oct 2017, In : Molecular and Cellular Proteomics. 16, 10, p. 1850-1863 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Novel Stool-Based Protein Biomarkers for Improved Colorectal Cancer Screening: A Case-Control Study

Bosch, L. J. W., De Wit, M., Pham, T. V., Coupé, V. M. H., Hiemstra, A. C., Piersma, S. R., Oudgenoeg, G., Scheffer, G. L., Mongera, S., Droste, J. T. S., Oort, F. A., Van Turenhout, S. T., Larbi, I. B., Louwagie, J., Van Criekinge, W., Van Der Hulst, R. W. M., Mulder, C. J. J., Carvalho, B., Fijneman, R. J. A., Jimenez, C. R. & 1 othersMeijer, G. A., 19 Dec 2017, In : Annals of Internal Medicine. 167, 12, p. 855-866 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection

Labots, M., van der Mijn, J. C., Beekhof, R., Piersma, S. R., de Goeij-de Haas, R. R., Pham, T. V., Knol, J. C., Dekker, H., van Grieken, N. C. T., Verheul, H. M. W. & Jiménez, C. R., 6 Jun 2017, In : Journal of Proteomics. 162, p. 99-107 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

2016

Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling

Tutakhel, O. A. Z., Jelen, S., Valdez-Flores, M., Dimke, H., Piersma, S. R., Jimenez, C. R., Deinum, J., Lenders, J. W., Hoenderop, J. G. J. & Bindels, R. J. M., 1 Feb 2016, In : American Journal of Physiology. Renal Physiology. 310, 3, p. F204-F216

Research output: Contribution to journalArticleAcademicpeer-review

Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer

Labots, M., Gotink, K. J., Dekker, H., Azijli, K., van der Mijn, J. C., Huijts, C. M., Piersma, S. R., Jiménez, C. R. & Verheul, H. M. W., 16 Dec 2016, In : Experimental & Molecular Medicine. 48, 12, p. e279

Research output: Contribution to journalArticleAcademicpeer-review

Multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus

Schouten, M., Bielefeld, P., Fratantoni, S. A., Hubens, C. J., Piersma, S. R., Pham, T. V., Voskuyl, R. A., Lucassen, P. J., Jimenez, C. R. & Fitzsimons, C. P., 16 Aug 2016, In : Scientific data. 3, p. 160068

Research output: Contribution to journalArticleAcademicpeer-review

Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes

van Winden, V. J. C., Ummels, R., Piersma, S. R., Jimenez, C. R., Korotkov, K. V., Bitter, W. & Houben, E. N. G., 2016, In : mBio. 7, 5

Research output: Contribution to journalArticleAcademicpeer-review

Novel diagnostic cerebrospinal fluid biomarkers for pathologic subtypes of frontotemporal dementia identified by proteomics

Teunissen, C. E., Elias, N., Koel-Simmelink, M. J. A., Durieux-Lu, S., Malekzadeh, A., Pham, T. V., Piersma, S. R., Beccari, T., Meeter, L. H. H., Dopper, E. G. P., van Swieten, J. C., Jimenez, C. R. & Pijnenburg, Y. A. L., 2016, In : Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring. 2, p. 86-94 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Peptide-mediated ‘miniprep’ isolation of extracellular vesicles is suitable for high-throughput proteomics

Knol, J. C., de Reus, I., Schelfhorst, T., Beekhof, R., de Wit, M., Piersma, SR., Pham, TV., Smit, EF., Verheul, HMW. & Jimenez, CR., Jun 2016, In : EuPA Open Proteomics. 11, p. 11-15

Research output: Contribution to journalArticleAcademicpeer-review

Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer

Warmoes, M., Lam, S. W., van der Groep, P., Jaspers, J. E., Smolders, Y. H. C. M., de Boer, L., Pham, T. V., Piersma, S. R., Rottenberg, S., Boven, E., Jonkers, J., van Diest, P. J. & Jimenez, C. R., 27 Sep 2016, In : Oncotarget. 7, 39, p. 63537-63548

Research output: Contribution to journalArticleAcademicpeer-review

Sensing of latent EBV infection through exosomal transfer of 5'pppRNA

Baglio, S. R., van Eijndhoven, M. A. J., Koppers-Lalic, D., Berenguer, J., Lougheed, S. M., Gibbs, S., Leveille, N., Rinkel, R. N. P. M., Hopmans, E. S., Swaminathan, S., Verkuijlen, S. A. W. M., Scheffer, G. L., van Kuppeveld, F. J. M., de Gruijl, T. D., Bultink, I. E. M., Jordanova, E. S., Hackenberg, M., Piersma, S. R., Knol, J. C., Voskuyl, A. E. & 4 othersWurdinger, T., Jimenez, C. R., Middeldorp, J. M. & Pegtel, D. M., 2 Feb 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 5, p. E587-E596

Research output: Contribution to journalArticleAcademicpeer-review

Sunitinib activates Axl signaling in renal cell cancer

van der Mijn, J. C., Broxterman, H. J., Knol, J. C., Piersma, S. R., De Haas, R. R., Dekker, H., Pham, T. V., Van Beusechem, V. W., Halmos, B., Mier, J. W., Jimenez, C. R. & Verheul, H. M. W., 15 Jun 2016, In : International Journal of Cancer. 138, 12, p. 3002-3010

Research output: Contribution to journalArticleAcademicpeer-review

2015

Abstract 4764: Transfer of regulatory protein networks via extracellular vesicles as a candidate mechanism of apoptosis-resistance in acute myeloid leukemia

Assaraf, Y. G., Zweegman, S., Cloos, J., Jansen, G., Knol, J., Schuurhuis, G. J., Jimenez, C. R., Piersma, S., Kessler, F. L., Wojtuszkiewicz, A. & Kaspers, G. L., 1 May 2015, In : Cancer Research. 74, 19 Supplement, p. 4764-4764 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria.

Ates, L. S., Ummels, R., Commandeur, S., van de Weerd, R., Sparrius, M., Weerdenburg, E., Alber, M., Kalscheuer, R., Piersma, S. R., Abdallah, A., Abd El Ghany, M., Abdel-Haleem, A. M., Pain, A., Jimenez, C. R., Bitter, W. & Houben, E. N. G., 2015, In : PLoS Genetics. 4, 11, 5.

Research output: Contribution to journalArticleAcademicpeer-review

Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics

van der Mijn, J. C., Labots, M., Piersma, S. R., Pham, T. V., Knol, J. C., Broxterman, H. J., Verheul, H. M. & Jimenez, C. R., 2015, In : Journal of Proteomics. 127, p. 259-263

Research output: Contribution to journalArticleAcademicpeer-review

Exosomal sorting of the viral oncoprotein LMP1 is restrained by TRAF2 association at signalling endosomes

Verweij, F. J., Heus, C., Kroeze, S., Cai, H. J., Kieff, E., Piersma, S. R., Jimenez, C. R., Middeldorp, J. M. & Pegtel, D. M., 2015, In : Journal of Extracellular Vesicles. 4, 26334.

Research output: Contribution to journalArticleAcademicpeer-review

Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines

Piersma, S. R., Knol, J. C., de Reus, I., Labots, M., Sampadi, B. K., Pham, T. V., Ishihama, Y., Verheul, H. M. W. & Jimenez, C. R., 2015, In : Journal of Proteomics. 127, p. 247-258

Research output: Contribution to journalArticleAcademicpeer-review

Genome-wide siRNA Screen Identifies the Radiosensitizing Effect of Downregulation of MASTL and FOXM1 in NSCLC

Nagel, C. R., Stigter-van Walsum, M., Buijze, M., van den Berg, J., van der Meulen, I. H., Hodzic, J., Piersma, S. R., Pham, T. V., Jimenez, C. R., van Beusechem, V. W. & Brakenhoff, R. H., 2015, In : Molecular Cancer Therapeutics. 14, 6, p. 1434-1444

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA-124 and-137 cooperativity controls caspase-3 activity through BCL2L13 in hippocampal neural stem cells

Schouten, M., Fratantoni, S. A., Hubens, C. J., Piersma, S. R., Pham, T. V., Bielefeld, P., Voskuyl, R. A., Lucassen, P. J., Jimenez, C. R. & Fitzsimons, C. P., 2015, In : Scientific Reports. 5, 12448.

Research output: Contribution to journalArticleAcademicpeer-review

miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo

Senol, O., Schaaij-Visser, T. B. M., Erkan, E. P., Dorfer, C., Lewandrowski, G., Pham, T. V., Piersma, S. R., Peerdeman, S. M., Strobel, T., Tannous, B., Saydam, N., Slavc, I., Knosp, E., Jimenez, C. R. & Saydam, O., 2015, In : Oncogene. 34, 14, p. 1790-1798

Research output: Contribution to journalArticleAcademicpeer-review

2014

Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer

van der Mijn, J. C., Sol, N., Mellema, W. W., Jimenez, C. R., Piersma, S. R., Dekker, H., Schulte, L. M., Smit, E. F., Broxterman, H. J., Skog, J., Tannous, B. A., Wurdinger, T. & Verheul, H. M., 2014, In : Journal of Extracellular Vesicles. 3, 25657.

Research output: Contribution to journalArticleAcademicpeer-review

Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector.

van der Woude, A. D., Stoop, E. J. M., Stiess, M., Wang, Q., Ummels, R., van Stempvoort, G., Piersma, S. R., Cascioferro, A., Jimenez, C. R., Houben, E. N. G., Luirink, J., Pieters, J., van der Sar, A. M. & Bitter, W., 2014, In : Cellular Microbiology. 16, 2, p. 280-295

Research output: Contribution to journalArticleAcademicpeer-review

Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling

de Wit, M., Kant, H., Piersma, S. R., Pham, T. V., Mongera, S., van Berkel, M. P. A., Boven, E., Ponten, F., Meijer, G. A., Jimenez, C. R. & Fijneman, R. J. A., 2014, In : Journal of Proteomics. 99, p. 26-39

Research output: Contribution to journalArticleAcademicpeer-review

Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture

Rajcevic, U., Knol, J. C., Piersma, S. R., Bougnaud, S., Fack, F., Sundlisaeter, E., Sondenaa, K., Myklebust, R., Pham, T. V., Niclou, S. P. & Jimenez, C. R., 2014, In : Proteome Science. 12, 39.

Research output: Contribution to journalArticleAcademicpeer-review

Decoration of outer membrane vesicles with multiple antigens using an autotransporter approach.

Daleke, M. H., Felix, T., Soprova, Z., ten Hagen-Jongman ten, C. M., Vikström, D., Majlessi, L., Beskers, J., Follman, F., de Punder, K., van der Wel, N. N., Baumgarten, T., Pham, T. V., Piersma, S. R., Jimenez, C. R., van Ulsen, P., de Gier, J. W., Leclerc, C., Jong, W. S. & Luirink, S., 2014, In : Applied and Environmental Microbiology. 80, 18, p. 5854-5864

Research output: Contribution to journalArticleAcademicpeer-review

Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset

Chiasserini, D., van Weering, J. R. T., Piersma, S. R., Pham, T. V., Malekzadeh, A., Teunissen, C. E., de Wit, H. & Jimenez, C. R., 2014, In : Journal of Proteomics. 106, p. 191-204

Research output: Contribution to journalArticleAcademicpeer-review

Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues

Knol, J. C., de Wit, M., Albrethsen, J., Piersma, S. R., Pham, T. V., Mongera, S., Carvalho, B., Fijneman, R. J. A., Meijer, G. A. & Jimenez, C. R., 2014, In : Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844, 5, p. 1034-1043

Research output: Contribution to journalArticleAcademicpeer-review