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OncoProteomics Laboratory VuMC

Contact Details

VU University Medical Center

VUmc-Cancer Center Amsterdam, Room CCA 1-60 De Boelelaan 1117 1081HV Amsterdam, The Netherlands

http://www.oncoproteomics.nl/

Prof.dr. C.R. Jimenez

c.jimenez@vumc.nl

0031 (0)20 4442340

Hotel Description

The OncoProteomics Laboratory is a clinical proteomics center specialized in (phospo)potein profiling and protein biomarker discovery/ validation by mass spectrometry and advanced data mining strategies.

We apply label-free (phospho)proteomics to solve biological and biomedical questions using a wide variety of sample types. Our research focus is on large scale profiling of human disease, most notably cancer and neurodegenerate diseases. In addition, in many different research collaborations a variety of topics is addressed (eg., subcellular analysis of human pathogens or basic research dissecting protein complexes or signaling pathways).

Proteomics
Public
  • Other
  • Biomedical & health
  • Industrial biotech
  • Proteomics
  • Mass spectrometry
  • Bioinformatics
  • Label-free protein quantitation
  • Phosphoproteomics
  • Biology, biochemistry
  • Oncoproteomics (cancer research, oncology)
  • Neuroproteomics (neuro-diseases)
  • Fundamental, Translational and Clinical research
  • Biomarker and target discovery

Expertise and Track Record

We are internationally recognized for our expertise in clinical and cancer proteomics. To this end, we pioneered and implemented robust label-free proteomics, which is a versatile approach that enables a flexible study design as well as analyses of large series of biological and clinical samples.

We are a multi-disciplinary team with complementary PhD-level expertises always working from the application side, thereby making pragmatic choices that turned out to be advantageous to answer the questions posed. The whole proteomics process is stream-lined from support and detailed protocols for sample preparation to data analysis and user-friendly reports including dedicated statistics that are returned to collaborators. The success of our approach has resulted in multiple co-authorships in collaborative projects (see below and http://www.oncoproteomics.nl/index.php/publications)

Five examples of collaborative projects :

1. CTMM valorisation project CRC-Bioscreen: stool protein biomarker discovery and validation (see also https://www.youtube.com/watch?v=e7JDDUlneLw ).

2. Proteomics data generated for a multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus (Sci Rep. 2015 5:12448; Sci Data. 2016 3:160068).

3. Identification of secretory components of pathogenic Mycobacteria in collaboration with the group of Wilbert Bitter (many publications eg., PLoS Genet. 2015 May 4;11(5):e1005190)

4. Unravelling the protein components of virus-modified exosomes in the context of host-pathogen interactions and inflammatory disease, collaboration with Dr. Pegtel (Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E587-96)

5. Sub-contractor for LeadPharma in context of EU Marie Curie project Growsperm (http://growsperm.eu; manuscript in prep.)

We have experience with the integration of proteomics with genomics data (transcriptome, arrayCGH, microRNA).
Also to enable “proteogenomics” we have implemented a data analysis pipeline to enable identification of disease variants by searching against dedicated (sample-specific) databases based on genome sequence data.

Published examples:

1. Integration proteomics and miRNA work
Senol O, Schaaij-Visser TB, Erkan EP, Dorfer C, Lewandrowski G, Pham TV, Piersma SR, Peerdeman SM, Ströbel T, Tannous B, Saydam N, Slavc I, Knosp E, Jimenez CR, Saydam O. miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo. Oncogene. 2014 May 26;0.

2. Integration proteomics and transcriptomics:
Snoeren N, Emmink BL, Koerkamp MJ, van Hooff SR, Goos JA, van Houdt WJ, de Wit M, Prins AM, Piersma SR, Pham TV, Belt EJ, Bril H, Stockmann HB, Meijer GA, van Hillegersberg R, Holstege FC, Jimenez CR, Fijneman RJ, Kranenburg OW, Rinkes IH. Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer. Br J Cancer. 2013 Sep 17;109(6):1636-47.

3. Validation of proteomics data in transcriptome datasets:
Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MP, Waisfisz Q, Rottenberg S, Boven E, Jonkers J, Jimenez CR. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer. Mol Cell Proteomics. 2012 Jul;11(7):M111.013334.

4. Integration proteomics with genomics to prioritize cell surface proteins as candidate biomarkers for colrectal adenoma-to-carcinoma progression:
de Wit M, Jimenez CR, Carvalho B, Belien JA, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Pontén F, Meijer GA, Fijneman RJ. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut. 2012
Jun;61(6):855-64. doi: 10.1136/gutjnl-2011-300511. Epub 2011 Sep 2. PubMed PMID: 21890811.

  • 1: Hassan C, Kester MG, Oudgenoeg G, de Ru AH, Janssen GM, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MH, Falkenburg JH, van Veelen PA. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J Proteomics. 2014 Jul 19;109C:240-244. doi: 10.1016/j.jprot.2014.07.009. [Epub ahead of print] PubMed PMID: 25050860.
  • 2: Senol O, Schaaij-Visser TB, Erkan EP, Dorfer C, Lewandrowski G, Pham TV, Piersma SR, Peerdeman SM, Ströbel T, Tannous B, Saydam N, Slavc I, Knosp E, Jimenez CR, Saydam O. miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo. Oncogene. 2014 May 26;0. doi: 10.1038/onc.2014.120. [Epub ahead of print] PubMed PMID: 24858044.
  • 3: van der Woude AD, Stoop EJ, Stiess M, Wang S, Ummels R, van Stempvoort G, Piersma SR, Cascioferro A, Jiménez CR, Houben EN, 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. 2014 Feb;16(2):280-95. doi: 10.1111/cmi.12221. Epub 2013 Nov 6. PubMed PMID: 24119166
  • 4: Snoeren N, Emmink BL, Koerkamp MJ, van Hooff SR, Goos JA, van Houdt WJ, de Wit M, Prins AM, Piersma SR, Pham TV, Belt EJ, Bril H, Stockmann HB, Meijer GA, van Hillegersberg R, Holstege FC, Jimenez CR, Fijneman RJ, Kranenburg OW, Rinkes IH. Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer. Br J Cancer. 2013 Sep 17;109(6):1636-47. doi: 10.1038/bjc.2013.489. Epub 2013 Sep 3. PubMed PMID: 24002600; PubMed Central PMCID: PMC3776998.
  • 5: Posthumadeboer J, Piersma SR, Pham TV, van Egmond PW, Knol JC, Cleton-Jansen AM, van Geer MA, van Beusechem VW, Kaspers GJ, van Royen BJ, Jiménez CR, Helder MN. Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery. Br J Cancer. 2013 Oct 15;109(8):2142-54. doi: 10.1038/bjc.2013.578. Epub 2013 Sep 24. PubMed PMID: 24064975; PubMed Central PMCID: PMC3798973.
  • 6: De Vries-van Leeuwen IJ, da Costa Pereira D, Flach KD, Piersma SR, Haase C, Bier D, Yalcin Z, Michalides R, Feenstra KA, Jiménez CR, de Greef TF, Brunsveld L, Ottmann C, Zwart W, de Boer AH. Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface. Proc Natl Acad Sci U S A. 2013 May 28;110(22):8894-9. doi: 10.1073/pnas.1220809110. Epub 2013 May 15. PubMed PMID: 23676274; PubMed Central PMCID: PMC3670367.
  • 7: van Dijk KD, Berendse HW, Drukarch B, Fratantoni SA, Pham TV, Piersma SR, Huisman E, Brevé JJ, Groenewegen HJ, Jimenez CR, van de Berg WD. The proteome of the locus ceruleus in Parkinson's disease: relevance to pathogenesis. Brain Pathol. 2012 Jul;22(4):485-98. doi: 10.1111/j.1750-3639.2011.00540.x. Epub 2011 Nov 8. PubMed PMID: 21988495.
  • 8: de Wit M, Jimenez CR, Carvalho B, Belien JA, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Pontén F, Meijer GA, Fijneman RJ. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut. 2012 Jun;61(6):855-64. doi: 10.1136/gutjnl-2011-300511. Epub 2011 Sep 2. PubMed PMID: 21890811.
  • 9: Skvortsov S, Jimenez CR, Knol JC, Eichberger P, Schiestl B, Debbage P, Skvortsova I, Lukas P. Radioresistant head and neck squamous cell carcinoma cells: intracellular signaling, putative biomarkers for tumor recurrences and possible therapeutic targets. Radiother Oncol. 2011 Oct;101(1):177-82. doi: 10.1016/j.radonc.2011.05.067. Epub 2011 Jun 21. PubMed PMID: 21700351.
  • 10: van Dijk FS, Nesbitt IM, Zwikstra EH, Nikkels PG, Piersma SR, Fratantoni SA, Jimenez CR, Huizer M, Morsman AC, Cobben JM, van Roij MH, Elting MW, Verbeke JI, Wijnaendts LC, Shaw NJ, Högler W, McKeown C, Sistermans EA, Dalton A, Meijers-Heijboer H, Pals G. PPIB mutations cause severe osteogenesis imperfecta. Am J Hum Genet. 2009 Oct;85(4):521-7. doi: 10.1016/j.ajhg.2009.09.001. Epub 2009 Sep 24. PubMed PMID: 19781681; PubMed Central PMCID: PMC2756556.

The OncoProteomics Laboratory participated in several national research consortia of the Center for Translational Molecular Medicine (DeCoDe, Airforce, CRC-Bioscreen, TraIT) and international EU consortia.

Participation in (inter)national networks:
2001 Founder of Netherlands Proteomics Platform
2001-present Steering Committee Member, Netherlands Proteomics Platform
2005-present General council member, European Proteomics Association
2013-2016 Council Member (Board of Directors) of the Human Proteome Organisation
2014-present Co-chair Cancer Initiative of the Human Proteome Organisation

Hotel Characteristics

  • Dedicated PhD level mass spectrometrist (1 fte)
  • Dedicated research technician with PhD in biochemistry for down-stream bioinformatics/ data mining (1 fte)
  • Dedicated research technicians/ lab manager (2 fte)
  • Dedicated biostatistician/ bioinformatician/ IT specialist with PhDs in computer science and physics ( 2 fte)
  • 8 fte research projects (4 post-docs and 4 PhD students)

~20-25%

  • 2 QExactive tandem mass spectrometry instruments (ThermoFisher)
  • 1 QExactive-HF (ThermoFisher)
  • Qtrap 5500 (Applied Biosystems)
  • All MS instruments on-line coupled to 4 Dionex nanoLC systems

we are in process of getting CCKL accreditation

we deposit raw and processed MS/MS data to ProteomeExchange