Action:Urine and Kidney Proteomics (EuroKUP, BM0702) Years:3 Participating countries: AT, BE, BG, CY, CZ, DE, DK, FI, FR, GR, IE, IT, LI, LU, MK, NL, NO, PL, ES, SB, SE, CH, UK, Australia Chair of the Action: Antonia Vlahou, GR, vlahoua@bioacademy.gr Rapporteur:Ursula Gundert-Remy, GE, Ursula.Gundert-Remy@bfr.bund.de Science Officer: Magdalena Radwanska, magdalena.radwanska@cost.eu Action Website: www.eurokup.org Scientific background ● Clinical proteomics has generated promising results, yet these have not been translated into the desired tangible clinical outcome. ● This observation underscores the need for a thorough evaluation of applied practices throughout the clinical proteomics workflow from biomarker discovery to validation and clinical implementation. ● Chronic renal disease at 10% (and continuously increasing) prevalence consists a major health problem in Europe in urgent need for novel diagnostic and therapeutic approaches. Objectives defined in the MoU Main objective: Facilitate translational research in kidney diseases by bringing together scientists and clinicians and achieving coordination and standardisation of steps for a clinical proteomics workflow Bioinformatics WG4 WG3: Urine proteomics Quantification Multiplex assays WG2: Kidney tissue proteomics LCM, Imaging MS EuroKUP Working Groups WG1: Biobanking ● Definition of clinically important research questions in the area of kidney diseases. ● Increase of inter-lab comparability in clinical proteomics through method standardisation ● Optimisation of methods for analysis of specific kidney structures ● Development of bioinformatics infrastructure (specialised databases, ontologies and analysis tools for kidney and urine proteomics) ● Training of young investigators in state-of-the-art proteomics and bioinformatics methods Scientific deliverables obtained due to networking ● Development of “Standard” Protocols for urine and kidney tissue collection (http://www.eurokup.org/node/138; Proteomics Clinical Applications, in press) ● Generation and characterisation of urine specimens to be used as “standards” in clinical proteomics ● Reporting of interdisciplinary (>45 authors) guidelines for biomarker discovery ● Fourteen collaborative manuscripts published (Including STSM results) ● Development of specialised ontology for kidney diseases (in collaboration with FP7 eLico) ● Funded collaborative projects: ProtoClin (MC IAPP) NefroBiobank (DESMI, Cyrpus), SeqAhead (COST), PRIORITY (FP7) ● Development of clinical study on CKD progression-submission of collaborative applications . Capacity building due to networking ● Links with relevant FP projects (E-Lico, DECanBio, SysKID) ● Links with other networks (HKUPP-HUPO), increase in participating countries (24 in Y3 vs 22 Y2 ), participation of investigators from US, Japan, Australia in WG meetings ● Links with Regulatory Agencies (EMA participation in EuroKUP meetings) ● Hands-on training schools on novel techniques-training days for ESR ● Build capacity on tissue imaging techniques-extensive interactions among labs-–rapid dissemination of know-how through COST instruments ● Funded collaborative projects-continuous submissions of collaborative proposals ● Expansion of interactions with all involved parties in biomarker pipeline underway (invitation of EMA, FP7 Eu Health, Biobanking, patient organizations, pharma companies, law-making bodies in upcoming EuroKUP meetings) ● EuroKUP non profit organization established to ensure continuation of activities Working Group 1: Standardisation in the clinical setting. This WG focuses on defining the major clinical questions in the area of kidney diseases. Chair: G. Spasovski (MK), co-Chair: M El Nahas (UK) Working Group 2: Method optimisation for kidney tissue proteomics analysis. WG2 targets the standardisation of state of the art methods for the proteomics analysis of specific kidney structures (coupling to laser capture microdissection techniques and imaging mass spectrometry). Chair: M Baumann (FI), co-Chair: G Allmaier (AT) Working Group 3: Standardisation of urine proteomics analysis. This WG targets standardisation of protocols for urine collection and increase in inter-laboratory data comparability Chair: H Mischak (DE), co-Chair: B Domon (LU) COST Visibility Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A,et al Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med. 2010; 2(46):46ps42 Mischak H, Kolch W, Aivaliotis M, Bouyssié D, Court M, et al Comprehensive human urine standards for comparability and standardization in clinical proteome analysis Proteomics Clinical Applications 2010;4(4):464-78 Dakna M, Harris K, Kalousis A, Carpentier S, Kolch W, Schanstra JP, et al Addressing the challenge of defining valid proteomic biomarkers and classifiers. BMC Bioinformatics 2010;11: 594-610 Makridakis M, Roubelakis MG, Bitsika V, Dimuccio V, Samiotaki M, et al Analysis of secreted proteins for the study of bladder cancer cell aggressiveness, Journal of Proteome Research 2010, 4;9(6):3243-59 (includes results of STSM) Special Issue on Urine and Kidney Proteomics edited by EuroKUP investigators Working Group 4: Development of bioinformatics infrastructure. This WG targets the generation of specialised ontology on kidney and urine -omics data and related diseases. Chair: E Bongcam-Rudloff (SE), co-Chair: T Attwood (UK)