European Kidney and Urine Proteomics

EuroKUP (Urine and Kidney Proteomics) (BM0702) is an Action sponsored by COST  (European Cooperation in the field of Scientific and Technical Research) focusing on facilitating translational proteomic research in kidney diseases by bringing together and promoting interactions between basic scientists and clinicians working in the broader areas of kidney and urine proteomics. EuroKUP currently fosters a multi-disciplinary network of more than 120 members from 26 countries. Four Working Groups (WG) focusing respectively on defining clinically important research questions in kidney diseases, kidney tissue proteomics, urine proteomics and bioinformatics have been generated. The decision-making body of EuroKUP is the Management Committee consisting of up to 2 representatives of participating COST countries. Scientific meetings and various training activities on cutting-edge techniques are regularly organized.  Short term scientific missions (STSM) for junior investigators are also financially supported. For more information please contact the Action Chair: A Vlahou

Working Groups

Working Groups: EuroKUP consists of 4 closely connected working groups.Working Groups: EuroKUP consists of 4 closely connected working groups.

Working group 1

Standardization in the clinical setting This Working Group will address and reach a consensus on the following issues:
  1. Definition of major kidney diseases and establishment of universally accepted pertinent terminology (staging system, definition of high risk patients etc)
  2. Review of state of the art in proteomics research for the selected renal diseases and definition of the special research needs in each case.  The latter include: a) definition of the most important clinically research questions (early diagnosis versus prognosis versus drug efficacy endpoint etc) and b) assessment of the stage of current proteomics (biomarker)  research (discovery phase, versus phases of confirmation or validation of already discovered biomarkers)
  3. Definition of optimal controls for each disease type so as to increase reliability of current and future biomarker discovery, confirmation or validation studies
  4. Definition of the sample sizes needed to reach statistically sound results for each of the biomarker discovery, confirmation and validation studies.
  5. Development of protocols for patient enrolment as well as for monitoring and evaluating participating centers.
  6. Standardization of biological sample collection (in collaboration with WG2 and 3). This also includes an assessment of the ability of participating centers to follow uniform protocols for sample collection and databasing.
  7. Establishment of criteria for the quality assessment of existing body fluid and tissue banks for kidney disease.
  8. Develop a network for the distribution of kidney disease-related biological material.
Chair: Goce Spasovski co-Chair: Meguid El Nahas Group Member Users

Working group 2

Method optimization for kidney tissue proteomics analysis and imaging mass spectrometry The field of biomarker and therapeutic target discovery for kidney diseases can greatly benefit from the development of innovative approaches for the proteomics analysis of pure kidney cell populations. EuroKUP addresses this need by setting as a very important scientific goal to optimize and standardize methods for the proteomics analysis of pure kidney cell populations either by coupling to laser capture microdissection techniques or by imaging mass spectrometry. Specifically, objectives of the activity of WG 2 include:
  1. Method optimization and standardization for the preparation of pure populations of all renal compartments from a) frozen and b) paraffin tissue sections following the use of Laser Capture Microdissection and imaging/profiling mass spectrometry
  2. Method optimization for protein extraction, separation, quantification and detection of post-translational modifications of kidney proteins
  3. Identification of existing infrastructure on nano-scale proteomics devices such as 2DE- lab on chip mini-devices and evaluation of their potential application for the analysis of starting material of limited amount, such as the protein extracts from LCM-isolated cells.
Chair: Joost Schanstra co-chair: Guenter Allmaier Group Member Users

Working group 3

Standardization of urine proteomics analysis To promote the use of urine as a biomarker discovery tool but also as the body fluid highly suitable for diagnostic/prognostic and disease monitoring tool several aspects of the proteomics analysis have to be improved.  The scientific focus of this WG is method optimization and standardization of protocols for the study of the different types (soluble, exosomal, proteins included in exfoliated cells) of urinary proteins. Specifically, objectives of WG3 include:
  1. Optimization and standardization of protocols for sample collection and storage for the analysis of the urinary soluble, exosomal and cellular proteins. This includes determination of the impact of sample preparation methods as well as of intra-individual and inter-individual variability on protein patterns.
  2. Method optimization for the enrichment of low abundance urinary proteins and their separation and identification.
  3. Optimization of quantification approaches for urinary proteins.
  4. Evaluation of the applicability of multiplex profiling proteomics platforms as routine urinary biomarker validation and/or renal disease detection tools.
Chair: Harald Mischak co-Chair: Bruno Domon Group Member Users

Working group 4

Development of a bioinformatics infrastructure for specialized research in kidney and urine proteomics. This WG will focus on computational issues pertinent to renal and urine proteomics data representation, sharing, retrieval, quality assurance and control, integration and analysis. Specific tasks that will be carried out include:
  1. Identification of all available knowledge and data sources concerning kidney and urine proteomics and other -omics.  This will be followed by the development of an integrated system for querying heterogeneous information sources relevant to the topic (structured knowledge bases (e.g. UniProt), document collections (e.g. MedLine), image databases, etc.),  in view of retrieving and extracting specific information related to kidney and urine proteomics.
  2. Creation, maintenance and update of a specialized “urine and renal proteomics” database that will integrate existing and newly acquired proteomics data.
  3. Development of a specialized ontology on kidney and urine -omics and all related diseases.  The ontology will be anchored to top level concepts of reference ontologies such as Gene Ontology (for gene products) or FMA (for anatomy), as well as other available ontologies (myGrid, UTOPIA) and terminological resources used by kidney/urine specialists (e.g., MeSH, ICD) . The initial or core ontology on kidney and urine proteomics will be developed by domain specialists together with computer scientists experienced in the development and deployment of biomedical ontologies. The latter will also develop web-service based mechanisms for incremental and collaborative refinement of this ontology by domain experts.
  4. Design, implementation and optimization of a set of tools for pre-processing of, and knowledge discovery from, proteomics experimental data. Issues to be addressed include: the data high dimensionality-small sample size problem, the inherently noisy nature of the data, the stability and reproducibility of the produced models, the incorporation of domain knowledge into the knowledge discovery process using innovative statistical/bioinformatic approaches.
  5. Investigation of strategies and development of a set of procedures to control for the quality of the experimental data and learned models.
Chair: Erik Bongcam-Rudloff co-Chair: Teresa Attwood Group Member Users

EuroKUP Members

  • Prof. Aasberg, A (NO)
  • Prof. Allmaier, G (AT)
  • Dr. Allory, Y (FR)
  • Dr. Arthur, J (USA)
  • Prof. Attwood, T (GB)
  • Prof. Banks, R (GB)
  • Prof. Barbas, C (ES)
  • Dr. Baumann, M (FI)
  • Dr. Benigni, A (IT)
  • Prof. Bezerianos, A (GR)
  • Dr. Bongcam-Rudloff, E (SE)
  • Dr. Campistol, JM (ES)
  • Dr. Candiano, G (IT)
  • Dr. Campistol, JM (ES)
  • Prof. Capasso, G (IT)
  • Dr. Carpentier, S (BE)
  • Prof. Cavouras, D (GR)
  • Dr. Charonis, A (GR)
  • Prof. D'Haese, P (BE)
  • Prof. d'Alche-Buc, F (FR)
  • Prof. Dadlez, M (PL)
  • Prof. Deltas, C (CY)
  • Dr. Djilianov, D (BG)
  • Prof. De Zeeuw, D (NL)
  • Dr. Decramer, S (FR)
  • Dr. Dihazi, H (DE)
  • Dr. Domon, B (CH)
  • Prof. Dominiczak, A (UK)
  • Dr. Edelman, A (FR)
  • Dr. Egido, J (ES)
  • Prof. El Nahas, M (GB)
  • Dr. Endlich, N (DE)
  • Dr. Farinazzo, A (IT)
  • Dr. Farfara, R (Israel)
  • Dr. Fernandez-Llama, P (ES)
  • Dr. Feldt-Rasmussen, B (DK)
  • Prof. Fliser, D (DE)
  • Prof. Frokiaer, J (DK)
  • Dr. Gansevoort, R (NL)
  • Dr. Garbis, S (GR)
  • Dr. Garin, J (FR)
  • Dr. Ghiggeri, GM (IT)
  • Dr. Gimenez, I (ES)
  • Dr. Granier, C (FR)
  • Dr. Goumenos, D (GR)
  • Dr. Haylor, JL (UK)
  • Dr. Hilario, M (CH)
  • Prof. Holthofer, H (IE)
  • Prof. Jankowski, J (DE)
  • Dr. Ioannou, K (CY)
  • Dr. Kentsis (USA)
  • Dr. Kalousis, A (CH)
  • Prof. Kaski, S (FI)
  • Dr. Knepper, M (USA)
  • Prof. Korneti, P (MK)
  • Dr. Kossida, S (GR)
  • Dr. Langham, R (Australia)
  • Dr. Loftheim, H (NO)
  • Dr. Lopez-Novoa, J (ES)
  • Prof. Luider, T (NL)
  • Dr. Maglogiannis, I (GR)
  • Prof. Magni, F (IT)
  • Dr. Malats, N (ES)
  • Dr. Martin, JL (ES)
  • Dr. Mayrhofer, C (AT)
  • Prof. Mischak, H (DE)
  • Dr. Monsarrat, B (FR)
  • Prof. Mueller, G (DE)
  • Dr. Nielsen, S (DK)
  • Mr. Norling, M (SE)
  • Dr. O'Connell, S (IE)
  • Dr. Ortiz, A (ES)
  • Prof. Paczek, L (PL)
  • Prof. Perunicic-Pekovic, G (SB)
  • Dr. Planelles, G (FR)
  • Prof. Polenakovic, M (MK)
  • Dr. Promponas, V (CY)
  • Dr. Rasic-Milutinovic, Z (SB)
  • Dr. Rehulka, P (CZ)
  • Dr. Rossing, P (DK)
  • Prof. Peter, K (Australia)
  • Prof. Righetti, PG (IT)
  • Prof. Ronco, P (FR)
  • Prof. Ryan, M (IE)
  • Dr. Sánchez-Carbayo, M (ES)
  • Dr. Schanstra, J (FR)
  • Dr. Schiffer, E (DE)
  • Dr. Semmes, J (USA)
  • Dr. Serra, A (CH)
  • Prof. Sheehan, D (IE)
  • Dr. Spasovski, G (MK)
  • Dr. Stenman, U-H (FI)
  • Ms. Stodkilde-Jorgensen, L (DK)
  • Dr. Tasic, V (MK)
  • Dr. Theodorescu, D (USA)
  • Dr. Thongboonkerd, V (Thailand)
  • Prof. Toncheva, D (BG)
  • Dr. Tsillibari, E (GR)
  • Dr. Tsiotis, G (GR)
  • Prof. Unwin, R (GB)
  • Prof. Vanholder, R (BE)
  • Prof. Vassilev, D (BG)
  • Dr. Vickers, ME (UK)
  • Dr. Verhulst, A (BE)
  • Dr. Vilasi, A (IT)
  • Dr. Vlahakos, D (GR)
  • Dr. Vlahou, A (GR)
  • Prof. Vonk, R (NL)
  • Dr. Wright, PC (UK)
  • Prof. Yamamoto, T (Japan)
  • Dr. Yutaka, Y (Japan)
  • Dr. Zielenkiewicz, P (PL)
  • Dr. Zürbig, P (DE)
  • Marija Ger (LT)
  • Francisco J. Lσpez-Hernαndez (E)
  • EuroKUP Executive Committee

    Chair: Antonia Vlahou
    Co-Chair: Joergen Frokiaer

    WG1:
    Chair: Goce Spasovski
    co-Chair: Meguid El Nahas

    WG2:
    Chair: Marc Baumann
    Joost Schanstra (5/2008-8/2010)
    co-chair: Guenter Allmaier

    WG3:
    Chair: Harald Mischak
    co-Chair: Bruno Domon

    WG4:
    Chair: Erik Bongcam-Rudloff
    co-Chair: Teresa Attwood

    Web-site coordinators: Erik Bongcam-Rudloff and Teresa Attwood
    STSM Coordinator: Sebastien Carpentier

    Management Committee

  • Prof. Aasberg, A (NO)
  • Prof. Allmaier, G (AT)
  • Prof. Attwood, T (GB)
  • Prof. Banks, R (GB)
  • Dr. Baumann, M (FI)
  • Dr. Benigni, A (IT)
  • Dr. Bongcam-Rudloff, E (SE)
  • Prof. Capasso, G (IT)
  • Dr. Carpentier, S (BE)
  • Dr. Charonis, A (GR)
  • Prof. D'Haese, P (BE)
  • Prof. Dadlez, M (PL)
  • Prof. Deltas, C (CY)
  • Dr. Dihazi, H (DE)
  • Dr. Domon, B (CH)
  • Dr. Edelman, A (FR)
  • Dr. Egido, J (ES)
  • Prof. El Nahas, M (GB)
  • Dr. Fernandez-Llama, P (ES)
  • Dr. Feldt-Rasmussen, B (DK)
  • Prof. Frokiaer, J (DK)
  • Dr. Granier, C (FR)
  • Prof. Holthofer, H (IE)
  • Prof. Luider, T (NL)
  • Prof. Magni, F (IT)
  • Dr. Mayrhofer, C (AT)
  • Prof. Mischak, H (DE)
  • Dr. Ortiz, A (ES)
  • Prof. Paczek, L (PL)
  • Prof. Perunicic-Pekovic, G (SB)
  • Prof. Polenakovic, M (MK)
  • Dr. Rehulka, P (CZ)
  • Prof. Righetti, PG (IT)
  • Dr. Sánchez-Carbayo, M (ES)
  • Dr. Schanstra, J (FR)
  • Dr. Spasovski, G (MK)
  • Ms. Stodkilde-Jorgensen, L (DK)
  • Prof. Toncheva, D (BG)
  • Prof. Unwin, R (GB)
  • Dr. Verhulst, A (BE)
  • Dr. Vlahou, A (GR)
  • Dr Ger, M (LT)
  • Prof Peter K (Australia)
  • COST DC Rapporteur: Prof. Gundert-Remy U (DE)
  • European Cooperation in the field of Scientific and Technical Research

    The European program COST (European Cooperation in the field of Scientific and Technical Research) was introduced in 1971 to promote the establishment of scientific networks in key thematic areas selected by scientists, in synergy with European Research Programs. COST is an open minded funding mechanism which supports financially networking activities including organization of meetings, workshops, schools as well as exchange visits and training of young investigators. EuroKUP is one of these actions.