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:
- Definition of major kidney diseases and establishment of universally accepted pertinent terminology (staging system, definition of high risk patients etc)
- 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)
- Definition of optimal controls for each disease type so as to increase reliability of current and future biomarker discovery, confirmation or validation studies
- Definition of the sample sizes needed to reach statistically sound results for each of the biomarker discovery, confirmation and validation studies.
- Development of protocols for patient enrolment as well as for monitoring and evaluating participating centers.
- 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.
- Establishment of criteria for the quality assessment of existing body fluid and tissue banks for kidney disease.
- 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:
- 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
- Method optimization for protein extraction, separation, quantification and detection of post-translational modifications of kidney proteins
- 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:
- 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.
- Method optimization for the enrichment of low abundance urinary proteins and their separation and identification.
- Optimization of quantification approaches for urinary proteins.
- 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:
- 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.
- Creation, maintenance and update of a specialized “urine and renal proteomics” database that will integrate existing and newly acquired proteomics data.
- 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.
- 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.
- 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