Urine and Kidney
Proteomics
Acronym:
EUROKUP (European Kidney and Urine
Proteomics)
Proposer: Antonia
Vlahou Ph.D
Biomedical
Research Foundation, Academy of Athens
Soranou Efesiou 4, 11527
Athens,
Greece
Tel:
30 210 65 97 506
Fax: 30 210 65 97 545
e-mail:
vlahoua@bioacademy.gr
COST
National Coordinator: Mrs Katerina Galanou
International Cooperation
Directorate
European Union Division
General Secretariat for Research and
Technology
14-18 Messogion Avenue, 11527
Athens, Greece
Tel. +30 210 7458092
Fax. +30 210 7714153
e-mail: kgal@gsrt.gr
A. Abstract (up to 200 words)
Renal
diseases constitute a major health threat in all societies. Proteomics is the large-scale analysis
of the proteins of biological samples. Application of proteomics methodologies
in the investigation of renal diseases will catalyze the development of optimal
diagnostic and prognostic tests. Despite preliminary successful efforts, the
interactions between the multidisciplinary teams of scientists working on
kidney diseases and proteomics are still limited in Europe. EUROKUP will foster
the generation of a strong and growing multi disciplinary network of scientists
from at least 20 European countries, focusing on renal and urine proteomics.
The objectives of the Action focus on the identification of reference clinical
centers for major kidney diseases and establishment of uniform clinical
databases, standardization and optimization of procedures, integration of data
to systems biology approaches and dissemination of information for application
to diagnostic/prognostic procedures. Multiple scientific, technological and
societal benefits to the European Union are expected, including but not limited
to setting the urgently needed standards for clinical proteomics and
translational research and improving the clinical situation in chronic renal
diseases.
Key Words
(max 5 keywords): Kidney, Urine, Clinical Proteomics, Standardization, Network
Europ
B. Background (up to 2250 words)
B1. General background
Impaired structure/function of the
kidneys is a major health problem of modern societies. Chronic renal diseases,
usually progress to end stage renal disease (ESRD) which requires renal
replacement therapy, currently costing more than 30.000 € per patient annually.
The prevalence of chronic renal disease in adult European populations is above
10%, posing a serious health threat. It may also be one of the leading causes
of cardiovascular disease (CVD), as failing renal function is one of the best
predictors of CVD. In the future it is expected that the number of patients
with chronic renal disease will even increase due to the increased number of
patients with type II diabetes and aging of the population.
Research aiming at the development
of urgently needed new diagnostic/prognostic biomarkers and understanding the
molecular mechanisms underlying kidney diseases is being carried on in many
European Clinics and Laboratories. In this effort, Urine plays a pivotal role;
Specifically, it is considered the ideal tool to monitor non-invasively the
kidneyfs health status, since even in normal conditions, 70% of its protein
content originates from the kidney or the urinary tract. However, this research area has
not yet made full use of the developing field of proteomics. Proteomics
is the large-scale analysis of the proteins of biological samples and involves
all aspects of protein analysis from the determination of amino acid sequence
to the identification of functional partners and ultimately assignment to
regulatory pathways. gClinical Proteomicsh defined as the application of
proteomic analysis to answer clinical questions is considered one of the most
important research fields in our days, promising to discover diagnostic and
prognostic biomarkers, therapeutic targets and unravel mechanisms of diseases.
In this field, the standardization of clinical specimen collection, of quality
controls, as well as the establishment of an interdisciplinary approach
involving clinicians and basic scientists are of paramount importance in order
to progress towards the development of gpersonalized medicineh. This need is
reflected in the establishment of the Human Proteome Organization (HUPO) in
2001, which is gan international consortium of national proteomics research
associationsh, aiming at promoting among others gthe development and awareness
of proteomics researchh. In 2005, the Human Urine and Kidney proteome
initiative was established within HUPO with the objective to map the urine and
kidney proteome in health and disease. This initiative highlights the strong
interest of the scientific community in urine and kidney proteomics, but it
does not provide funding for regular networking activities, needed to achieve
its objectives.
Why COST Action?
The proposed Action provides the
unique opportunity to expand the HUPO initiative, enhances its networking
activities and promotes research in this field in Europe. As shown by a Medline
Search using the terms gproteomics, kidney and urineh out of 379 entries, 175
had originating (corresponding)
institutions in North America (46.17%), 142 in Europe (37.46%), and 62 in Asia
and Australia (16.35%). These numbers indicate that
there is a strong basis in Europe.
The proposed Action is the only way to: a) establish maximal
networking activity and b) boost research and help establishing Europe
as a place of Scientific Excellence in the field of renal and urine
proteomics. To demonstrate the competitive nature of this field, it should be
noted that the American Society of Nephrology recently organized a series of
retreats with the objective to define priorities in renal research and to make
specific recommendations to the National Institute of Health for the
development of core facilities (including proteomics) for kidney research.
Importantly, the Action is highly
complementary to running European projects (see below), and falls within
the guidelines of the European Science Foundation (ESF) since it tackles
Functional Genomics and their integration into Systems Biology in an
interdisciplinary approach; via standardization of approaches from the clinical
specimen collection all the way up to the data acquisition, handling and
analysis, the Action targets the smooth transition from basic to
clinical research and the establishment of translational approaches in the
area of kidney diseases. It is obvious that at this stage, these ambitious
objectives cannot be achieved through research frameworks with limited partner
numbers; to bring them into fruition, the first and most crucial step is to
accrue the interested vastly multidisciplinary team of scientists, including
clinicians, statisticians, bioinformaticians, protein chemists, molecular/cell
biologists, to provide their expert opinion and disseminate their
gknow-howh. This can be only
achieved through the open-minded and flexible COST mechanism.
B2 Current state of knowledge
Kidney proteomics
The application of proteomics
methodologies in order to understand the molecular mechanisms of renal diseases
and to develop improved biomarkers is continuously expanding. Applications on
the investigation of metabolic diseases like diabetic or hypokalemic
nephropathy, fibrotic processes including glomerulosclerosis, renal cancer, IgA
nephropathy and other diseases have been reported. Proteomics methodologies are
extensively used in the investigation of cultured cells obtained from human
patients and models for kidney diseases. Collectively these experiments strongly
support that (a) extensive proteomics investigations of kidney tissue will
provide useful diagnostic/prognostic markers and drug/therapeutic targets for
renal diseases; and (b) coordination of these efforts is absolutely necessary.
Urine Proteomics
Urine is excreted by the kidneys, is
non-invasively and easily attainable and largely reflects renal function,
making an ideal substrate for biomarker research. The protein content of urine is low under normal conditions
and derives mainly from human plasma proteins filtered through the renal
glomeruli and not absorbed at the proximal tubule level, exfoliated cells,
degradation of extracellular matrix as well exosomes secreted from epithelial
cells of the urinary track.
Multiple individual research efforts
in the investigation of the urine proteome are currently being conducted. These
involve the application of a series of proteomics technologies including
two-dimensional electrophoresis (2DE), various forms of liquid chromatography
in combination to mass spectrometry (LC-MS), MALDI-TOF or SELDI-TOF profiling and
capillary electrophoresis coupled to mass spectrometry (CE-MS). Nevertheless,
in comparison to other proteomics samples, urinary
proteome analysis is still in its early stages. It
been shown that variations in the
protein content of urine exist depending on the collection time, the age, sex,
diet and health of the donor.
Despite this variability, protein markers for kidney and other diseases
of major clinical importance (cancer, diabetes, atherosclerosis etc) have been
detected in urine and in many cases have been approved to be utilized in the
clinic for disease diagnosis and prognosis. This justifies and triggers a
coordinated in-depth analysis of the urinary proteome, particularly with the
advent of contemporary proteomics technologies, with the objective to identify
novel disease biomarkers. Even more, to fully exploit the potential of urine as
a diagnostic/prognostic tool, a concerted effort to develop standardized
protocols for urine collection and processing is extremely urgent.
Proteomics methodologies
Undeniably, advances in the fields
of chemistry, physics and computer sciences in the last decades have greatly
facilitated proteomic studies. Significant improvements in the protein
separation methodologies such as planar two-dimensional and capillary
electrophoresis and chromatography, as well as in mass spectrometry systems, in
the last decades have greatly increased the resolution, sensitivity and
accuracy in protein detection. In addition, novel approaches such as CE-MS,
MALDI-TOF-MS profiling and Multiple Reaction Monitoring (MRM) expand for the
first time the application of mass spectrometry from a research-biomarker
discovery tool to a biomarker quantification tool with potential direct
clinical applications.
As expected,
these technological/methodological improvements have given rise to new research
challenges: the reproducibility, portability and general applicability of each
methodology as a clinical diagnostic/prognostic tool has to be carefully
evaluated by well designed multi-institutional studies. Each separation
methodology and MS technology has distinct strengths and limitations and
extensive complementarity between them exist. Given the proteome complexity, a combined
approach that entails collaboration of different centers of expertise for each
methodology, will be therefore required for the successful characterization of
the human proteome in the normal and disease state. The detection of low abundance protein molecules
remains a big challenge; In this field, nano-technologies and microfluidics,
currently in development provide a highly promising avenue for improvement. Last
but not least, the use of innovative bioinformatic tools is mandatory to make
the most from all data generated by proteomics.
Innovation of the Action:
Coordination of activities and
standardization of processes are clearly needed at all levels of investigation
in the Renal/Urine Proteomics field. The Action fully addresses this need by
bringing together the experts in the field with the objective to synthesize
their input into a set of standardized approaches so as to maximize research
efficiency and knowledge extraction. In addition, the Action recruits and
brings together innovative proteomics, statistical and bioinformatics
techniques with the objective to identify new biomarkers and therapeutic
targets and develop non-invasive urine-based tests for kidney diseases.
B3 Reasons for the action
The critical mass of researchers
working on a) the investigation of kidney diseases, b) exploring urine in disease
diagnostic/prognostics, and c) developing/optimizing proteomics technologies
for the investigation of clinically important questions, is clearly emerging in
Europe. It is of paramount
importance to bring these teams of scientists together with a clear focus on
urine and kidney proteomics. Such an Action will have immediate and long-term
benefits on multiple scientific/technological as well as economic/societal
aspects in Europe:
Immediate Scientific/Technological
benefits
1) The establishment of appropriate
standards and quality controls in all aspects of urine and renal proteomics
research, from clinical specimen collection
and databasing to proteomics analysis and data processing will greatly increase
the effectiveness and comparability of running studies in individual research
centers.
2) Optimized protocols for sample
processing, fractionation, protein identification and data analysis will be
readily disseminated to the scientific community promoting proteomics research
in general.
Future scientific/technological
benefits
1) The foundation for future
biomarker validation and translational studies will be set up, including
working out their special statistical, clinical and methodological needs as
well as establishing unified clinical biobanks.
2) The basis for the establishment
of core facilities dedicated to proteomic kidney research in Europe will be set
up. Such effort has already been initiated in the United States and is urgently
needed in order to enhance the visibility and excellence of European research
in this field.
3) The
new proteomic approaches will provide insights in renal disease, which will
subsequently lead to innovative therapeutic targets/approaches
4) Through the dissemination of the
optimized protocols/novel proteomics approaches and the need for commercialization of the novel findings,
enhancement of the activities of the private sector is anticipated.
5) The promotion of collaborations
achieved during the Action will give rise to competitive research proposals to
the European Framework programs and other funding organizations.
Future societal/economic benefits
1) The foundation for the
exploration of urine in the clinical arena will be established with clear
societal and economic benefits: urine diagnostic/prognostic tests for the
highly prevalent kidney diseases may replace current invasive and costly
approaches; they will also facilitate early detection and disease monitoring,
reducing the number of patients and associated cost with end-stage disease.
2) Young researchers will be trained
on the use of state-of the art proteomics technologies which are widely used in
the pharmaceutical and medical industry.
3) Through the dissemination
activities of the Action, public awareness on the potential of novel proteomics
technologies in disease diagnosis and prognosis will increase.
B4. Complementarity with
other research programs
The proposed Action, with a clear focus on Clinical
Proteomics and specifically on Urine and Kidney has no direct overlap with any
other European project; however, it is considered highly complementary with
multiple running projects. A search of the CORDIS FP6 website using the
keywords grenal proteomicsh returned one entry: EUGINDAT. The project employs
various –omics technologies with the objective to study Primary Inherited
Aminoacidurias, a rare disease that affects renal reabsorption of amino acids. In
addition, when individually utilized, the keywords gurineh, grenalh, gkidneyh
or gproteomicsh brought up various projects aiming at investigating renal disease
at the genome level (EUROGENE,
Cells into Organs), involving
urine analysis for prostate cancer diagnostic purposes (P-MARK), or focusing on
the development of bioinformatics (ADDNET, BioInfoGrid, Diamonds, EMBnet, EMBRACE and HealthGrid ) or proteomics platforms (NanoSpad,
Interaction Proteome, Loccandia, ProteomeBinders) for biological data. In
addition, a COST Action on plant
proteomics (EuPP) was recently funded. A clear synergy between the
Action and these projects is envisaged: Tools developed and experience
accumulated in these projects will be of interest to the Action, and vice
versa: clearly the standards, proteomics tools and databases developed in the
Action will facilitate the realization of the objectives of these projects,
leading to more efficient use of European Resources. Leading scientists
of these projects are participating or will be invited to the workshops
organized by the Action so as to bring this synergy into fruition. As
the 2006-10 Strategic Plan of ESF involves translational research and renal
diseases, the timing for launching this Action is considered highly
appropriate.
(words: 2107)
C. Objectives and Benefits (up to 1500)
C.1 Main/primary objectives
The main objective of the Action is to
catalyze translational research in kidney diseases via standardization in all
aspects of urine and kidney proteomics analysis from specimen collection and databasing up to data processing and
analysis.
C.2 Secondary objectives
1) Identify reference clinical centers in Europe and develop unified
biobanks and a network for distribution of kidney disease-related clinical
specimens (tissue-urine). Specific research areas will include glomerulopathies
and tubulointerstitial diseases all leading to chronic renal disease and renal
failure.
2) Evaluate the applicability of
selected proteomics technologies (SELDI-TOF-MS, MALDI-TOF-MS, CE-MS, MRM) as
urinary biomarker quantification and profiling tools to be utilized in the
clinical setting. This will be achieved by dissemination of the expertise from
the respective centers and designing the appropriate portability and
reproducibility studies.
3) Optimize methodologies for the
proteomics analysis of pure kidney cell populations. This is a very important
research area since the analysis of selected cell types (rather than whole
tissues) greatly facilitates the discovery of novel biomarkers and therapeutic
targets.
4) Establish bioinformatics
infrastructure specialized for urine and kidney proteomics
5) Train young investigators in
state of the art proteomics and bioinformatics methodologies employed for
Clinical Proteomics applications.
6) Disseminate the information
gathered to the scientific community and increase the public awareness about
the potential of proteomics in the development of non-invasive
diagnostic/prognostic procedures
C.3 How will the objectives be achieved?
The objectives of the Action will be
achieved by bringing together scientists working on relevant fields, in a
manner that will allow fruitful interactions, dissemination of expertise and
promotion of collaborations. It is
characteristic that several scientific meetings in the fields of renal research
and proteomics take place in Europe and internationally every year. However,
the missing factor is a focus on urine and kidney proteomics and exchange of
valuable information in this field.
The Action will have a very strong interdisciplinary nature and will
foster and promote the interaction of basic scientists (biologists, protein
chemists, biochemists, statisticians, bioinformaticians), with clinicians
(nephrologists, urologists, pathologists, epidemiologists). Centers of
expertise in all aspects of the kidney disease proteomics analysis including
clinical/patient enrolment centers, proteomics laboratories as well as biostatistical,
data analysis and bioinformatics centers in Europe and internationally have
been and will be continuously identified and recruited to the Action. Dissemination of the individual
gknow-howh and promotion of collaborations will be achieved through
organization of workshops, summer schools, conferences, short term scientific
missions and exchange visits of junior scientists. To this end, special efforts
will be made to employ infrastructure developed in European Framework programs
(e.g. available e-learning platforms such as the European Multimedia
Bioinformatics Educational Resource-EMBER)
C4. Benefits
Considerable scientific,
technological and societal benefits are expected.
At the scientific level:
Standardized approaches for tissue
and urine collection will be defined and homogeneous clinical databases will be
developed that will catalyze sample exchange between different researchers and
consequently biomarker validation studies. Methodologies for urine and kidney
tissue proteomics analysis will be optimized and respective standards will be
set that will increase the effectiveness and comparability of current research
efforts. Proteomic databases
generated through this effort will be reference points for researchers and
clinical nephrologists and will form the basis towards the development of
personalized medicine approaches. Cross-correlation of these databases with
genomic, transcriptomic and metabolomic data will form the basis for kidney and
urine systems biology. The parallel analysis of urine and kidney proteome will
lead to a better understanding of the biological processes in renal cells and
more efficient exploitation of urine in disease diagnostics/prognostics.
At the technological level, the basis for the establishment of
core facilities for kidney research in Europe including reference clinical
settings for selected kidney diseases, facilities for tissue and urine specimen
processing, proteomics and bioinformatics analysis will be set. Undeniably,
such a major task will require further funding for infrastructure expansion.
The roots however, for such collaborative research projects will be implanted
and grown during the Action. In addition, the protocols and data to be
generated will facilitate the development of new therapeutic approaches as well
as of novel, non-invasive (and cost effective), diagnostic and treatment
monitoring tests, mainly but not limited to renal diseases, since urine
frequently reflects metabolic alterations stemming from other diseases.
Therefore, extensive interactions with the private sector will be set-up for
the exploitation of the findings. The latter interactions will also focus on
the dissemination of the new proteomics approaches developed in the Action, which
will enhance the activities of existing industries and/or lead to the establishment
of new „start-upgcompanies.
At the level of the society, the Action will contribute to the
reduction of the severity of renal pathologies and of the huge ESRD related
costs, by setting up the basis for the development
of non invasive early diagnostic tests and new therapeutic approaches.
As a result of their
training through the workshops, short-term scientific missions, and exchange
visits during the Action, young researchers will increase their competitiveness
in job hunt in medical and pharmaceutical industries. Public awareness on the
exciting new field of proteomics and its potential applications in the clinical
setting will increase through the dissemination activities of the Action.
In summary, by bringing together
experts from a variety of scientific fields and bridging the existing gap in
information exchange between them, the Action will reach the following high
quality outputs:
1. Increase efficiency of current
and future research activities involving urine and kidney proteomics by
optimizing and standardizing processes.
2. Set the pavement for the
discovery and validation of novel therapeutic targets and diagnostic and
prognostic biomarkers/biomarker profiles for the non-invasive detection of the
highly prevalent kidney diseases.
3. Set the foundation for kidney and
urine systems biology.
4. Catalyze translational research
in this field.
C5. Target groups/ End users
The anticipated end users of the
results of the Action include:
1. Basic scientists working in the
Clinical Proteomics field,
2. Physicians and nurses involved in
biological sample collection for research purposes,
3. Private sector which in
collaboration with basic scientists will be involved in the commercialization
of the novel diagnostic/prognostic approaches,
4. Patients suffering from kidney
diseases and their families
(words: 1029)
D. Scientific focus and workplan (up to 3000 words)
D1. Scientific focus (guidelines: describe the most
important research tasks; provide a structured (not too detailed) workplan,
explain the human and technical means- in lay terms)
To reach its major objective, the
scientific focus of the Action includes the following 3 major research tasks:
1)
Establishment of standardized procedures for acquiring, databasing and storing
urine and kidney samples related to clinically important research questions.
This task tackles one of the main
problems of current renal research which is lack of comparability of individual
research studies due to differential use or misuse of clinical terminology,
different biological specimen processing and storage mechanisms, and improper
case-control study design including insufficient statistical power and
sub-optimal control selection.
2)
Definition of quality controls and optimized protocols for the various
proteomics methodologies in use in urine and kidney tissue research.
This task addresses the
optimization/development of protocols for the proteomic analysis of pure populations of kidney cells by the
use of innovative approaches; it also tackles major difficulties that current
researchers encounter in evaluating and reproducing the results from individual
proteomics laboratories. The latter problem partially stems from the lack of
appropriate quality controls and of knowledge on the technical characteristics
(accuracy, resolution, reproducibility, linearity etc) of each proteomics
technology. Another factor contributing to this problem is the presence of a
plethora of technical protocols for protein extraction, fractionation and
separation. The use of
different protocols is undeniably needed due to the enormous complexity of the
human proteome. At the same time however, optimization of a single protocol for
each specific type of experiment and coherence of different laboratories to
that is needed to allow direct data comparability.
3) Formation
of bioinformatics infrastructure specialized for kidney and urine proteomics
data and establishment of procedures for its continuous maintenance and
updating.
The vast amount of data acquired by
the contemporary proteomics methods require databases and mining tools that will allow
comparisons of different samples, generation of reference profiles as well as
both statistical and graphical information about the sample under examination.
Along the same lines, various types of kidney or urine related 2DE protein maps
have been generated and become available through the world wide web. These
tools greatly facilitate research by providing protein map resources and
efforts are underway towards their expansion. There is a definite need for
urine and kidney database integration from multiple sources and development of
user interfaces that allow new data entry, visualization and retrieval. Simply stated, an gopen-mindedh
database has to be established to allow continual additions of data and
integration of information acquired by different centers of expertise.
Summary of workplan
The Action will achieve its
objectives by bringing together scientists with an in-depth knowledge on the
various aforementioned aspects of renal disease, proteomics and bioinformatics
analysis. As expected, the Action
is characterized by a very strong multidisciplinary character since it includes
nephrologists, urologists, pathologists, epidemiologists, statisticians,
molecular/cell biologists, protein chemists and bioinformaticians. The
gknow-howh and the necessary infrastructure, including a wide range of state-of
the art proteomics technologies (2DE, quantitative 2DE, various quantitative
LC-MS approaches, CE-MS, SELDI/MALDI MS platforms) are available by the
participating investigators. As
described in detail below (section D2), four working groups (WG) will be
formed; dissemination of the expertise and individual results, and synthesis of
the input from various partners will be carried out through scientific meetings
and short term scientific missions always with a clear focus on reaching the
objectives outlined above.
D2. Scientific workplan .
The working plan has been discussed
with all partners. To reach optimal efficiency in achieving the objectives,
four working groups (WG) have been conceived:
WG1:
Focusing on standardization in the clinical setting.
WG2:
Addressing the special needs and protocol optimization for kidney tissue
proteomics analysis.
WG3:
Focusing on method optimization and standardization for urine proteomics
analysis.
WG4:
Addressing the bioinformatics issues pertinent to the urine and kidney
proteomics analysis.
These working groups will be
strongly linked together as shown on Figure 1. Clearly each of them has distinct tasks which also define
the main type of expertise required in each case: clinical and expertise on
statistics in WG1, kidney proteomics (WG2), urine proteomics (WG3) and bioinformatics
(WG4). It should be emphasized
however, that completion of the tasks of each group can only be achieved
through continuous information exchange between them. For example, the clinical
and statistical information accumulated in WG1 will have to be passed on to the
basic researchers of WG 2 and 3 so as to design their studies accordingly, and
to the bioinformaticians of WG4 to formulate the specific domains required for
databases and ontologies.
Similarly, WG2 and 3 will have to disseminate their expertise to WG 1
and 4 so as define the requirements for sample collection and storage (WG1) and
the special needs for proteomics data deposit and analysis (WG4). Finally WG4 will have to work closely
with the rest of the groups to integrate the accumulated data and increase
knowledge extraction from them.
Figure 1:
WGs in (acronym). The major objectives and
main research tools within each group are shown. The WGs are strongly linked
together and extensive information exchange between exists.
The specific objectives and workplan
for each of the WGs are outlined below
WG1: Standardization in the clinical
setting
This working group will address and
reach a consensus on the following issues:
These
research questions will be addressed by a series of teaching activities (summer
schools, Working Group meetings) focusing on each of these issues. It should be emphasized that courses on
the principles of statistical design of biomarker discovery and translational
studies are urgently needed in order to increase the efficiency of the large
number of discovery and validation studies currently being conducted and
anticipated to be conducted in the future.
WG2: 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. The Action 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.
The urgent need to address this
issue stems from the multiple distinct structural elements forming the kidney: There is a cortex,
containing glomeruli and tubules, the medulla, containing tubules with
different characteristics than the ones in the cortex, and finally there is the
vascular system that provides blood supply to both the cortex and the medulla.
All these structural differentiations reflect functional differences.
Proteomic approaches so far have
been hampered by our limited ability to study each of these compartments
separately and within its biological context. Most of the studies performed so
far, deal with a piece of biopsy tissue or a part of an animal model renal
tissue, analyzed by the classical methodologies. Therefore, these analyses
cannot discriminate between the different cell types and their specific
structural/functional alterations in a pathologic process.
In an effort to overcome this
problem, some studies have introduced the purification of either glomeruli
(where filtration takes place) or tubules (where re-absorption takes place).
This is a clear improvement, however, this approach requires lengthy isolation
procedures that lead to stress and therefore alter substantially the proteomic
profile of the compartments under study.
The Action will address the above mentioned limitations
by coupling the proteomics analysis to the Laser Capture Microdissection (LCM)
technology. Alternatively
peptide/protein imaging approaches of kidney tissue slices by mass spectrometry
will also be developed. With
these approaches, the proteomic profiles of specific compartments or even
specific cell types can be determined greatly facilitating the study of specific categories of
renal diseases (cystic diseases, glomerular diseases either of primary or
systemic aetiology, tubular/tubulointerstitial diseases, vascular diseases).
Groups with expertise on the
combinatorial use of LCM with proteomics or imaging mass spectrometry are
participating in the Action. They will disseminate their gknow-howh to other
partners by organization of workshops, short-term scientific missions and
summer schools. In parallel, in collaboration with the clinicians and the
proteomics experts in the Action the improvement of several aspects of the technique
will be addressed. Specifically, the optimal storage, fixation and staining of
tissue sections need to be determined and standardized. Current protocols
employ primarily frozen fixed tissue as starting material. However, in many
occasions, renal tissue from humans even dating back to the middle of the 20th
century and classified by expert pathologists as well as tissue from animal
models for diseases have been fixed in formalin and embedded in paraffin.
The Action will focus on the development of novel techniques for the
proteomics analysis of such material. This would allow retrospective
prognostic and diagnostic biomarker investigations of a vast archive of
pathologically characterized clinical samples that exist in most Pathology
departments worldwide.
The LCM technology has a low yield
of proteins and their further analysis is consequently quite challenging. It is
anticipated that for obtaining the maximal information, the coordinated use of
different techniques (e.g. 2DE, SELDI and LC-MS) as well as the recruitment of
developing nano-scale proteomics devices (such as lab-on chip miniaturized 2DE
systems) is necessary. Regardless of whether the analysis involves kidney pure
cell populations or whole tissue, the detection of low abundance molecules such
as growth factors, transcription factors, as well as of specific protein
classes such as hydrophobic/membrane proteins or post-translationally modified
proteins (glycosylated, phosphorylated etc) remains technically difficult. To
address these issues, the expertise from groups working on the development of
proteomics nano-devices as well as on sample enrichment techniques for specific
type of proteins (glycoproteins etc) will be indispensable; It is anticipated
that workshops and training
activities for young investigators on these issues will be organized throughout
the course of the Action.
Collectively, 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.
.
WG3: Standardization
of urine proteomics analysis
To promote the use of urine as a
biomarker discovery 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.
Protocols employed for the study of
each of the above protein types will be discussed so as to establish clinically
feasible guidelines for urine specimen collection and processing (in
collaboration with WG1). It should
be emphasized that the analysis of the urinary proteome is considered
challenging due to the variations in urine composition (intra-individual and
inter-individual variabilities) as
well as due to the presence of many proteins in low abundance and in modified
forms. Various protein
preparation/extraction methodologies are being applied in the investigation of
the urinary proteome including, ultra-filtration, precipitation, solid phase
extraction, dialysis, ultracentrifugation or combinations thereof. Each of
these protein preparations methods may be combined with different protein
separation techniques (2DE, LC-MS, SELDI, CE-MS, MALDI profiling etc). Partners
in the Action have an in-depth knowledge on various urinary protein preparation
techniques; their input will be synthesized into a set of optimized urinary
protein extraction protocols to be shared among all partners and to the wider
scientific community.
Besides optimization/standardization
of sample collection, storage and urinary protein extraction protocols, this
WG will also address the employment of urine in multiplex protein profiling
studies. Recent reports
support the potential of proteomics platforms such as MRM, CE-MS and
MALDI/SELDI-MS in biomarker validation and even direct clinical application, as
novel diagnostic/prognostic approaches. In several cases, application of these
techniques has provided significantly higher accuracy rates in disease
detection compared to available diagnostic/prognostic means. In the course of
the Action, experts in the field will bring in their experience from the
application of these methods with the objective to disseminate their gknow-howh
through workshops and training activities and set the pavement for future
method portability and validation studies. In addition, studies involving the
analysis of the same set of urine samples by the different technologies will be
conducted, so as to directly compare the generated proteomic profiles.
Summarizing, 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.
As described above, WG2 and WG3 have
distinct objectives pertinent to the special needs of the biological sample
under investigation (kidney tissue in WG2, urine in WG3). Nevertheless, these two working groups share a
very important main objective: To get a clear understanding and establish the
analytical performance characteristics of each of the employed proteomics
methodologies (various types of LC-MS approaches, CE-MS, MALDI profiling, 2DE
in combination to different detection methods), as applicable. These
characteristics are extremely important for the design of appropriate quality
controls and include:
1) Reproducibility of analysis, ie.
repeatability and long-term stability
2) Achievable separation efficiency
(protein resolution)
3) Limit of detection, limit of
quantification, linearity
4) Mass accuracy
5) In collaboration with WG4, data
normalization and interpretation approaches.
WG4: 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 (e.g. UroProt, http://intramural.niddk.nih.gov/research/uroprot/) 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. To this end, software tools developed under
running European projects (e.g., UTOPIA (User-friendly Tools for OPerating
Informatics Applications)) will be recruited.
2) Creation, maintenance and update of a specialized gurine and renal
proteomicsh database that will integrate existing and newly acquired proteomics
data. This task includes a review of the state-of the art in available
pertinent bioinformatics platforms, definition of the special needs that such a
dedicated database entails and establishment of standardized approaches for
proteomics data deposit. The database schema will be designed in conformity
with the ontology to be developed in Task 3.
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.
5) Investigation of strategies and development
of a set of procedures to control for the quality of the experimental data and
learned models.
(2992 words)
E. ORGANIZATION
E1. Coordination and Organization
The Action will be coordinated by
the Management Committee (MC), according to the published rules and procedures
and with the support of the Scientific Secretariat in Brussels. To better
organize and promote interactions between the multidisciplinary teams of
scientists participating in the Action, 4 working groups will be established as
described below (E2).
.
The Management Committee will have as main responsibilities:
---Appointment of chair,
vice-chair(s), and WG co-ordinators; This will be carried out during the
kick-off meeting
---Appointment of a scientist
responsible for generating and frequently updating the Action-specific website
(web-site coordinator).
---Decision-making on the
distribution of funds to the various activities of the Action
---Planning and coordination of
several types of meetings and teaching activities, detailed below
---Evaluation of meetings and other
activities necessary to meet the set objectives
---Evaluation and report of the
progress of the different WGs and the Action as a whole. Preparation of Annual
Reports
---Promotion of collaboration
between the different WG members
---Establishment of extensive
collaborations between members of the WGs and members of other related Actions
and Scientific programs in Europe and world-wide.
– Increase the visibility of the
Action and promote interactions with medical and proteomics societies.
--Promote interactions with the private
sector and dealing with issues related to exploitation of results
A Steering Group (SG) consisting of the Chair, vice-chair(s),
web-site coordinator and the WG coordinators will be established. Members of
this group will be in frequent (at least once every two-months) communication
via e-mail and/or telephone conferences to discuss on the progress and ensure
good coordination of the activities of the different WGs. The Chair will be
contacting members of the MC during inter-meeting periods to inform them about
SG discussions as needed, and to recruit the necessary elements for achieving
the milestones. Besides these checkpoints, the MC/WG meetings will also play a
very crucial role in evaluating the progress of the Action (see below)
MC/WG meetings
The Management Committee will
convene at least four times, (once or twice every year) to ensure efficient
coordination, evaluate the
progress and make specific plans for future activities. These meetings with the
exception of the first one (kick-off meeting) will coincide with the Working
Group meetings. They will take place in different locations reflecting the
geographical distribution of the current and future members of the Action.
Efforts will be made so that the MC/WG meetings coincide with larger meetings
in the field (for example, the Human Proteome Organization (HUPO), Siena
Proteomics meetings etc) so as to increase the visibility of the Action and
attract more participants. Their
duration is expected to be 3-days. To ensure efficiency in meeting the
WG-specific needs as well as in promoting the communication and reaching
maximum possible exchange of information among different WGs, the meetings will
include 1-2 day-long WG-specific sessions and at least 1 day-long plenary
sessions involving the participation of representatives of all WGs. These will involve presentations
of individual research results, as well as presentations and discussions on
later developments in the field.
Emphasis will be given on the inclusion of young scientists and women in
these activities (oral presentations, chairmanship of sessions etc). Based on
these presentations, the MC will be evaluating the progress of the Action
towards reaching its objectives and will be deciding on future plans
accordingly.
Short Term Scientific Missions and other teaching activities
The STSMs consist a major tool for
the dissemination of gknow-howh to young investigators and the promotion of
collaborations between different research teams. Candidates to participate in
these activities will be selected following an application process and
assessment by the MC members. In addition the organization of about 5-day long
summer schools and workshops for young investigators will be conducted. These
will include (but will not be limited to) presentations on biomarker discovery
and translational study design, proteomics analysis of LCM cells and urine
proteomics. For these training activities special efforts will be made to
utilize available e-learning infrastructures, such as EMBER (European Multimedia Bioinformatics
Educational Resource), developed under European Framework programs. It should be emphasized that participants in the Action have the
infrastructure and gknow-howh on a very wide range of state-of the art
methodologies and technologies. These teaching activities provide the unique
opportunity to disseminate this knowledge to young researchers in Europe,
promoting scientific Excellence in the fields of clinical proteomics and
translational research.
E2. Working Groups
Four working groups will be formed
based on the scientific workplan described in section D2 of the Technical
Annex:
WG1:
Focusing on standardization in the clinical setting.
WG2:
Addressing the special needs and protocol optimization for kidney tissue
proteomics analysis.
WG3:
Focusing on method optimization and standardization for urine proteomics
analysis.
WG4:
Addressing the bioinformatics issues pertinent to the urine and kidney
proteomics analysis
Each Working Group will have a
co-ordinator to be appointed by the Management Committee during the kick-off
meeting. The WG-coordinator will play a pivotal role in reaching the objectives
of the Action.
Specifically, the main
responsibilities of the WG- coordinators
include:
--Interact frequently with the other
SG members and the members of the respective WG to discuss on WG-related issues
--Coordinate the activities within
each WG so as to meet the objectives of the Action
--Suggest to the MC the organization
of scientific activities (for example workshops, summer schools, STSM) related
to the specific WG.
--Promote interactions and
collaborations of different researchers within the WG and with the other WGs.
--Report on the progress of the WG
to the Action chair and the MC.
E3. Liaison and interaction with other research programmes
Interactions with scientists
participating in Framework Programs and Actions with complementary interests to
the Action will be of major interest to achieve maximum efficiency in using the
European Resources. As described in section B leading participants of projects
focusing on the development of proteomics tools (NanoSpad, Interaction
Proteome, Loccandia, ProteomeBinders), or bioionformatics platforms for
biological data (ADDNET, BioInfoGrid, Diamonds, EMBnet,
EMBRACE and HealthGrid ), that involve urine analysis
(P-MARK), or study kidney diseases at different –omics (genomics etc) levels (EUROGENE, Cells into Organs) as well
as from the Action on plant proteomics (EuPP) are already
participating in the Action or will be invited to the activities organized by
the Action. Through these
interactions the experience and tools acquired in these projects will be
recruited for the investigation of kidney diseases and the development of
urinary tests, and vice versa: the standards, optimized protocols, databases,
ontologies etc generated in the Action will facilitate the realization of the
objectives of these projects.
E4: Gender balance and involvement of early-stage researchers
This COST Action will respect an
appropriate gender balance in all its activities and the Management Committee
will place this as a standard item on all its MC agendas. This Action will also
be committed to considerably involve early-stage researchers. This item will
also be placed as a standard item on all MC agendas.
It is worth emphasizing that early
stage female scientists have already played a major role in the conception and
delineation of the objectives of the Action. It is therefore expected that
young female scientists will also play leading roles in the management of the
Action. As described above, gender balance will be observed in the Workshops,
Teaching Activities and Short Scientific Missions where also early stage
researchers are expected to form the overwhelming majority of
participants.
(1230 words)
F. TIMETABLE
The proposed duration for this
Action is 4 years. The Kick-off meeting will mark the start-point of the Action
where the chair, co-chair(s), WG co-ordinators and web-site coordinator will be selected. The Action-specific
website will be generated the first trimester and will be updated every
trimester. Reports will be generated at the end of every year. Details about
the frequency and the timing of MC meetings, WG meetings, Workshops, Short-Term
Scientific Missions and Teaching activities are indicated in the table below.
Please note that WG/MC meetings are planned to take place once a year;
nevertheless depending on the available budget and the specific needs of the
Action their frequency may increase to twice a year.
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YEAR 4 |
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Based on
the description in Section D and the above timetable, the following Milestones
will be reached
Type of Milestone |
Description |
Month(s) |
Evaluation |
Progress
Report |
12,
24, 36, 48 |
Dissemination |
Website
Generation |
3 |
Dissemination |
Generation
of brochure describing the Action |
4 |
Didactic |
Working
Group Meetings, Workshops, Summer Schools, Final conference |
12,
24, 36, 48 |
Dissemination |
Publication
of WG meeting and final conference proceedings on special issues of
peer-reviewed scientific journals |
12, 24, 36, 48 |
Dissemination |
Publication
of material of summer schools to the website |
18, 28, 40, 48 |
Research |
Standardizing
clinical terminology for major kidney diseases |
12, 24 |
Research |
Definition
of principles for study design |
12 |
Research |
Identification/Establishment
of Biobanks for kidney diseases |
12, 24, 36, 48 |
Research |
Definition
of optimized protocols/standards for analysis of pure kidney cell populations |
12, 24, 36, 48 |
Research |
Definition
of optimized protocols/standards for the analysis of urinary proteins |
12, 24, 36, 48 |
Research |
Definition
of optimized bioinformatics tools for proteomics data pre-processing and analysis |
12, 24, 36, 48 |
Research |
Establishment
and updating of kidney and urine specialized proteomics database and ontology |
12, 24, 36, 48 |
(406 words)
G. Economic dimension
The following
20 COST countries have actively participated in the preparation of the Action
or otherwise indicated their interest: AT, BE, BG, CY, CZ, DK, FI, FR, DE, GR, HU, IE,
IT, MK, NL, PT, ES, SE, CH, UK.
It is
expected that more participants will join this Action.
On the
basis of national estimates provided by representatives of these countries, the
economic dimension of the activities to be carried out under the Action has
been estimated at roughly EUR 32 Millions
for the total duration of the Action.
This
estimate is valid under the assumption that all the countries mentioned above,
but no other countries, will participate in the action. Any departure from this
will change the total cost accordingly.
H. DISSEMINATION PLAN
H.1 Who?
The
activities of the Action will be disseminated as widely as possibly to diverse
groups of people including basic scientists from academic- research
institutions and industrial settings, clinicians and general public. Target
groups specifically include:
---Fellow
researchers working in the fields of Clinical Proteomics and Proteomics, in
general.
---Fellow
researchers working on renal diseases and urine diagnostics, not using
proteomic approaches
---Other
European research groups participating in projects with complementary interests
to the Action (described in B4)
---Hospitals
and Clinics specializing in renal and urological diseases as well as medical
societies (European Renal Association, European Association of Urology (EAU), Board of the European Society for Urological Research,
Medical Research Council etc)
---Small
and Medium Enterprises focusing on the development of novel diagnostic kits
---European,
National and Regional policy makers
---The
general public
H.2 What?
---An
Action-specific website will be
constructed in order to provide information to the international scientific
community, to industries (proteomics technologies providers, pharmaceutical,
biotechnology settings) and general public. The Management Committee will assign this task to a partner
(web-site coordinator). Part of the website will be accessible to the general
public, whereas a section will be password-protected for the exchange of
specific information and unpublished data between partners. The website will also contain
information on the Action activities (meetings, workshops, etc), proceedings of
meetings, links to publications of
participants, job/STSMs announcements as well as material and
presentations from the didactic activities.
---A brochure will be generated at the beginning
of the Action describing its objectives and planned activities. This will be
distributed to scientists, representatives from the industry and society in
major international conferences on proteomics (for example HUPO) and kidney
diseases (for example European Renal Association- European Dialysis and
Transplant Association meetings etc)
---Scientific publications in peer-reviewed scientific journals generated as a
result of collaborative research during the Action either in the form of
original, review, or technical articles. To increase the visibility of the
Action, the publication of the proceedings of WG-meetings and final conference
to highly cited peer-reviewed journals in the field will be pursued.
---Combined Management Committee and Working
Groups meetings and other scientific
conferences; The MG/WG meetings are planned to take place on a regular
basis, ideally every six months, in various geographic regions, in order to
encourage participation of all interested members. To increase the visibility
of the Action, they will be preferably organized as satellites to major
scientific conferences in the field, such as the HUPO, the Siena Proteomics,
and the European Renal Association-European Dialysis and Transplant Association
(ERA-EDTA) meetings.
---Short-Term Scientific Missions,
targeting young scientists especially originating from developing regions, in order to foster
exchange of ideas and technology transfer.
---Teaching activities (Workshops and
summer schools), in order to disseminate the latest developments in the
proteomics field and also combine hands-on practical training with theoretical
information. These will be offered mainly to young investigators.
.
H.3
How?
The
Management Committee (MC) will be responsible for implementing all of the above
activities. The representative members of each country will be responsible for
disseminating the activities of the Action to research groups within their
countries, industrial partners, medical societies and representatives of the
society. Each MC member is
therefore, expected to generate, regularly update and circulate to other MC
members a list of target groups with contact information. For regional meetings
and other activities, the MC will delegate responsibilities to WG-coordinators
and members of the WGs depending on their specialty. In addition, the MC will
be responsible for providing all necessary information regarding the above
mentioned activities and their outcome as well as revise the dissemination plan
according to the Domain Committee (DC) recommendations.
(618 words)