News & updates

M6 Lay Version

Project Update May 2010 - Lay Version

 

Introduction: The BIO-NMD project is a collaboration of 12 European partners working together with the common aim of trying to identify possible biomarkers in people with neuromuscular disease. Once the potential biomarkers are identified, they will be validated in animal and cell models and in human body fluids.

The project is currently in its 6th month and much progress has been made. This report summarises the activities of the partners during that time. It is intended only as a brief update and summary.

 

University of Ferrara (UNIFE)
Leader: Alessandra Ferlini

Summary: The University of Ferrara is coordinating the BIO-NMD project. In addition, they are trying to discover biomarkers by looking at DNA and RNA. The team is also involved in providing patients' samples.

Update: During these first months the UNIFE has:
• finalised the BIO-NMD web site.
• got approval from Local Ethics Committees together with licences for animal experiments.
• finalised the creation of a patient friendly section on the project website.
• set-up a task force for selecting a limited number of patients to be studied.
• built-up a list of genes for Duchenne muscular dystrophy and collagen-VI myopathies to be analysed using ARIADNE software.

At the London meeting (8-9 July 2010) UNIFE has organised a dedicated session for industry in which the project impact and possible outcomes will be presented and described. Links for future collaborations will also be identified.

 

Leiden University Medical Centre (LUMC)
Leader: Peter Bram ‘t Hoen

Summary: LUMC is looking for biomarkers in cells, muscle tissue and body fluids.

Update: LUMC has screened the serum of Duchenne patients for possible protein biomarkers. They have so far found two proteins with elevated levels in DMD patients compared to healthy age-matched controls.

 

University of Newcastle upon Tyne (UNEW)
Leader: Volker Straub

Summary: The Institute for Human Genetics at Newcastle University is involved in three areas of the project: organising the collection and use of patients’ samples; social and ethical aspects of the project; and dissemination of information.

Update: In recent months, the patient-friendly part of the project’s website has been created in collaboration with patients’ groups. Other parts of the website have been created or improved in order that it can be used as a dissemination tool and discussion forum for BIO-NMD.

The project ethics board (PEB) has arranged its first meeting in Barcelona in June and a summary of the outcomes will be posted onto the website.

UNEW has been liaising with local and international biobanks to ascertain biomaterial availability, how much more is needed and when.

They have also been working as part of the clinical task force in selecting criteria for the various patient subgroups. In addition, UNEW has been discussing with partners the need for a standard procedures when collecting samples from patients across the different centres.

 

University of Padova (UNIPD)
Leader: Paolo Bonaldo

Summary: The University of Padova is working on biomarkers in animal models.

Update: During the first 6 months UNIPD has:
• Studied mice with a genetic mutation which means they do not produce collagen VI (COL6 null mice) in order to gain new insight into the molecular mechanisms of collagen VI disease. These molecular mechanisms may provide interesting biomarkers.
• Looked at the effect of switching collagen VI production back on in an animal model.
• Carried out experiments aimed at throwing new light on the mechanisms responsible for muscle cell death.
• Assessed muscle function and levels of various known biomarkers in mice after exercise.
• Built up a list of candidate genes for COL6 myopathies to be used by Ariadne for the generation of a knowledge base.

 

Institute of Child Health, University College London (UCL)
Leader: Francesco Muntoni

Summary: UCL Institute of Child Health will be involved in the collection and distribution of biomaterials for the research (e.g. muscle cells, blood and urine from Duchenne muscular dystrophy patients).

They will also be involved in the search for both genetic and protein biomarkers that would show differences in disease progression and in response to drugs.  The goal is to have a non-invasive way of monitoring disease severity or treatment benefit, e.g. by measuring levels of a protein in the blood or urine.

Update: Prof. Francesco Muntoni has been actively involved in the design of the study for biomarker selection, in particular the selection of patient characteristics.

UCL has recently recruited two full-time staff to work on the BIO-NMD project - Dr. Cirak has started the recruitment of patients for the study and Dr. Zaharieva has started to establish full RNA sequencing.

UCL will host the BIO-Consortium Meeting in June 2010 in London.

 

University of Rome Tor Vergata (UNIROMA)
Leader: Giuseppe Novelli

Summary: The university will be responsible for monitoring the results obtained across the labs involved in the BIO-NMD project. They will ensure that the methods used follow rules set out by the European Medicines Agency (EMEA).
 
Update: Prof. Novelli’s team is keeping up to date with work in progress at the European regulatory agency regarding new rules, new documents and guidelines about genomic biomarkers.

This is in order to guide the future the work of the other partners in the BIO-NMD project who will identify new genomic biomarkers and assisting them in applying for biomarker regulation and qualification.

 

Institut National de la Santé et de la Recherche Médicale (INSERM)
Leader: Christophe Béroud

Summary: INSERM will identify the tools used by other partners in their research. They will create new bioinformatics tools and databases to handle data generated during the project and coordinate the use of software by partners.

Update: As the biomarker discovery process involves different fields (looking at genetic material, cells, muscle tissue and body fluids), the first step will be to identify key tools used by partners in order to standardize data collection. A questionnaire has been sent to all partners and will be used to define the database structure.

At the same time, the INSERM team has started development of the UMD-Predictor® software that will be able to predict the effects of certain genetic mutations. It will be used in addition to other tools that are able to predict the impact of other mutations (Human Splicing Sequences Finder tool, HSSF®) as well as data from public databases.

 

University of Milan (UNIMI)
Leader: Cecilia Gelfi

Summary: The University of Milan will be mostly involved with biomarker discovery by studies on patient cells, muscle tissues and body fluids as well as biomarker discovery and validation in animal models.

Update: To better understand the consequences of collagen VI mutations UNIMI have focused attention on studies of mice deficient in the protein. This will provide new information about the effect that different protein expression has on the animal model.

Preliminary results have indicated that different muscles are affected in a different way by collagen VI mutations. The analysis is due to be completed by the first week of July 2010.

 

Royal Institute of Technology Stockholm (KTH)
Leader: Mathias Uhlen

Summary: The Royal Institute of Technology (KTH) is involved in checking that biomarkers discovered during the BIO-NMD project are specific to the muscular dystrophies under study. This will involve comparing samples from patients at different stages of the diseases and under different treatment programmes with healthy controls and with patients with unrelated NMDs.

Update: KTH has installed a new LUMINEX instrument which enables analysis of 384 samples in one single run. The instrument has been tested and calibrated ready for the start of biomarker analysis.

During the first 6 months they have also been in contact with BIO-NMD partners to discuss which type of patient samples (blood, serum or plasma) should be analyzed, the amount required for the analysis and the number of the samples to ensure that the planned analysis will provide meaningful results.

 

Ariadne Genomics Inc (ARIADNE)
Leader: Nikolai Daraselia

Summary: ARIADNE's role within BIO-NMD is to develop a literature-derived  knowledge base focusing on Neuromuscular Diseases (NMD).

Update: ARIADNE have been analyzing NMD-related literature in order to identify relevant concepts.

They have also started outlining the molecular mechanisms of various muscular dystrophies and are looking into public repositories of genetic data to identify and use that which is relevant to BIO-NMD.

 

AppliedBiosystems (AB)
Leader: Simone Guenther

Summary: AppliedBiosystems will provide technological support for methodological development using their SOLiD Next Generation Sequencing technology. The methods will allow analysis of BIO-NMD samples.

Update: AB have been working with Professor Ferlini’s laboratory at the University of Ferrara to set up and optimize a method for the re-sequencing of 80 genes related to NMD.

The plan is to get samples and a list of genes from the University of Ferrara and start designing the exact technique to be used for sequencing and analysis. They will then check their results in order to decide on the conditions and techniques required to achieve the most accurate and useful sequencing results.

 

Projets et Reseaux de Recherche (P2R/ACIES)
Leader: Loïc Courtot

Summary: ACIES/P2R will act as support to the project coordinator in strategic and operational management. More specifically, ACIES/P2R will accompany the project coordinator in monitoring, evaluating, consolidating and submitting the project targets and periodic reports as well as monitoring the project progress in terms of quality, costs, schedule and risks, in accordance with EU regulations and the grant agreement.

Update: During the last 6 months ACIES/P2R as the partner responsible for operational management, organised the Kick-Off Meeting for the project along with the project coordinator (UNIFE).

The management team has also monitored the achievement of the first 6  month’s targets and related reports, and supported the BIO-NMD partners in their work on a daily basis.

ACIES/P2R is currently working on some legal issues and organisational matters such as the upcoming meeting in London (July 8/9 2010). Part of this event will also be opened to Industry.

 




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