Department of Bioinformatics – BiGCaT

Research projects



Metabolic Diseases

EuroDISH (Determinants – Intake – Status – Health)

About

Europe is suffering an increasing incidence of diet-related public health problems, including obesity, heart disease, stroke, cancer, type 2 diabetes and mental disorders. The European Union (EU) and its member states, therefore, face major challenges in promoting health and reducing this disease burden.

Improving health through lifestyle, food and nutrition can help combat such issues but high quality research to design effective strategies is required. EU-wide research collaborations and innovations are essential to improve the efficiency of the, mainly public, research resources and will provide competitive advantage at the global level. To support this, EuroDISH will assess the current needs for food and health research infrastructures in Europe.

Research infrastructures are facilities, resources or services which support the scientific community to conduct top-level research.
They can be divided into
a) hard research infrastructures; major buildings, equipment and instruments, knowledge-containing resources (e.g. e-platforms and data banks), and
b) soft research infrastructures; unique data management, interpretation and handling capacities, harmonisation of data and procedures, training staff, professional networks and knowledge transfer.

EuroDISH is a three year project funded under the EU 7th Framework Programme. It will focus on the integration of existing food and health research infrastructures, as well as the development of new ones. It will consider the needs of different stakeholders, such as EU and national policy makers, and researchers from a range of disciplines in both the public sector and industry.

Website

http://www.eurodish.eu/

Funding

 


Micronutrients

Vitamin D in diseases

 


MICROGENNET

Extension, enhancement and strengthening of established collaborations for the purpose of a community-driven knowledge base for micronutrient genomics

About

MICROGENNET is an EU funded exchange program that is closely related to the micronutrient genomics project (MGP).

MICROGENNET is a collaboration of 16 distinguished universities and research institutes worldwide. The overall aim of the exchange programme is to build, extend and strengthen sustainable collaborations between the partners so as to create a community driven knowledge base for micronutrient genomics research. Currently, the data on nutrient effects on health are scattered in publications and databases around the world. The aim of this work is to provide a public portal and bioinformatics toolbox to access and analyse collaborative and publicly available data. Ultimately the goal is to develop individualized intake recommendations for specific micronutrients to promote prevention of both acute illness and chronic disease.The exchange objective is provide researchers with: an international platform to learn novel techniques and methods, the opportunity to formulate new joint collaborative research and funding proposals and international exposure and intercultural understanding. The exchange programme consists of visits ranging from 1-7 months for ESRs and ERs. The expertise and facilities of the partners are highly complementary and the synergy lies in the combination of expertise on identifying metabolic and functional target pathways for a range of micronutrients (Selenium, Zinc, Vitamins and vitamin-related compounds anti-oxidants) and bioinformatics expertise on pathway analysis and data integration. The concise work plan consists of 4 work packages, 2 related to data collection concerning minerals and vitamins, a third over-arching bioinformatic workpackage and one for management. The consortium will be sustainable through its close association with the Micronutrient Genomics Project and the Europe-led NuGO association. MICROGENNET contributes to the EC priorities because it uses mobility to transfer knowledge and will create a network through which European centres of excellence will enhanced through links with researchers from the rest of the world.

Website

Link to MICROGENNET website

Funding

MICROGENNET  is funded by the EU Marie Curie action program IRSES grant 269210.

Mariecurie


Systems Toxicology and Risk Assessment

EU-ToxRisk

An Integrated European ‘Flagship’ Programme Driving Mechanism-based Toxicity Testing and Risk Assessment for the 21st century.

Websites

OpenRiskNet

OpenRiskNet is a 3 year project with the main objective to develop an open e-Infrastructure providing resources and services to a variety of communities requiring risk assessment, including chemicals, cosmetic ingredients, therapeutic agents and nanomaterials. OpenRiskNet will work with a network of partners, organized within an Associated Partners Programme.

Websites

Funding

The OpenRiskNet project is funded by the European Union’s H2020 (H2020-EINFRA-2016-1) under grant agreement no. 731075.

NanoSolveIT

NanoSolveIT aspires to introduce a ground-breaking in silico Integrated Approach to Testing and Assessment (IATA) for the environmental health and safety of Nanomaterials (NM), implemented through a decision support system packaged as both a stand-alone open software and via a Cloud platform.

Websites

Funding

The NanoSolveIT project is funded by the European Union H2020 (NMBP-14-2018) under grant agreement no. 814572.

RiskGONE

RiskGONE is a H2020 project aiming at providing solid procedures for science-based inter-disciplinary risk governance of nanotechnology, based on a clear understanding of risks, risk management practices and the societal risk perception by all stakeholders.

Websites

Funding

The RiskGONE project is funded by the European Union H2020 (H2020-NMBP-13-2018 RIA) under grant agreement no. 814425.

eNanoMapper

Creating community framework to accelerate collaboration – Supporting “Safe by Design” engineered nanomaterials development – Accelerating knowledge exchange through ontologies

Websites

Funding

The eNanoMapper project is funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration (FP7-NMP-2013-SMALL-7) under grant agreement no. 604134.


Rare diseases

Rett syndrome

Rett syndrome is caused by a detrimental mutation of the MECP2 gene. MECP2 is a central signaling gene which influences neuronal growth, differentiation, and development in many ways. MECP2 sits like a spider in the center of a biological network and acts as transcription regulator (activator or silencer), and it influences alternative splicing, chromatin structure and epigenetic imprinting.

To investigate the biological pathways which lead from the gene to the different phenotypes which occur in Rett females the methods of systems biology are especially useful. Their advantage is the holistic approach that investigates the whole process and gives an unbiased overview of changes in the cellular metabolism, gene interaction and protein production process. The data sources for these methods are usually high throughput data from genome, transcriptome, epigenome, or metabolome analysis. These are typically very long lists of genes or metabolites which are different from control samples. For visualization, analysis and interpretation of this huge amount of data specialized programs are developed and used at the Bioinformatics department.

The current work focuses on Rett patient’s transcriptomics data and to analyze them using prior knowledge databases like WikiPathways – a database for biological pathways. This method allows checking whether a group of changed genes belong to the same metabolic or signaling pathway and therefore allows a conclusion whether this pathway is affected. There are already several pathways known to lead to a certain phenotype e.g. energy metabolism or neuronal differentiation. Several pathways are also known to be susceptible for drugs so using this method new potential drugs could be identified which may contribute to handle the Rett syndrome symptoms.

We expect that application of systems biology methods is going to improve the understanding of MECP2 mechanism and we hope to provide explanation for some typical Rett symptoms like impaired sleeping patterns or nutrient uptake. We also hope to get more information about other neurological diseases and contribute to a better understanding of neurological physiology in general.

Collaboration

GCK – Rett Expertise Centre, Maastricht University Medical Centre

Funding

Stichting Terre – Rett Syndroom Fonds http://www.stichtingterre.nl/home/

 

EJP-RD (see http://www.ejprarediseases.org/) is a large project that will support research in rare disease aiming to substantially improve diagnosis and treatment. EJP RD is a 5-year project, it has 88 partners in 35 different European and non-European countries and the total budget is about 110M Euro; part of that reserved for calls opened by the project itself.

Within the EJP-RD we are coordinating WP13 – A cross-omics analysis work package. As one of the main pillars of this project will develop and test a bioinformatics framework and infrastructure for rare diseases. It will use earlier ELIXIR experiences on FAIR data and BBMRI experiences with private patient data catalogues, and EJP RD was already selected as a new driver project for the Global Alliance for Genomics and Health (GA4GH). After all that data organisation we will apply bioinformatics interoperability approaches for integrative data evaluation. The work package on this latter cross-omics and data integration approach is lead by the Department for Bioinformatics at UM. Next to tool development, this work will include the following steps:

  • Create disease-specific pathways on a new WikiPathways rare disease portal (see http:///raredisease.wikipathways.org for the first version). This will be done based on database and literature evaluation and in collaboration with existing European expert networks (ERNs), quite a few of these are also active in our MUMC.
  • Evaluate omics and other relevant data-availability on selected rare diseases and perform pathway (enrichment) analysis (likely already improving understanding of disease mechanisms. Omics data types already identified include genomics (largely exomes and single gene variants), transcriptomics and metabolomics.
  • We will combine affected pathways into data and knowledge supported rare disease networks, evaluate these for things like active nodes and make them available on NDEX.
  • Allow extension of these networks with relevant regulatory information (e.g. transcription factors and miRNAs) and where available evaluate data on such regulatory factors.
  • Use the networks to evaluate drug targets and thus come up with ideas for drug repurposing with some special interest in orphan drugs (building on our IMI collaborations).
  • Evaluate the network for intrinsic lifestyle factors (e.g. micronutrients present in or known to affect the networks) or processes known to be affected by exercise (building on our NuGO and other nutrition-related collaborations).
  • Allow extension with external environmental factors like chemical exposure (toxicology) and evaluate overlap with so-called adverse outcome pathways (building on toxicology collaborations).
  • Create complete workflows and make these available, including component containers and specific networks resulting from the analysis.

In this project, we will collaborate with various partners, The ones with central roles are: Franz Schaefer (WP co-lead, Heidelberg representing the ERN research group, Peter-Bram t Hoen (leads proof of principle task, RUMC Nijmegen, Marco Roos (link to FAIR work, LUMC Leiden), Anais Baudot (nutrient evaluation in networks, INSERM-AMU, Aix en Provence), Alberto Mantovani (toxicology evaluation, Istituto Superiore di Sanita (ISS), Rome), plus currently about 20 other participants. It will probably be clear that the project also links to most, if not all, activities that we currently have at BiGCaT. We expect that this project can thus also become a driver project for the department as a whole making the interlinks between various activities more tangible.

Funding

This project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement N° 825575, EJP-RD.


Education in health and life sciences

Helis academy  is a project that started in April 2018 (until April 2021). 10 Partners from academia and industry are now working together to 1. Assess the teaching and training needs of health and life science companies in the region and 2. To develop and to offer courses to provide the desired skills and competences. Its main purpose is to bridge the large “gap” between the required competences in the life sciences jobs and the existing competence / training programs.
Collaboration
Flanders.bio, Maastricht University, VIB, TU Eindhoven, DTL, VIVES-Noord/Vives Zuid, Hyphen Projects, Health House, TU Delft, LBSPf – Biotech Training Facility
Funding