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ImmRisk SIGNED

Defining how environmental factors influence downstream effects of immune-mediated disease risk-SNPs

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

ImmRisk project word cloud

Explore the words cloud of the ImmRisk project. It provides you a very rough idea of what is the project "ImmRisk" about.

public fungal direction integration stimuli snps methodology functional 1 downstream exogenous diseases me variants conduct genome hypothesize analysing cells group immune trigger molecular person seq modulating predispose analytical rheumatoid absence white blood datasets evident re gt expression genetic risk bacterial arthritis framework viral eqtls combine single triggers interact interplay alter data mediated collection computational few am rna revealed samples context association frameworks disease mediate crohn qtl regulated last cell individuals interacting critical presumably generate environmental genomics thousands

Project "ImmRisk" data sheet

The following table provides information about the project.

Coordinator	ACADEMISCH ZIEKENHUIS GRONINGEN Organization address address: HANZEPLEIN 1 city: GRONINGEN postcode: 9713 GZ website: www.umcg.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Netherlands [NL]
Project website	https://molgenis58.target.rug.nl/scrna-seq/
Total cost	1˙496˙690 €
EC max contribution	1˙496˙690 € (100%)
Programme	1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
Code Call	ERC-2014-STG
Funding Scheme	ERC-STG
Starting year	2015
Duration (year-month-day)	from 2015-09-01 to 2020-08-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	ACADEMISCH ZIEKENHUIS GRONINGEN ACADEMISCH ZIEKENHUIS GRONINGEN Organization address address: HANZEPLEIN 1 city: GRONINGEN postcode: 9713 GZ website: www.umcg.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (GRONINGEN)	coordinator	1˙496˙690.00

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Project objective

In the last few years genome-wide association studies have revealed thousands of genetic variants associated to immune-mediated diseases, such as rheumatoid arthritis and Crohn's disease. Although it is evident that non-genetic factors can also trigger these diseases, presumably by interacting with the risk SNPs, we do not know what these factors are or how they affect risk-SNPs.

I hypothesize that environmental factors that increase disease risk also mediate the downstream molecular effects of disease-associated genetic variants. Since I am able to identify the downstream molecular effects of many risk-SNPs, and can identify molecular pathways regulated by specific exogenous factors like viral, bacterial or fungal stimuli, I now propose to combine these two approaches into a new analytical framework that will allow me to identify some of the exogenous factors that interact with risk-SNPs and together predispose to immune-mediated diseases.

My aim is to determine how exogenous triggers alter molecular pathways that are critical in immune-mediated diseases. For this we will generate single-cell RNA-seq data on white blood cells from 100 individuals (~1,000 cells per person) and conduct expression QTL analyses. We will then use this information to identify exogenous risk factors for immune-mediated diseases by re-analysing public RNA-seq data from >20,000 samples generated in the presence and absence of different (disease) stimuli.

This project is given direction by three developments by my research group: (1) our collection and integration of large functional genomics datasets, (2) our ability to develop computational frameworks for identifying the downstream consequences of SNPs using such datasets, and (3) my methodology to identify context-specific eQTLs.

This research will improve insight into the complex interplay between risk-SNPs and exogenous factors in modulating the molecular pathways that are crucial for the development of immune-mediated diseases.

Publications

List of publications.
year	authors and title	journal	last update
2017	Rocio Acuna-Hidalgo, Pelagia Deriziotis, Marloes Steehouwer, Christian Gilissen, Sarah A. Graham, Sipko van Dam, Julie Hoover-Fong, Aida B. Telegrafi, Anne Destree, Robert Smigiel, Lindsday A. Lambie, HÃ¼lya Kayserili, Umut Altunoglu, Elisabetta Lapi, Maria Luisa Uzielli, Mariana Aracena, Banu G. Nur, Ercan Mihci, Lilia M. A. Moreira, Viviane Borges Ferreira, Dafne D. G. Horovitz, Katia M. da Rocha, Aleksandra Jezela-Stanek, Alice S. Brooks, Heiko Reutter, Julie S. Cohen, Ali Fatemi, Martin Smitka, Theresa A. Grebe, Nataliya Di Donato, Charu Deshpande, Anthony Vandersteen, Charles Marques LourenÃ§o, Andreas Dufke, Eva Rossier, Gwenaelle Andre, Alessandra Baumer, Careni Spencer, Julie McGaughran, Lude Franke, Joris A. Veltman, Bert B. A. De Vries, Albert Schinzel, Simon E. Fisher, Alexander Hoischen, Bregje W. van Bon Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies published pages: e1006683, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1006683	PLOS Genetics 13/3	2019-05-29
2018	Monique G. P. van der Wijst, Harm Brugge, Dylan H. de Vries, Patrick Deelen, Morris A. Swertz, Lude Franke Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs published pages: 493-497, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0089-9	Nature Genetics 50/4	2019-05-29

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The information about "IMMRISK" are provided by the European Opendata Portal: CORDIS opendata.