The aims and coming activities of the EAACI Interest Group on OMICS and Systems Medicine are:
- To provide a communication platform for allergy and immunology researchers to share and develop knowledge about functional genomics and proteomics. This entails making a survey of researchers with this interest. Also to follow how functional genomics is applied in other disciplines.
- To promote understanding and recognition of functional genomics and proteomics among other researchers in the field of allergy and immunology.
- To promote development of standardized protocols in order to facilitate functional genomics and proteomics research, as well as comparisons between different studies.
- To have a symposium about functional genomics and proteomics at the EAACI Meeting in Vienna 2006 where researchers in the field can present their work.
- Hot topics in Functional Genomics and Proteomics
Complex diseases like allergy depend on altered interactions between multiple genes and environmental factors. At a recent meeting arranged by the Welcome Trust and Nature Genetics researchers compared notes from genome-wide association studies of complex diseases (http://www.nature.com/ng/meetings/genomics). It was predicted that hundreds or even thousands of genes could be involved in each complex disease. On top of this complexity different genes may be involved in different patients that appear to have the same disease. If it were possible to get a grip on this complexity it might be possible to gain increased understanding of disease mechanisms as well as to find new diagnostic or therapeutic targets.
Recent studies indicate that this may be achieved by network-based analysis of genomic high-throughput data. Essentially disease-associated genes are identified and organized in networks that are analyzed in a top-down manner. First, modules of interacting genes with distinct biological functions are identified. Then the modules are dissected to find pathways and finally upstream genes with key regulatory functions. Network-based analyses of cancer and allergic disease have resulted in the identification of new disease mechanisms, genes, single nucleotide polymorphisms and diagnostic markers.
Hot topics in allergy research are to apply network-based analysis to study disease mechanisms in different cells and tissues as well to find new diagnostic and therapeutic targets. Another challenge is to integrate data from different forms of high-throughput studies to form modules that describe disease-associated changes on multiple levels, ranging from DNA to protein.
- Current international allergy projects in Functional Genomics and Proteomics
Ø The EU project ComplexDis (http://www.complexdis.org.gu.se/) aims to develop methods to find markers for personalized medication in complex diseases. Seasonal allergic rhinitis is used as a disease model. Allergen-challenged CD4 + cells are examined with high-throughput techniques and the data subjected to network-based analysis. Candidate diagnostic markers are tested in clinical studies of SAR. The bioinformatic methods will be made freely available on the Internet.
The project which has a budget of 1.8 million Euro involves three pediatric allergists from Italy, Hungary and Sweden and experts in genomics, bioinformatics, modeling, computer science and systems biology from Spain, Italy, Belgium, Norway and the US.
Ø Sens-it-iv, the acronym for “Novel Testing Strategies for In Vitro Assessment of Allergens” is an EU funded consortium within the 6th framework, consisting of 28 European universities, institutes, companies and organizations which aims to design a human cell-based assay to test the propensity of new chemicals and proteins used by the e.g. the cosmetic and pharmaceutical industries to cause allergy (www.sens-it-iv.eu). The test system will be based on in vivo-like human epithelial and DC lines, cultured together to mimic the environment in lung or skin, and will hopefully reduce the need for animal experiments. Mechanisms for allergen recognition and markers involved will be identified with functional genomics, proteomics and metabolomics. All data generated are collected in an inductive database allowing queries for data patterns and predictive models, which will be freely available after project completion.
- Upcoming events
The IG is organizing a workshop in functional genomics and proteomics (FGP) in May 2008. The aim is to introduce FGP to allergy researchers in order to promote its application in different research fields. To this end leading experts in allergology, genomics, bioinformatics, computer science and systems biology have been invited to give lectures and seminars. To get an informal and interactive workshop the number of participants has been restricted to 35.
There are several FGP related events at the EAACI conference in Barcelona symposium. These are summarized
Symposium - Novel Developments in Genetics of Allergic Diseases
Update on asthma genetics
Stephen Holgate, United Kingdom
Genetics of atopic dermatitis
Stefan Weidinger, Germany
New genes influencing specific immunoglobulin E response
Luis Caraballo, Colombia
Meet the Expert 16 - Molecular Allergy, the Future is Now
Adriano Mari, Italy
Functional Genomics & Proteomics IG - Business Meeting and Session
Computation is the Key to Unraveling Disease Mechanisms in High-throughput Studies of Allergic Disease
Michael Langston, United States
Symposium - How Will New Genomic Technologies Help Allergists in the Next Decade?
Microarrays to find biomarkers
Marsha Wills-Karp, United States
A new approach to complex allergies: how rapid desensitisation turns off signal transduction
Mariana Castells, United States
Will new technologies result in biomarkers and drugs to prevent disease in early life?
Reto Crameri, Switzerland
- Comment on the must read papers of the last 3-6 months
A summary of a recent meeting about genome-wide studies of complex diseases addresses the huge challenges and possible solutions:
Petretto E, Aitman TJ. A gene harvest revealing the archeology and complexity of human disease. Nature Gen 2007; 39: 1299-3002
This study is a very elegant example of how integrated network-based analysis of high-throughput data from humans and model organisms as well as data from the public data can be used to identify new disease mechanisms, genes and polymorphisms:
Pujana et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007;39:1338-1349
This article is a conceptually brilliant discussion about how different complex diseases can be described as nodes in network. The nodes are described both geno- and phenotypically and there is considerable overlap:
Barabasi AL. Network medicine--from obesity to the "diseasome".
N Engl J Med. 2007
- Important relevant research centers across Europe