FINE MAPPING OF REGULATORY GENETIC VARIATION INVOLVING COMMON AUTOIMMUNE DISEASE ASSOCIATED HAPLOTYPES IN THE HUMAN MHC

Lead Research Organisation: University of Oxford
Department Name: Wellcome Trust Centre for Human Genetics

Abstract

Autoimmune diseases such as type I diabetes, multiple sclerosis and Crohn?s disease involve the body attacking itself through the immune system. Such diseases are common, particularly among younger people, for whom the consequences can be devastating. We know that autoimmune diseases occur more commonly in particular families and recent research has shown that many different genes are involved. In particular, scientists have found that a region of the human genome called the major histocompatibility complex on chromosome 6 is critically important in determining genetic susceptibility to autoimmune disease. We know that this part of our genome contains many genes involved in the immune response. The MHC is also a remarkably variable portion of the genome. It has proved very hard to define the particular genetic variants that are associated with developing disease within the MHC, or how such variants act to cause disease. In this research project we propose to investigate how genetic variation associated with disease affects the way genes are expressed. Genes are the blueprint of life, providing a code from which proteins are synthesized via an intermediary molecule called RNA. We will study how RNA is produced from DNA. We will do this in cells from the blood which are important in the immune response. We will study healthy volunteers who have different genetic backgrounds to see how this affects the process of gene expression. In particular we will study people with genetic backgrounds associated with autoimmune disease. We will also measure chemical changes in the DNA itself called methylation which can affect how genes are expressed. DNA methylation is an important control mechanism for the body to regulate expression of particular genes in particular cells at particular times. We know that this process may become dysregulated in disease and we plan to investigate this for genes in the MHC involved in autoimmunity. Overall our research will help scientists to better understand how genetic differences between people control the way our genes are regulated and define our risk of developing autoimmune diseases. This should help doctors to find new ways of treating these very important diseases and to target therapies to those who will benefit most. The work will be carried out at the University of Oxford. Our research will be published in scientific journals and promoted to the public through presentations at schools, the local and national media, and by providing information on the University website.

Technical Summary

There is a significant inherited component in susceptibility to autoimmune disease with the most striking and robust genetic associations involving sequence variation in the major histocompatibility complex (MHC) on chromosome 6p21. However fine mapping these disease associations and resolving specific functional variants has proved a significant roadblock in the field. This is made more challenging at this locus due to the remarkably polymorphic nature of the MHC and extensive coinheritance or linkage disequilibrium between variants. There is also a need for a more integrated approach to the resolution of genetic determinants of common disease, recognising the importance of epigenetic mechanisms and context-specific regulation of gene expression. Here we propose to define functionally important genetic variants modulating gene expression for common autoimmune disease associated haplotypes spanning the MHC. We know that there is significant heritable variation in gene expression involving the MHC. Our data from lymphoblastoid cell lines HLA-homozygous for HLA-A1-B8-Cw7-DR3, A3-B7-Cw7-DR15 and A26-B18-Cw5-DR3-DQ2 demonstrates that haplotype-specific differences in gene expression are common and often involve differences in alternative splicing. We propose to extend this analysis to carry out transcript profiling using RNA-seq for B lymphocytes and monocytes from HLA-homozygous healthy volunteers selected by genotype for eight common autoimmune disease associated haplotypes. These haplotypes were completely re-sequenced as part of the MHC Haplotype Project and are strongly implicated in autoimmune diseases including type I diabetes, systemic lupus erythematosus and multiple sclerosis. We will then confirm haplotype-specific differences and define specific local (likely cis-acting) or distant (likely trans-acting) variants by expression quantitative trait mapping combined with allele-specific transcript quantification. Specific regulatory variants will be characterised in the context of the local regulatory landscape based on chromatin profiling together with reporter gene analysis, assays of protein-DNA interactions, small interfering RNAs and assays to define allele-specific expression of alternatively spliced isoforms. Our analysis of transcription will be complimented by epigenetic profiling to define haplotype-specific differences in DNA methylation involving the MHC. This work will provide unique insights into the functional basis of observed associations with autoimmune disease for commonly occurring haplotypes in European populations. This has significant translational importance in advancing our understanding of disease pathogenesis and defining patients at risk of disease or most significantly benefiting from specific therapies.

Publications

10 25 50
 
Description Wellcome Trust Investigator Award
Amount £1,575,666 (GBP)
Funding ID 204969/Z/16/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2017 
End 09/2022
 
Description GenEXPRESSID 
Organisation University of Oxford
Department Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Diseases (NDORMS)
Country United Kingdom 
Sector Academic/University 
PI Contribution I have set up the necessary ethics and clinical collaboration for patient recruitment to enable the proposed studies. The GenEXPRESSID study is now listed in the UKCRN Portfolio (ID 12320) and at www.genexpressid.org. This is the mechanism where by patients are recruited.
Collaborator Contribution My clinical collagues have contributed to study design, setup and research nurse recruitment.
Impact Ethics approval, adoption on UKCRN Porfolio, beginning patient enrolment.
Start Year 2011
 
Description "All in the genes". Science Oxford Live 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 50 people attended this talk on genetics and health at Oxford Science Live which involved a presentation and a facilitated question and answer session

Significant interest and discussion among the group
Year(s) Of Engagement Activity 2013
URL http://www.scienceoxford.com/live/watch-us-archive/all-in-the-genes-interview
 
Description Cheltenham National Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Our genetics stand was very popular, particular with school children and stimulated much interest and debate

Interest from school teachers in genetics related 'hands on activities' for classes
Year(s) Of Engagement Activity 2014
URL http://www.well.ox.ac.uk/wtchg-at-cheltenham-science-festival
 
Description GenEXPRESSID workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach Local
Primary Audience Health professionals
Results and Impact Research nurses, information technology support workers and secretarial staff

Facilitated patient recruitment
Year(s) Of Engagement Activity 2012
 
Description Oxfordshire Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Stimulated questions and interest through activities

Interest and questions from public
Year(s) Of Engagement Activity 2013,2014
URL http://www.ndm.ox.ac.uk/oxfordshire-science-festival
 
Description Science Uncovered at the Natural History Museum London 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Stall generated significant interest

Requests for information
Year(s) Of Engagement Activity 2014
URL http://www.well.ox.ac.uk/a-night-at-the-museum
 
Description Seminar for non-scientists 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 30 administrative and support staff from the Wellcome Trust Centre for Human Genetics

Engagement with research of Centre. Very strong positive feedback.
Year(s) Of Engagement Activity 2012
 
Description The Naked Scientists podcast 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Generated The Naked Scientists podcast, Naked Genetics episode 'Genes, infections and immunity' (supported by the Genetics Society)

Raised awareness of genetics and disease
Year(s) Of Engagement Activity 2013
URL http://www.thenakedscientists.com/HTML/podcasts/genetics/show/20130814/
 
Description Work experience student 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Workshop Facilitator
Geographic Reach Local
Primary Audience Schools
Results and Impact Work experience for an A-level student from a local comprehensive school for a week spent in my laboratory

Enthusiasm from the student to apply for a degree course in genetics or biological sciences
Year(s) Of Engagement Activity 2012