Functional Genomics in SLE: A Transancestral Approach

Lead Research Organisation: King's College London
Department Name: Genetics and Molecular Medicine

Abstract

Systemic lupus erythematosus (SLE), or lupus is an autoimmune disease, by this we mean one in which the immune system targets the body's own organs. The spectrum of illness is wide, from considerable fatigue with skin rash and joint pains at one end of the spectrum to severe renal disease, which may cause renal failure and early death, at the other end. Lupus tends to occur in young women and affects all human populations; it is more common in those with Asian and African ancestry. We have a limited understanding of what causes the immune system to start this inappropriate attack on the body. The disease has a strong genetic component; there are many genes involved in influencing lupus: each gene exerting a modest effect on risk. If we can identify the genes and establish how they affect immune function, we can gain fundamental insight into how the disease develops and how best to treat individuals who suffer from it.

Considerable advances in genetics have been made over the last decade: examples include the sequence of human genetic material, DNA (Human Genome Project) and increasing understanding and cataloging of how this DNA sequence varies between people. DNA can be pictured as a code; variations in DNA code (or sequence) alter the structure and function of genes that are coded in the DNA. Genes affect the growth, function and development of the body, including the immune system. It is hardly surprising therefore that difference in the DNA code alters immune function and thereby influences the development of immune-related diseases, such as lupus.

We can compare the pattern of variation in DNA between healthy subjects and those with any particular disease, such as SLE. If we perform these studies in large numbers of subjects (thousands) we can build up a list of differences in DNA code that are much more likely to occur in individuals with disease when compared with healthy people. Studies in SLE reveal about 50 such examples, many of which are shared by other diseases such as rheumatoid arthritis. The next important question is to determine how these genetic differences affect immune function and by implication how they alter disease risk. One major hurdle preventing progress on this question is identifying the exact difference in the DNA code that affects disease. Although we state that 50 such differences across all human DNA have been established, we are not able to pinpoint the actual disease-causing genetic difference. This is because gene differences that a close to one another are usually inherited together. Thus, the 50 genetic factors in lupus are actually strings of 50 correlated gene DNA differences. Untangling some of these strings is the purpose of this project.

How do we achieve this unraveling? The pattern of these related strings varies according to inheritance and ancestry. We propose therefore to investigate a subgroup of 7 of the 50 lupus DNA regions by sequencing the DNA from people with SLE from European, Indian, west African and Chinese ancestries. This will provide a comprehensive catalogue of all the DNA differences that exist. We will then compare these pattern and frequency of these differences in SLE cases and healthy controls from these four ancestries. We know that the length and composition of the associated strings of correlated DNA variations differ in these ancestries. By lining them up against one another we can determine which DNA differences are consistently present in the disease group. Once we have established what the precise location and nature of the DNA code that affects disease, we can begin the process of working out how the genetic factors influence immune function. If we do not precisely locate the causal alteration in the DNA code that affects disease all subsequent experiments to pursue function will be flawed. This study is an essential component of future work on the genetics of autoimmune disease.

Technical Summary

SLE is a generalized autoimmune disease whose aetiology is incompletely understood. It exhibits complex genetics with approximately 50 known susceptibility loci. The disease appears to be most common in non-European populations. Data from GWAS suggest that the majority of loci are shared, but it is unlikely that this sharing extends to the allelic level. Like many others in the field, we have ben successful in mapping disease loci, but have not convincingly identified susceptibility alleles at the majority of these loci. This lack of resolution in mapping is a major impediment to functional analysis.

We aim to use transancestral mapping to identify causal alleles at lupus susceptibility loci. This approach exploits the variable patterns of linkage disequilibrium (LD) that are present in different human populations. The experimental plan is as follows. Resequence, to a high density, a set of seven functionally related SLE loci in 200 cases and 200 controls from each of four ancestries: European, African, Southeast Asian and north Indian. The libraries for sequencing will be generated by long range PCR. These data will generate a comprehensive panel of genetic variation at the loci, including insertion-deletion polymorphisms. Based on LD and functional annotation, a common set of markers across each locus will be assembled. This marker set will be genotyped in larger cohorts, each comprising 1800 cases and 1800 controls in the same four ancestries. Using sharing and regression-based approaches we will compare the association patterns across the populations with the aim of identifying causal common alleles. Rare coding variants will also be investigated, if identified and enriched in cases, they have a strong likelihood of causality in view of the known association of each locus with disease. We propose to commence experimental investigation of the functional effect of one or two of the causal alleles that we identify.

Planned Impact

The impact of this project will be most fully realised through engaging with the wider public, seeking ways to influence genetic policy and furthering our collaboration with an industrial company.

The ImmunoGenetics group at KCL run by Tim Vyse, has a good track record in publicising the results of its research, through the contribution of articles to the newsletters distributed by our other funders, Arthritis Research UK and the Wellcome Trust. DSCG wrote a "News and Views" article for Lupus UK following publication of the TNSF4 paper in Nature Genetics. TJV has also appeared on BBC1's South East TV News and on Radio 4's Today programme. The Vyse group also has a presence on FaceBook through the LupusUK website, a charity currently funding our Research Co-ordinator. The group also has an active programme of offering work experience to sixth formers and longer-term placements for other interested people, wishing to pursue a career in genetics.

The work proposed by the project has two major impact foci:
1) lupus patients and their friends
2) inspiration of the next generation of students
Lupus patients have life-long illness, which can seriously impact their quality of life. The relapsing-remitting disease course makes clinical management difficult and requires repeated medication changes. Disease management is easier when the patients and their close friends and family, have greater understanding of the causes of their disease, the options for medication and importance of seeking medical attention during lupus flares. This information can be important in increasing compliance to drugs with when the side effects may be unpleasant and interfere with the quality of life. Lupus patients can feel isolated by their disease and its effects on their day-to-day life. We plan to establish whether there is a need for patient support groups, either face to face or online. The goal is to educate the patients about their disease, encourage them to seek treatment at an earlier stage and thereby ensure that medical intervention is kept to a minimum. This has the added benefit of reducing the cost to health services.

Inspiration of future students - the region around Guy's Hospital contains some regions of poor social housing and disadvantaged children. We want to build on our programme of work experience by exploring the possibilities of directly engaging with children/sixth-formers to inspire them with a love of science and give them an insight into what being a scientist is really like. Since this is a new venture, we have set up a preliminary meeting with a representative of a local Education Board in order to discuss possible areas for involvement and arranged to meet with the Outreach for Medicine programme at KCL. Depending on the age of the students, our input may involve talks and discussion directly about the importance of genetics, either based within the school or at KCL. Alternatively it could take the form of a mentoring system, either face-to-face or electronically, using an e-mentoring system such as Brightside. KCL run mentoring schemes for both existing students and for would-be students in the Division of Medicine. We have made contact with the organisers of these programmes to explore ways in which we could be involved.

Influencing genetic policy - The PI/co-applicants will discuss with the Genetic Alliance potential avenues for being involved in the society's role in influencing policy decisions within Government. LupusUK is not currently part of this umbrella organization.

Application and exploitation - The Vyse group has developed an industrial partnership with Oxford Gene Technology (http://www.ogt.co.uk), to look for correlations between antibody profiles and clinical features of SLE, but also to examine the impact of genetics on antibody profiles e.g.) how genetically-driven MHC restriction may change antibody profiles, including against lupus susceptibility loci.

Publications

10 25 50
 
Description Arthritis Research UK Project grant Targeted DNA sequencing in Indian and European samples contributes to causal allele identification for lupus
Amount £215,000 (GBP)
Funding ID 20580 
Organisation Versus Arthritis 
Start 01/2015 
End 01/2017
 
Description MRC project grant: Functional genomics of SLE: A transancestral approach
Amount £150,000 (GBP)
Funding ID MR/L002604/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 01/2014 
End 01/2015
 
Description African ancestry analyses 
Organisation Oklahoma Medical Research Foundation (OMRF)
Country United States 
Sector Charity/Non Profit 
PI Contribution Sequencing data from associated genetic loci
Collaborator Contribution Sequencing data from associated genetic loci in African Americans
Impact Collaboration still ongoing and analyses have yet to be completed
Start Year 2013
 
Description Cross ancestry genetic comparison study 
Organisation Anhui Medical University
Department Institute of Dermatology
Country China 
Sector Academic/University 
PI Contribution genetic data in SLE in Europeans
Collaborator Contribution genetic data in SLE in Chinese
Impact Additional genetic factors in SLE
Start Year 2013
 
Description Genetic analysis of Indian SLE Lucknow 
Organisation Sanjay Gandhi Post Graduate Institute of Medical Sciences
Country India 
Sector Academic/University 
PI Contribution provision of novel genetic variants provided by sequencing at SLE risk loci
Collaborator Contribution provision of DNA samples for genetic analyses in Indian SLE cases, local PI Dr Ramnath Misra, SGPI, Lucknow
Impact Theis collaboration is under development
Start Year 2014
 
Description Genetics analysis of SLE in South African populations 
Organisation University of the Witwatersrand
Department Department of Rheumatology
Country South Africa 
Sector Hospitals 
PI Contribution We provide genetic data and analyses
Collaborator Contribution Partner provides DNA samples and clinical data,
Impact No outputs yet, the disciplines collaborating are: clinical rheumatology, genetics and statistics
Start Year 2016
 
Description Investigation of SLE in South Africa 
Organisation University of the Witwatersrand
Department Department of Rheumatology
Country South Africa 
Sector Hospitals 
PI Contribution Undertajke genetic analysis of DNA samples from collaborator
Collaborator Contribution proviso of DNA samples and clinical information on SLE subjects and controls
Impact Disciples: genetics, immunology , statistics and rheumatology
Start Year 2016