Regulation of keratinocyte innate immune genes by psoriasis susceptibility alleles

Psoriasis is a common skin disease that affects approximately 1,000,000 people in the UK. It usually begins during early adulthood and may last for a whole lifetime. It presents as red, scaly patches on the skin generating much discomfort. It is associated with joint and heart disease and can have a large impact on the emotional health and wellbeing of sufferers, so poses a major social and economic burden on society. Current treatments cannot cure the disease and may cause unpleasant, serious side effects.

The skin provides a barrier to the outside world, to limit damage from infection and chemicals. It is known that the cells in the uppermost layer of the skin contribute to psoriasis through their ability to communicate closely with neighbouring immune cells. They help to set up an exaggerated immune response which results in the skin changes seen in psoriasis. Exactly how their function is altered in psoriasis is not yet known, but would provide important information to guide the development of treatments in the future.

Although the exact cause of psoriasis is unclear, it is known to run in families. Research suggests that multiple genes are involved. Identifying which genes these are and how these genes contribute to disease by affecting skin and immune cells is a major current challenge. Through studying the DNA of patients with psoriasis and comparing it to healthy individuals, we have identified numerous, large areas of the genetic map that are involved in causing psoriasis, however each area contains many genes of interest. We aim to analyse these areas in detail in order to discover the genes that cause psoriasis. We are particularly interested in how changes in genes may affect the function of the cells in the uppermost layer of the skin and contribute to disease. We will investigate this by studying skin cells from volunteers with psoriasis who have agreed to take part in our study.

Interestingly, some of the areas of the genetic map that increase risk of psoriasis also appear to increase risk of other immune-related conditions, such as Crohn's disease and rheumatoid arthritis. If we can understand more about the genes and immune pathways that are common and unique to these conditions, we may be able to streamline the design of future research studies and develop new, more effective treatments that have fewer side effects. Our research therefore has far-reaching relevance that spans many healthcare disciplines.

The group of researchers at King's College London led by Professor Jonathan Barker, Professor Richard Trembath and Dr Francesca Capon, have developed the critical mass and experience to support programmes and projects to resolve the genetic basis of medical disorders including psoriasis. The group have access to blood samples from a large number of patients with psoriasis and healthy individuals (all of whom have agreed to participate in our work), in-house state-of-the-art equipment to analyse DNA and computer-based technology for processing the results. Using cutting edge laboratory-based techniques, we will also explore how the changes in genes may affect the function of skin cells and the body's immune system.

We will make our results available to scientists, doctors and members of the public and hope to demonstrate the importance of high quality medical research in improving how we understand and treat common long-term diseases.

Aim
Identify common, regulatory variants underlying psoriasis genetic association signals that affect the expression of innate immune genes in keratinocytes

Objectives
1. Refine the localisation of disease associated signals containing innate immune genes
2. Determine the impact of candidate causal variants on keratinocyte gene expression

Methodology
1.1 Association analysis of a dataset (6600 cases/15000 controls) of SNPs genotyped on the Immunochip. Loci containing innate immune genes will be analysed using software e.g. PLINK. Genotypes of additional SNPs will be derived using 1000 Genomes Project. Sample divergence (confounders) will be controlled using principal component analysis. Stepwise logistic regression conditioning on the most significant variant within each locus will be repeated to derive all signals reaching genome-wide significance. Risk variants will be functionally annotated using ENCODE and correlated with phenotypes.

2.1 To analyse the impact of candidate causal variants on transcription factor-DNA interactions, involved and uninvolved skin will be sampled from patients harbouring variants in the regulatory regions of innate immune genes. Each patient will be heterozygous for the regulatory variants. To ensure robust results, I will repeat the analysis of each variant in >3 patients. Chromatin immunoprecipitation-sequencing (ChIP-seq) will be performed using antibodies to transcription factors, as informed by bioinformatic analysis. Reads from sequenced ChIP products will be analysed using MACS. The effects of the susceptibility loci on gene expression will be determined by correlation with quantitative RNA sequencing from keratinocytes available in expression quantitative trait loci databases.

Opportunities
The research may lead to drug discovery, clinical trials and disease stratification. Given the overlap between autoimmune disease genetic determinants, cross-disciplinary medical and scientific opportunities will arise.

Psoriasis is a common, stigmatising chronic inflammatory skin disease that poses a major global public health problem. It causes significant morbidity as it is associated with systemic diseases and severe psoriasis has increased mortality risk. The high impact on quality of life and emotional health is further testament to the social and economic burden the disease places on society. Current therapies are non-curative, expensive and associated with side effects. The proposed research has translational potential as improved understanding of the genetic and molecular mechanisms involved in psoriasis pathogenesis will open new avenues for disease stratification and highlight novel drug targets for clinical studies, resulting in health, wellbeing and financial benefits for society. The research has a wide range of beneficiaries, including investigators and clinicians interested in dermatology, autoimmune diseases, genetics and immunology, patients with psoriasis and other autoimmune diseases (and their families), private sector biotechnology/pharmaceutical companies, the media, government and general public.

The public, media and government are aware and very interested in the wealth of genetic information now available, which is in part attributable to recent, highly publicised advances in genomic technology and release of data from initiatives such as 1000 Genomes Project. My proposal is therefore of major current interest as it utilises state-of-the-art technology and computational approaches to advance our understanding of the genetic basis of psoriasis. By engaging with the general public, media and government, facilitated by the press/communications offices of King's College London (KCL), MRC, British Association of Dermatology and British Skin Foundation, I will increase awareness and understanding of chronic disease and the potential impact of cutting-edge medical research on health and wellbeing. My experimental techniques and analytical approaches are widely applicable to other areas of biomedical research and I will share techniques developed in this project through collaboration, publications and presentations at national/international meetings. Staff working on the project will develop skills in computation/statistics, team-working and communication, all of which are applicable in other employment sectors.

KCL is a world leader in genomic research and the large scale datasets that I will analyse will ensure my findings have the highest impact on a global scale. As part of a NIHR-funded Biomedical Research Centre, KCL has an advanced translational research programme. I hope, therefore, that observations made during the fellowship are developed into clinical studies in parallel with the project. This may require engagement with biotechnology/pharmaceutical companies, who would be key beneficiaries. Communication with industry representatives will be facilitated by attendance at MRC 'showcases'.

Recent studies confirm shared susceptibility loci between psoriasis and other autoimmune diseases, so my research is of interest and relevance to patients affected by a range of diseases, their families and the general public. Investigation into the innate antiviral immune molecular mechanisms contributing to psoriasis and regulatory pathways in keratinocytes may provide insights into the body's early response to pathogens and skin tumourigenesis. This may forge new angles of investigation into infective diseases (relevant to public health research/policy) and skin malignancy, further enhancing the project's quality of life and health outputs.

There is much interest in genomic medicine, with rapidly increasing trends towards personalising management of common diseases and stratified use of medicines based on genomic data, which represent major shifts in practice. There is also interest in the manipulation of immune pathways using immunotherapies. My research is thus very timely and has major translational potential.