Uncovering how ‘dark matter’ regions of the genome affect inflammatory diseases

Uncovering how ‘dark matter’ regions of the genome affect inflammatory diseases

Key points:

  • Genetic variations associated with increased susceptibility to inflammatory diseases are often hidden away in non-coding ‘dark matter’ regions of the genome.
  • An in-depth study of one such region reveals a key genetic switch that helps immune responses remain in check.
  • The study, published in the journal Nature, identifies a target protein GARP that is controlled by the switch, and that plays a key role in enabling immune cells to suppress inflammation.
  • This new knowledge helps to understand the contribution of non-protein coding ‘dark matter’ regions in disease, and identifies a promising new target for the treatment of autoimmune and allergic diseases.

A study led by researchers at the Babraham Institute in collaboration with the Wellcome Sanger Institute has uncovered how variations in a non-protein coding ‘dark matter’ region of the genome could make patients susceptible to complex autoimmune and allergic diseases such as inflammatory bowel disease. The study in mice and human cells reveals a key genetic switch that helps immune responses remain in check. Published today in the leading scientific journal Nature, the research, involving collaborations with research institutions in the UK and worldwide, identifies a new potential therapeutic target for the treatment of inflammatory diseases.

Over the last twenty years, the genetic basis of susceptibility to complex autoimmune and allergic diseases, such as Crohn’s disease, ulcerative colitis, type 1 diabetes and asthma, has been narrowed down to a particular region of chromosome 11. This work has involved large scale genome-wide association studies (GWAS), a genome-wide ‘spot-the-difference’ comparison between the genomes of individuals with or without a disease, to highlight regions of variation in the DNA code. This can identify potential genetic causes, and reveal possible drug targets. 

However, most of the genetic variations responsible for the susceptibility to complex immune and allergic diseases are concentrated within regions of the genome that don’t encode proteins - the genome’s ‘dark matter’. This means there’s not always a clear gene target for further investigation and the development of treatments.

Recent advances in sequencing-based approaches have shown that these disease-associated genetic changes are concentrated within regions of DNA called enhancers, which act as switches to precisely regulate the expression of genes. Further technological developments have allowed scientists to map physical interactions between different remote parts of the genome in 3D, so they can connect enhancers in non-coding regions with their target gene.

To gain insight into inflammatory disease, a large team of researchers used these methods to study an enigmatic non-protein-coding region of the genome whose genetic variations are associated with increased immune disease risk. They identified an enhancer element that is required for the immune system’s ‘peace-keepers’ and immune response mediators, regulatory T cells (Tregs), to balance an immune response.

Lead researcher and Babraham Institute group leader, Dr Rahul Roychoudhuri said: “The immune system needs a way of preventing reactions to harmless self- and foreign substances and Treg cells play a vital role in this. They’re also crucial in maintaining balance in the immune system, so that our immune responses are kept in check during infections. Tregs only represent a small percentage of the cells making up our complete immune system but they’re essential; without them we die from excessive inflammation. Despite this important role, there has been little evidence that unequivocally links the genetic variations that cause certain individuals to be susceptible to inflammatory diseases to changes in Treg function. It turns out that non-protein-coding regions provided us with the opportunity to address this important question in the field.”

Evolution gave the researchers a helping hand. The researchers took advantage of an approach called shared synteny, where not just genes are conserved between species, but a whole section of the genome. Similar to finding part of your book collection duplicated in your neighbour’s house, including the order of their arrangement on the bookshelf.

They used this genomic similarity to translate what was known about the enhancer in the human genome and find the corresponding region in mice. They then explored the biological effect of removing the enhancer using mouse models.

The researchers found that the enhancer element controls the expression of a gene in Treg cells, which encodes a protein called GARP (Glycoprotein A Repetitions Predominant). They showed that deleting this enhancer element caused loss of the GARP protein in Treg cells, and an uncontrolled response to a triggered inflammation of the colon lining. This demonstrated that the enhancer is required for Treg-mediated suppression of colitis, with a role for the GARP protein in this immune system control.

There was a similar effect in human Treg cells from healthy blood donors. The researchers identified an enhancer region whose activity was impacted by genetic variation specifically in Treg cells. The enhancer directly interacted with the human form of the same gene, and the genomic variations occurring in the enhancer element were associated with reduced GARP expression.

Dr Gosia Trynka, a senior author on the paper from the Wellcome Sanger Institute and Open Targets, said: “Genetic variation provides important clues into disease processes that can be targeted by drugs. In our joint efforts here, we combined human and mouse research to gain invaluable insight into complex processes underlying immune diseases. This has identified GARP as a promising new drug target and brings us a step closer to developing more efficient therapies for people suffering from diseases such as asthma or inflammatory bowel disease.”

Dr Roychoudhuri concludes: “Decades of research have now identified the variations in our genomes that make some of us more susceptible to inflammatory diseases than others. It has been very difficult, however, to make sense of how these variations relate to immune disease since many of them occur in non-protein-coding regions, and therefore the implications of these changes are poorly understood. Studies such as these will enable us to link the genetic switches that commonly reside in such disease-associated non-coding regions with the genes they control in different cell types. This will yield new insights into the cell types and genes underlying disease biology and provide new targets for therapeutic development.”

 

Notes to Editors

Publication reference
Nasrallah, R. & Imianowski, C.J. et al. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells. Nature. DOI: 10.1038/s41586-020-2296-7

Press contact
Dr Louisa Wood, Communications Manager, Babraham Institute, louisa.wood@babraham.ac.uk

Image description
Gut inflammation in mice lacking a homologue of a distal enhancer found at the human chromosome 11q13.5 disease risk locus. Credit: Babraham Institute.

Affiliated authors (in author order):
Rabab Nasrallah, postdoc, Roychoudhuri lab
Charlotte Imianowski, PhD student, Roychoudhuri lab
Francis Grant, previous PhD student, Roychoudhuri lab
Paula Kuo, postdoc, Roychoudhuri lab
Firas Sadiyah, PhD student, Roychoudhuri lab
Sarah Whiteside, postdoc, Roychoudhuri lab
Panagiota Vardaka, research assisant, Roychoudhuri lab
Carly Whyte, postdoc, Liston lab
Teresa Lozano, postdoc, Roychoudhuri lab
Adrian Liston, group leader in the Immunology research programme
Simon Andrews, Head of the Institute's bioinformatics facility
Jie Yang, postdoc, Roychoudhuri lab
Rahul Roychoudhuri, group leader in the Immunology research programme. Visit the Roychoudhuri lab website here: http://www.roychoudhurilab.org 

Research funding
The research was supported by a Wellcome Trust / Royal Society Fellowship, funding awarded from the Wellcome Trust including a Wellcome Trust Major Award, Institute Strategic Programme Grant funding and responsive mode funding from the Biotechnology and Biological Sciences Research Council, and funding from the following sources: Cancer Research UK, Medical Research Council, Associazione Italiana per la Ricerca sul Cancro and US National Institutes of Health (NIH).

Additional/related resources:
News item, 6 June 2018. Breaking through a tumour's defenses
Press release, 24 July 2017. Rahul Roychoudhuri awarded prestigious Lister Prize
Press release, 15 May 2017. How bacterial toxins could treat autoimmune disease

Animal research statement
As a publicly funded research institute, the Babraham Institute is committed to engagement and transparency in all aspects of its research. The research presented here used mice in which a small genomic region had been deleted to understand the effect of this deletion on immune cells and the mice’s response to an inflammation trigger. The mice were humanely killed to investigate the effects on different immune cell types and the mice’s immune response was measured by health and welfare monitoring while they were alive, and by analysis of cells and tissues after they had been humanely killed.

Please follow the link for further details of our animal research and our animal welfare practices.

About the Babraham Institute
The Babraham Institute undertakes world-class life sciences research to generate new knowledge of biological mechanisms underpinning ageing, development and the maintenance of health. Our research focuses on cellular signalling, gene regulation and the impact of epigenetic regulation at different stages of life. By determining how the body reacts to dietary and environmental stimuli and manages microbial and viral interactions, we aim to improve wellbeing and support healthier ageing. The Institute is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through an Institute Core Capability Grant and also receives funding from other UK research councils, charitable foundations, the EU and medical charities.

The Wellcome Sanger Institute
The Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. We are open and collaborative; our data, results, tools and technologies are shared across the globe to advance science. Our ambition is vast – we take on projects that are not possible anywhere else. We use the power of genome sequencing to understand and harness the information in DNA. Funded by Wellcome, we have the freedom and support to push the boundaries of genomics. Our findings are used to improve health and to understand life on Earth. Find out more at www.sanger.ac.uk or follow us on TwitterFacebookLinkedIn and on our Blog.

About Wellcome
Wellcome exists to improve health by helping great ideas to thrive. We support researchers, we take on big health challenges, we campaign for better science, and we help everyone get involved with science and health research. We are a politically and financially independent foundation. www.wellcome.ac.uk

Open Targets
Open Targets is a pioneering public-private collaboration that aims to transform drug discovery through the systematic identification and prioritisation of drug targets to improve the success rate for developing new medicines. The consortium is a unique, pre-competitive partnership between pharmaceutical companies and not-for-profit research institutes. The partners are GSK, Takeda, Bristol Myers Squibb, Sanofi, the Wellcome Sanger Institute and the EMBL’s European Bioinformatics Institute (EMBL-EBI). Open Targets combines the skills, knowledge and technologies of its partner organisations, offering a critical mass of expertise that does not exist in any single institution. Large-scale genomic experiments and computational techniques developed in the public domain are blended with formal pharmaceutical R&D approaches to identify causal links between targets, pathways and diseases. This enables the partners to systematically identify drug targets, and prioritise them for further exploration. Find more at https://www.opentargets.org/science/or follow @targetvalidate