Dissecting the mechanisms of immune-mediated inflammation: a systems-immunology approach

A better understanding of the early mechanisms that affect the immune response and induce inflammation in immune mediated inflammatory diseases (IMIDs) would help in developing better strategies for their treatment, prevention, and early diagnosis. Until now, research has mainly focused on patients already affected by specific IMIDs, and sometimes at later stages of the disease. Thus, important insights on the common early mechanisms of IMIDs may have been missed. We hypothesize that these early mechanisms are caused by a dysregulation of the same mechanisms that are involved in the normal immune regulation of inflammation in healthy subjects. Consequently, we propose to a) identify the main players involved in the immune regulation of inflammation in unaffected individuals, and b) verify their role in IMIDs using a very large sample of patients affected by specific and multiple IMIDs.

We have already finely characterised the immune blood cells of 2,000 twins from the TwinsUK cohort, of which 274 are affected by IMID. We have collected up to 9 years of follow up data, with a large number of clinical and biochemical variables, including variables that allow quantification of the underlying inflammation state. Follow up information has identified an additional 130 twins that developed the disease after collection. This well-characterised sample, which also includes 172 identical twins of whom only one of them was already or become affected, is ideal to investigate the relationship between immunity and inflammation.
A further limitation of current research is that immunological studies are often focused on the independent analysis of individual components. This approach does not take into account the real complexity of the immune system, whose function relies on the concerted action of multiple immune cells. We will use computational models to analyse altogether the immune cells and their interactions and to identify groups of immune cells associated with inflammation. To increase the power of our study, we will further characterise a number of chemical compounds that are key mediators of the communication with and between immune cells.
We have previously shown that the abundance of immune cells is controlled by genes. We will use genetics as an instrument to distinguish which of these groups of immune cells is a consequence of the inflammation state, and which are a cause of it - increasing IMID risk. Indeed, if a set of genetic changes affects the composition of a group of immune cells, and these cause inflammation and increases IMID risk, then the same set of genetic changes are likely to be more frequent in subjects who have developed IMID. To investigate this, we will use already available genetic data in 500,000 people from the UKBiobank, which includes 50,000 IMIDs patients. After identifying the genetic changes controlling the different groups of inflammation-associated immune cells in TwinsUK, we will use the UKBiobank sample to test their effect on IMID, and to prioritise their importance in increasing IMID risk.

Finally, in TwinsUK, we have already characterised both composition and function of the gut bacterial community. Our gut hosts trillions of microbes, which mutually interact with the immune system. We will investigate the interplay between the gut bacteria and the prioritised sets of IMID-associated immune cells, to identify bacteria that could be potentially targeted to modify immune cell composition.

In summary, by taking advantage of already available data and advanced statistical modelling, this project will pinpoint novel mechanisms of immune-mediated inflammation shared by different IMIDs, and will further explore the interplay between the microbiome and the involved immune cells. These results will constitute the basis for further investigations using disease-specific cohorts and to identify and validate potential therapeutic targets, that will be validated through interventional studies.

Our current understanding of the early mechanisms of immune-mediated inflammation has largely built on reductionist strategies, and studies focussed on specific diseases. We hypothesize that the early mechanisms of IMIDs dysregulate the same pathways involved in the normal immune regulation of inflammation. Moreover, novel insight can be gained through holistic systems approaches better-suited to modelling the complexity of the immune response. We have finely characterised immune cell composition in 1,726 healthy and 274 IMID-affected twins (124 discordant monozygotes[dMZ]) from TwinsUK, generating 90,000 variables describing cell types and their surface proteins. Longitudinal data on these subjects identified 130 additional subjects developing IMID (48 dMZs) after sampling. We further characterised: a)inflammation markers, from classical CRP to plasma metabolomics and glycomics; b)gut microbiome composition/function, through 16S, metagenomics, and faecal metabolomics; c)GWAS and WGS data.

We propose to take advantage of this unique deeply-phenotyped sample to:
1-Identify networks of immune cells, cytokines, and their interactions, associated with underlying inflammation (inflamModules)
2-Assess disruption of inflamModules in IMID
3-Exploit the UKBiobank resource to investigate through complementary approaches the shared genetic contribution between specific and multiple IMIDs and each inflamModule, to prioritise their putative involvement in IMID risk
4-Investigate association between prioritised inflamModules and the microbiome

We have previously shown, using a 4-times smaller sample, that genetic variants affecting the immunophenotypes also associate with inflammatory diseases. With this much larger sample, by integrating cytokines, and by exploiting the powerful UKBiobank resource, we would be in a strong position to identify novel mechanisms of early inflammation shared by IMIDs, and to explore the interplay between the microbiome and inflammation.

Who will benefit from the research?

IMIDs are apparently unrelated conditions, targeting different organs and encompassing such diverse disorders as Type 1 diabetes, psoriasis, or multiple sclerosis. Their prevalence is on the rise, and results in significant morbidity, reduced quality of life, and premature death. Increased disability and illness result in increased costs for the NHS and social care system, and long-term care also affects patients and their families, which are estimated to pay about 40% of the costs from income and savings.

Seemingly unrelated IMIDs conditions have been shown to benefit from common treatments, as in the case of the tumour necrosis factor-alpha inhibitors. This supports the involvement in distinct IMID of common underlying mechanisms, whose characterization would help the development of new strategies for widespread treatment and prevention. Therefore, the identification of such common mechanisms, as wells as generating valuable scientific data of importance to a variety of stakeholders in both the private and public sectors, has the potential to impact on the nation's health and welfare.

Beneficiaries of the research will be:

- The public sector, if these results help in developing more efficient strategies for prevention, early diagnosis and interventions for a wide range of IMID diseases
- The NHS, which may be able to use already-collected next-generation sequencing data for disease prediction and prevention
- The public, if translation of these results to clinical practice results in improved health outcome
- Private stakeholders (pharma and biotechnology) that can exploit the results for the development and marketing of novel diagnostic and therapeutic assays, and of pre- and probiotics

Cytokines and their receptors are particularly appealing targets for drug companies. They are able to modulate and boost the immune system, and cytokine-targetting drugs are already in therapeutic use for immune and infectious diseases, and cancer.

Finally this research will be an opportunity for the researchers involved in this research to test and validate computational medicine approaches aimed at data integration between functionally well-characterised cohorts and diseased cohorts. The research will allow further assessment of the translational value of existing statistical approaches for genetic risk prediction and patient's stratification. Additionally, this research will help to better understand whether microbiome research in IMID should focus on the effects on risk of singular species (with conflicting results often arising from different studies) rather than on the concerted metabolism of the microbial community as a whole.

It is important to highlight that while this research will provide novel insights on the mechanisms of immune-mediated inflammation and their putative involvement in IMID risk, a proper distinction between causal and reactive inflamModules as well as the identification of their key players, would require further investigation in disease-specific cohorts, interventional studies, and particularly the assessment of their effect over time. This includes a targeted follow-up of individuals in our longitudinal TwinsUK cohort - both those already included in this study and those for whom data and biological samples have already been collected. Particularly, individuals with immunophenotypes included in this study have been generated on samples collected on average 5 years ago, and up to 9 years ago. Given an incidence of IMID of 5% it would be expected that further subjects would develop the disease, thus allowing additional longitudinal comparison of immune cells and cytokines composition, and of the inflammation biomarkers.