Transcriptional profiling of circulating leukocyte populations in primary biliary cholangitis

Primary biliary cholangitis (PBC) is chronic liver disease that mainly affects middle-aged and older women. It is an autoimmune condition in which the body's own immune system causes progressive damage to the small bile ducts inside the liver. This leads to progressive scarring of the liver. Many patients eventually develop cirrhosis. Only two medications are licensed for treatment of PBC: ursodeoxycholic acid (UDCA) and obeticholic acid (OCA). Up to 20% of patients will have inadequate response to both medications, increasing their risk of developing cirrhosis. PBC therefore remains a major cause of liver-related problems, accounting for almost 20% of liver transplants performed in women in the UK.

Studies have shown that in PBC, the patient's prognosis is accurately predicted by the liver blood tests repeated at least 12 months after starting treatment with UDCA. This is known as the UDCA response. In patients with adequate UDCA response, life expectancy is the same as that of the general population, whereas in those with inadequate UDCA response, life expectancy without a liver transplant is significantly reduced. For this reason, current guidelines recommend using the UDCA response measured after at least 12 months of treatment to determine whether patients need second-line treatment (for example, with OCA). The problem with this approach is that the patients who need second-line treatment the most (i.e. patients destined to have inadequate response to UDCA) end up waiting longest to receive it. We need a way to predict which patients will or will not respond to UDCA, so that high risk patients can start second-line treatment at the earliest opportunity.

In our group, we have access to genetic and clinical information about several thousand patients with PBC. In my study, I will analyse these data, looking for genetic factors associated with UDCA response. Having identified these genetic factors, I will develop a 'genetic risk score' to predict UDCA response, which I will test in other large groups of patients.

Further to my work I will identifiy PBC patients at the start of their disease diagnosis prior to treatment initiation using our groups recently developed scoring system to identify two likely groups of patients, whose who will respond to UDCA therapy and those who will response inadequately. I will take blood samples from these patients to identify genes that are differentially expressed in immune blood cells that are associated with UDCA response. These results will then be validated and used to find a set of genes that could be used as a test to identify patients who will adequately respond to UDCA treatment and those who will have an inadequate response.

The aim of this two areas to my project will be to accurately characterise patients at diagnosis to identify those who will respond to first line therapy and achieve the greatest benefit and those who will not respond and will receive greater benefit from second line or newly developed therapies.

Primary biliary cholangitis (PBC) is an autoimmune liver disease characterised by destructive cholangitis affecting the small, intrahepatic bile ducts, leading in many patients to end-stage liver disease with attendant need for liver transplantation. The only licenced therapies are ursodeoxycholic acid (UDCA) and obeticholic acid (OCA). It is well-established that the liver biochemistry on treatment with UDCA (so-called 'UDCA response') strongly predicts long-term outcome. Current guidelines therefore recommend that UDCA response after 12 months of treatment be used to risk-stratify patients and determine eligibility for second-line treatment, e.g. with OCA. The problem with this step-up approach is that patients in greatest need of second-line treatment end up waiting longest to receive it. Methods are needed to identify high-risk patients at baseline for early introduction of second-line agents. Our group previously developed the UDCA Response Score (URS) to predict UDCA response - but this is a complicated equation, which might inhibit its use in practice.

In the proposed CRTF, I aim to discover and validate genetic and transcriptional biomarkers for UDCA response. I will undertake genotype-phenotype analysis of 5,700 well-characterised, genotyped cases in the UK-PBC Research Cohort to identify variants associated with UDCA response, from which I will derive a genetic risk score (GRS) with validation in external cohorts. I will undertake transcriptional profiling using RNA-sequencing of peripheral blood leukocyte subsets isolated from newly-diagnosed PBC patients prior to their starting treatment with UDCA, aiming to identify the minimum panel of differentially expressed genes (DEGs) that best classifies subsequent UDCA response, which may in future be developed as transcriptional biomarkers. I will determine whether the GRS or DEGs outperform or improve the URS, and where appropriate, work with industry to develop these biomarkers for clinical application.

In the proposed project I will aim to develop precision medicine (PM) for primary biliary cholangitis (PBC). PM is needed for PBC as in other chronic diseases as there is currently no system of treatment stratification; all patients start with UDCA monotherapy irrespective of baseline characteristics with OCA added only if the patients still has active disease more than 12 months later. The obvious disadvantage is patients with the greatest need of enhanced treatment end up waiting the longest to receive it. Recognising this need for PM our recently used clinical data from 2,703 UDCA-treated patients to derive the UDCA Response Score (URS), a logistic regression model based on pre-treatment clinical parameters that accurately predicts the likelihood of achieving adequate UDCA Response - but it is a complicated equation, which might inhibit use in practice.

Of note, however, one the variables in the URS model that impacts on UDCA response is the time from diagnosis to the start of treatment, such that if effective treatment is delayed, patients are less likely to respond to it. Moreover, patients with highly active disease, with marked duct injury, frequently experience worse symptoms. It follows that if timely introduction of effective treatment increases the likelihood of adequate treatment response this will lead to improved patient quality of life, improved long term disease outcome, reduction in disease associated complications and a decreased cost for healthcare systems.

It is clear that timely effective treatment is important, therefore, to improve the likelihood of achieving disease remission, and to reduce symptom burden I aim to undertake a project to identify the genetic basis behind patient response to UDCA therapy to identify genetic biomarkers to derive a genetic risk score (GRS) to predict UDCA response and also transcriptional profiling to identify differentially expressed genes associated with UDCA response with the aim to identify transcriptional biomarkers to distinguish patients who will subsequently achieve adequate versus inadequate response to UDCA therapy.

This will allow a more comprehensive precision medicine approach to treatment stratification in PBC whereby patients who will achieve an adequate response to UDCA will be identified at the time of diagnosis and started on appropriate therapy and whose patients identified as likely to have an inadequate response to UDCA will be started on second line or newer therapies to aim to improve their disease activity in a more timely manner. This stratified treatment approach will lead to improved disease outcomes and a more cost-effective approach to patient care.