Medical biotechnology to improve hepatocellular carcinoma diagnostics

We propose a project in the field of hepatocellular carcinoma diagnostics that will build on and bring together several research lines in our lab: N- and O-glycomics and methylomics (see below for more methodological details). These methods have been designed with clinical applicability in mind (both with respect to implementation and cost) and have now reached a point of maturity that they are being used for biomarker discovery in several clinical settings.

The current research project would pursue the discovery of biomarkers for early HCC diagnosis and HCC risk stratification in liver cirrhosis patients using these omics technologies. A large number of high quality samples from several Belgian university hospitals are already available. Further targets are biomarkers for treatment follow-up and prediction of drug response. For the latter, we will expand our collaboration with the hepatology department at UZ Ghent (prof. dr. Hans Van Vlierberghe and dr. Xavier Verhelst), who are experts in the field of hepatocellular carcinoma.

Over the past 3 years, liquid biopsies have being prospectively collected at the hepatology departments in three clinical centers (UZ Gent, UZ Antwerp and UZ Leuven). These samples enable a full multi-omics characterization of cirrhosis and early HCC patients and should give this project a kick start. In particular, these samples will be characterized with epigenomics (methylomics) and glycomics workflows developed in our lab. These give access to a layer of molecular information that is not directly genetically coded and thus carries physiologically relevant information.

First, we have a two decade-long experience using glycomics in chronic liver disease. Most of the plasma proteome and thus also the plasma glycome is produced by the hepatocytes. The glycome changes with the physiological state of the cells and consequently carries disease information. Our research has resulted in a cirrhosis biomarker and a HCC risk stratification marker based on the N-glycans in the plasma proteome (Callewaert N. et al. Noninvasive diagnosis of liver cirrhosis using DNA sequencer-based total serum protein glycomics. Nat Med 10, 429–434 (2004), Verhelst X. et al. A Glycomics-Based Test Predicts the Development of Hepatocellular Carcinoma in Cirrhosis. Clin Cancer Res 23, 2750–2758 (2017)). Currently we are developing a method that allows to characterize the O-glycome on tissue and secreted proteins. Via this method, we should be able to collect valuable information of cell-surface glycoproteins markers that are tumor-specific.

On the methylomics side, we have developed cfRRBS, cell-free reduced representation bisulphite sequencing, that allows to profile methylation of cell-free DNA (De Koker A. et al. A versatile method for circulating cell-free DNA methylome profiling by reduced representation bisulfite sequencing. bioRxiv 663195; doi: https://doi.org/10.1101/663195). CpG methylation has a profound regulatory effect on protein expression and often changes during oncogenesis. The goal is to find early HCC detection biomarkers and, based on the specific tumor epigenomics profile, enable the prediction of drug response.
Much of the clinical work in the past has been done in collaboration with the hepatology department at UZ Ghent and we intend to continue this work together. The combination of our experience in method development with the clinical expertise in the hepatology field of Dr. Van Vlierberghe and Dr. Verhelst ensure an environment in which this project can be brought to fruition successfully.

Chronic liver disease is a major cause of morbidity and mortality worldwide, with increasing prevalence. In terms of total years of life lost, it is now the 13th most burdensome disease overall and the 5th leading cause of death in the young adult age group of 25-50 years. HCC costs 800,000 lives per year. The main etiologies are chronic hepatitis B and C virus infection (HBV, HCV), alcohol abuse and, rapidly increasingly, nonalcoholic fatty liver disease (NAFLD) that is associated with insulin resistance and obesity. NAFLD is dramatically increasing in the last decades, in parallel with the obesity epidemic that is hitting hard in countries with a western diet.

In this setting, there are several unmet clinical needs with respect to diagnosis and follow up. In particular demand are biomarkers for early detection of HCC, while it is still in a stage amenable to curative treatment (as opposed to life-prolonging and supportive treatment). During treatment, there is a need for accurate disease monitoring biomarkers; how is the disease progressing? Does the treatment have a beneficial effect? Taking it one step further towards personalized medicine, (methylomics ) profiling of a patient’s HCC should allow to predict future drug responses and we can even envisage designing a personalized immunotherapy based on glycoprotein targets that we identify.

Experience in clinical or translational research in the field of hepatology or pathology in general. Experience or keen interest in exploring novel wet lab technologies, and (omics) data analyses.