Functional characterization of non-collagenous extracellular matrix proteins as a potential molecular target and novel biomarker of liver fibrosis

Detailed information about the project:

Project Duration: 01.09.2015-28.08.2019
Project number: UMO-2014/15/D/NZ5/03421
Project title: “Functional characterization of non-collagenous extracellular matrix proteins as a potential molecular target and novel biomarker of liver fibrosis”
Project leader: Michal Pawlak, PhD; Investigators: Eugeniusz Tralle, MSc
Source of funding: National Science Centre, Poland, SONATA
Budget: 541 875 PLN

Project decription and main findings:

Fibrosis characterized by exaggerated synthesis and accumulation of connective tissue in the organ leading to its progressive dysfunction are associated with a wide range of chronic diseases. Among them liver fibrosis and its final stage liver cirrhosis is the major and the most severe hallmark of chronic liver disease leading to cancer development and organ failure. Liver cirrhosis affects nearly 0.1% of European population. The predominant cause of liver fibrosis are excessive alcohol consumption, hepatitis B and C virus and non-alcoholic fatty liver disease (NAFLD), which prevalence is drastically increasing over last decades due to epidemic of obesity.

Currently, no approved and efficient liver fibrosis therapy is approved, therefore liver transplantation is often needed in individuals with high grade of pathological changes. Despite growing understanding of the mechanisms driving liver fibrosis, there is lack of specific molecular biomarkers and molecular targets providing non-invasive diagnosis and safe targeted therapy. Transcriptomics, proteomics, metabolomics and other ‘omics’ have emerged as valuable tools to elucidate the mechanisms of multiple diseases and search for novel molecular markers and therapy targets.

By applying transcriptomics of liver biopsies from healthy patients and patients with liver fibrosis, we have identified genes related to this pathological condition including dermatopontin (DPT), a gene encoding extracellular matrix protein with yet unknown role in fibrogenesis. Functional tests in model organisms such as zebrafish and mouse established a clear association between DPT expression and liver fibrosis. DPT gene loss-of-function experiments including CRISPR-Cas9 genome editing, revealed that the lack of functional Dpt protein protects the animals from liver fibrosis development. Moreover, next-generation sequencing (NGS) techniques such as RNA-seq and ATAC-seq performed at single-cell type resolution in zebrafish model allowed to identify genes and epigenetic landscapes related to physiological conditions and liver injury.

Finally, we have identified novel protein associated with liver fibrosis both in human and in animal models of chronic liver injury. DPT appears as a promising molecular marker of liver fibrosis with a strong potential in  development of non-invasive diagnostics of liver fibrosis. Moreover, DPT is a potential molecular target of liver fibrosis therefore our findings can contribute in identifying novel preventive and therapeutic strategies of liver fibrosis.

Conferences:

1. Fishing for novel targets of liver fibrosis by using danio rerio model. Michal Pawlak, Katarzyna Kedzierska, Cecilia Winata. Liver fibrosis: The next goal of targeted therapy? European Association for the Study of the Liver, 17-18 JUNE 2016 Porto, Portugal. Poster presentation

2. The role of a novel extracellular matrix protein in zebrafish liver development and repair. E Tralle. M Pawlak, C Winata. 10th European ZebraFish Meeting, Budapest, Hungary, 3-7 July 2017. Poster presentation

3. Establishing a zebrafish liver fibrosis model. E Tralle. M Pawlak, C Winata. 2nd International FishMed Conference on Zebrafish Research, FishMed2018, March 25-27, 2018. Poster presentation

Publications:

1. PPARs in obesity-induced T2DM, dyslipidaemia and NAFLD. Gross B, Pawlak M, Lefebvre P, Staels B. Nature Reviews Endocrinology. 2017 Jan;13(1):36-49. doi: 10.1038/nrendo.2016.135. Epub 2016 Sep 16

2. Interspecies NASH disease activity whole-genome profiling identifies a fibrogenic role of PPARα-regulated dermatopontin. Lefebvre P, Lalloyer F, Baugé E, Pawlak M, Gheeraert C, Dehondt H, Vanhoutte J, Woitrain E, Hennuyer N, Mazuy C, Bobowski-Gérard M, Zummo FP, Derudas B, Driessen A, Hubens G, Vonghia L, Kwanten WJ, Michielsen P, Vanwolleghem T, Eeckhoute J, Verrijken A, Van Gaal L, Francque S, Staels B. Journal of Clinical Investigation Insight. 2017 Jul 6;2(13). doi: 10.1172/jci.insight.92264. [Epub ahead of print].

3. Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Pawlak M, Kedzierska K, Migdal M, Abu Nahia K, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Genome Research, Accepted article, 2019 Jan 9.

4. Transcriptome and chromatin landscapes of hepatocytes, stellate cells and endothelial cells in vivo during liver injury. Pawlak et al. [Manuscript in preparation].