Thomas Mohr*
Institute of Analytical Chemistry, University of Vienna
thomas.mohr [at] univie.ac.at
Abstract
In 2024, Gribben et al published a paper, “Acquisition of epithelial plasticity in human chronic liver disease”. This paper includes a single-nucleus RNASeq experiment spanning all stages of chronic liver disease, from healthy tissue to Metabolically Dysfunctional-Associated Steatotic Liver Disease (MASLD), Metabolic Dysfunction-Associated Steatohepatitis (MASH), liver cirrhosis, and end-stage liver cirrhosis. Samples from at least 4 patients represent each stage; MASH encompasses samples from 27 patients. The size of the dataset (>80.000 cells, with ~20.000 genes sequenced) poses special challenges but also enables the application of state-of-the-art network-based reengineering of gene regulatory networks.
In this talk, we will explore workflows available for these data and examine co-expression network-based determination of gene modules and structural equation model-based pathway perturbation analysis. This talk will give a brief overview of available methods, their strengths and limitations, and will present initial results on gene modules associated with disease progression, hub genes and pathways that change during chronic liver disease progression.
Keywords: MASH, MASLD, SEM, WGCNA
Acknowledgement: We want to thank Christopher Gerner and Samuel Meyer-Menches (both University of Vienna) for valuable input and Vorenica Moreno-Viedma (Medical University of Vienna) for pointing out the dataset,