A systems biology approach to deciphering the etiology of steatosis employing patient-derived dermal fibroblasts and iPS cells

• ¹ Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
• ² Institute of Pathology, Medical University of Graz, Graz, Austria
• ³ Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
• ⁴ Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
• ⁵ Cancer Stem Cell Group, Institute for Pathology and Comprehensive Cancer Center, Charité – Universitätsmedizin, Berlin, Germany
• ⁶ Magnetic Resonance Center, University of Florence, Florence, Italy
• ⁷ Department of Molecular Cell Biology, Netherlands Institute for Systems Biology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
• ⁸ Doctoral Training Centre ISBML, The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
• ⁹ Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
• ¹⁰ Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany
• ¹¹ Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf, Germany

Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis. As a result of increases in the prevalences of obesity, insulin resistance, and hyperlipidemia, the number of people with hepatic steatosis continues to increase. Differences in susceptibility to steatohepatitis and its progression to cirrhosis have been attributed to a complex interplay of genetic and external factors all addressing the intracellular network. Increase in sugar or refined carbohydrate consumption results in an increase of insulin and insulin resistance that can lead to the accumulation of fat in the liver. Here we demonstrate how a multidisciplinary approach encompassing cellular reprogramming, transcriptomics, proteomics, metabolomics, modeling, network reconstruction, and data management can be employed to unveil the mechanisms underlying the progression of steatosis. Proteomics revealed reduced AKT/mTOR signaling in fibroblasts derived from steatosis patients and further establishes that the insulin-resistant phenotype is present not only in insulin-metabolizing central organs, e.g., the liver, but is also manifested in skin fibroblasts. Transcriptome data enabled the generation of a regulatory network based on the transcription factor SREBF1, linked to a metabolic network of glycerolipid, and fatty acid biosynthesis including the downstream transcriptional targets of SREBF1 which include LIPIN1 (LPIN) and low density lipoprotein receptor. Glutathione metabolism was among the pathways enriched in steatosis patients in comparison to healthy controls. By using a model of the glutathione pathway we predict a significant increase in the flux through glutathione synthesis as both gamma-glutamylcysteine synthetase and glutathione synthetase have an increased flux. We anticipate that a larger cohort of patients and matched controls will confirm our preliminary findings presented here.