Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue

• Verfasst von: Godoy, Patricio [VerfasserIn]
• Verfasst von: Meyer, Christoph [VerfasserIn]
• Verfasst von: Hammad, Seddik [VerfasserIn]
• Verfasst von: Dooley, Steven [VerfasserIn]
• Titel: Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue
• Verf.angabe: Patricio Godoy, Agata Widera, Wolfgang Schmidt-Heck, Gisela Campos, Christoph Meyer, Cristina Cadenas, Raymond Reif, Regina Stöber, Seddik Hammad, Larissa Pütter, Kathrin Gianmoena, Rosemarie Marchan, Ahmed Ghallab, Karolina Edlund, Andreas Nüssler, Wolfgang E. Thasler, Georg Damm, Daniel Seehofer, Thomas S. Weiss, Olaf Dirsch, Uta Dahmen, Rolf Gebhardt, Umesh Chaudhari, Kesavan Meganathan, Agapios Sachinidis, Jens Kelm, Ute Hofmann, René P. Zahedi, Reinhard Guthke, Nils Blüthgen, Steven Dooley, Jan G. Hengstler
• E-Jahr: 2016
• Jahr: 23 June 2016
• Umfang: 17 S.
• Fussnoten: Gesehen am 08.07.2019
• Titel Quelle: Enthalten in: Archives of toxicology
• Ort Quelle: Berlin : Springer, 1930
• Jahr Quelle: 2016
• Band/Heft Quelle: 90(2016), 10, Seite 2513-2529
• ISSN Quelle: 1432-0738
• DOI: doi:10.1007/s00204-016-1761-4
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: Bioinformatics
• Sach-SW: Differentiation
• Sach-SW: Gene arrays
• Sach-SW: Inflammation
• Sach-SW: Metabolism
• K10plus-PPN: 1668739828

Abstract

It is well known that isolation and cultivation of primary hepatocytes cause major gene expression alterations. In the present genome-wide, time-resolved study of cultivated human and mouse hepatocytes, we made the observation that expression changes in culture strongly resemble alterations in liver diseases. Hepatocytes of both species were cultivated in collagen sandwich and in monolayer conditions. Genome-wide data were also obtained from human NAFLD, cirrhosis, HCC and hepatitis B virus-infected tissue as well as mouse livers after partial hepatectomy, CCl4 intoxication, obesity, HCC and LPS. A strong similarity between cultivation and disease-induced expression alterations was observed. For example, expression changes in hepatocytes induced by 1-day cultivation and 1-day CCl4 exposure in vivo correlated with R = 0.615 (p < 0.001). Interspecies comparison identified predominantly similar responses in human and mouse hepatocytes but also a set of genes that responded differently. Unsupervised clustering of altered genes identified three main clusters: (1) downregulated genes corresponding to mature liver functions, (2) upregulation of an inflammation/RNA processing cluster and (3) upregulated migration/cell cycle-associated genes. Gene regulatory network analysis highlights overrepresented and deregulated HNF4 and CAR (Cluster 1), Krüppel-like factors MafF and ELK1 (Cluster 2) as well as ETF (Cluster 3) among the interspecies conserved key regulators of expression changes. Interventions ameliorating but not abrogating cultivation-induced responses include removal of non-parenchymal cells, generation of the hepatocytes’ own matrix in spheroids, supplementation with bile salts and siRNA-mediated suppression of key transcription factors. In conclusion, this study shows that gene regulatory network alterations of cultivated hepatocytes resemble those of inflammatory liver diseases and should therefore be considered and exploited as disease models.