Background: Liver transplantation leads to non-alcoholic fatty liver disease or non-alcoholic steatohepatitis in up to 40% of graft recipients. The aim of our study was to assess transcriptomic profiles of liver grafts and to contrast the hepatic gene expression between the patients after transplantation with vs. without graft steatosis. Methods: Total RNA was isolated from liver graft biopsies of 91 recipients. Clinical characteristics were compared between steatotic (n = 48) and control (n = 43) samples. Their transcriptomic profiles were assessed using Affymetrix HuGene 2.1 ST Array Strips processed in Affymetrix GeneAtlas. Data were analyzed using Partek Genomics Suite 6.6 and Ingenuity Pathway Analysis. Results: The individuals with hepatic steatosis showed higher indices of obesity including weight, waist circumference or BMI but the two groups were comparable in measures of insulin sensitivity and cholesterol concentrations. We have identified 747 transcripts (326 upregulated and 421 downregulated in steatotic samples compared to controls) significantly differentially expressed between grafts with vs. those without steatosis. Among the most downregulated genes in steatotic samples were P4HA1, IGF1, or fetuin B while the most upregulated were PLIN1 and ME1. Most influential upstream regulators included HNF1A, RXRA, and FXR. The metabolic pathways dysregulated in steatotic liver grafts comprised blood coagulation, bile acid synthesis and transport, cell redox homeostasis, lipid and cholesterol metabolism, epithelial adherence junction signaling, amino acid metabolism, AMPK and glucagon signaling, transmethylation reactions, and inflammation-related pathways. The derived mechanistic network underlying major transcriptome differences between steatotic samples and controls featured PPARA and SERPINE1 as main nodes. Conclusions: While there is a certain overlap between the results of the current study and published transcriptomic profiles of non-transplanted livers with steatosis, we have identified discrete characteristics of the non-alcoholic fatty liver disease in liver grafts potentially utilizable for the establishment of predictive signature.

1st Faculty of Medicine The General University Hospital Institute of Biology and Medical Genetics Charles University Prague Czechia

Centre for Experimental Medicine Institute for Clinical and Experimental Medicine Prague Czechia

Department of Hepatogastroenterology Institute for Clinical and Experimental Medicine Prague Czechia

Zobrazit více v PubMed

Bedogni G, Miglioli L, Masutti F, Tiribelli C, Marchesini G, Bellentani S. Prevalence of and risk factors for nonalcoholic fatty liver disease: the Dionysos nutrition and liver study. Hepatology. (2005) 42:44–52. 10.1002/hep.20734 PubMed DOI

Chalasani N, Younossi Z, Lavine JE, Diehl AM, Brunt EM, Cusi K, et al. . The diagnosis and management of non-alcoholic fatty liver disease: practice Guideline by the American Association for the Study of Liver Diseases, American College of Gastroenterology, and the American Gastroenterological Association. Hepatology. (2012) 55:2005–23. 10.1002/hep.25762 PubMed DOI

Neuschwander-Tetri BA, Caldwell SH. Nonalcoholic steatohepatitis: summary of an AASLD Single Topic Conference. Hepatology. (2003) 37:1202–19. 10.1053/jhep.2003.50193 PubMed DOI

Ong JP, Pitts A, Younossi ZM. Increased overall mortality and liver-related mortality in non-alcoholic fatty liver disease. J Hepatol. (2008) 49:608–12. 10.1016/j.jhep.2008.06.018 PubMed DOI

Friedman SL, Neuschwander-Tetri BA, Rinella M, Sanyal AJ. Mechanisms of NAFLD development and therapeutic strategies. Nat Med. (2018) 24:908–22. 10.1038/s41591-018-0104-9 PubMed DOI PMC

Targher G, Byrne CD, Lonardo A, Zoppini G, Barbui C. Non-alcoholic fatty liver disease and risk of incident cardiovascular disease: a meta-analysis. J Hepatol. (2016) 65:589–600. 10.1016/j.jhep.2016.05.013 PubMed DOI

Mantovani A, Zaza G, Byrne CD, Lonardo A, Zoppini G, Bonora E, et al. . Nonalcoholic fatty liver disease increases risk of incident chronic kidney disease: a systematic review and meta-analysis. Metabolism. (2018) 79:64–76. 10.1016/j.metabol.2017.11.003 PubMed DOI

Abenavoli L, Greco M, Milic N, Accattato F, Foti D, Gulletta E, et al. . Effect of mediterranean diet and antioxidant formulation in non-alcoholic fatty liver disease: a randomized study. Nutrients. (2017) 9:E870. 10.3390/nu9080870 PubMed DOI PMC

Papandreou D, Andreou E. Role of diet on non-alcoholic fatty liver disease: an updated narrative review. World J Hepatol. (2015) 7:575–82. 10.4254/wjh.v7.i3.575 PubMed DOI PMC

Salomone F, Godos J, Zelber-Sagi S. Natural antioxidants for non-alcoholic fatty liver disease: molecular targets and clinical perspectives. Liver Int. (2016) 36:5–20. 10.1111/liv.12975 PubMed DOI

Marchesini G, Petta S, Dalle Grave R. Diet, weight loss, and liver health in nonalcoholic fatty liver disease: pathophysiology, evidence, and practice. Hepatology. (2016) 63:2032–43. 10.1002/hep.28392 PubMed DOI

Dumortier J, Giostra E, Belbouab S, Morard I, Guillaud O, Spahr L, et al. . Non-alcoholic fatty liver disease in liver transplant recipients: another story of “seed and soil”. Am J Gastroenterol. (2010) 105:613–20. 10.1038/ajg.2009.717 PubMed DOI

Lim LG, Cheng CL, Wee A, Lim SG, Lee YM, Sutedja DS, et al. . Prevalence and clinical associations of posttransplant fatty liver disease. Liver Int. (2007) 27:76–80. 10.1111/j.1478-3231.2006.01396.x PubMed DOI

Seo S, Maganti K, Khehra M, Ramsamooj R, Tsodikov A, Bowlus C, et al. . De novo nonalcoholic fatty liver disease after liver transplantation. Liver Transpl. (2007) 13:844–7. 10.1002/lt.20932 PubMed DOI

Dureja P, Mellinger J, Agni R, Chang F, Avey G, Lucey M, et al. . NAFLD recurrence in liver transplant recipients. Transplantation. (2011) 91:684–9. 10.1097/TP.0b013e31820b6b84 PubMed DOI

Malik SM, Devera ME, Fontes P, Shaikh O, Sasatomi E, Ahmad J. Recurrent disease following liver transplantation for nonalcoholic steatohepatitis cirrhosis. Liver Transpl. (2009) 15:1843–51. 10.1002/lt.21943 PubMed DOI

Hejlova I, Honsova E, Sticova E, Lanska V, Hucl T, Spicak J, et al. . Prevalence and risk factors of steatosis after liver transplantation and patient outcomes. Liver Transpl. (2016) 22:644–55. 10.1002/lt.24393 PubMed DOI

Bhanji RA, Watt KD. Fatty allograft and cardiovascular outcomes after liver transplantation. Liver Transpl. (2017) 23:S76–80. 10.1002/lt.24843 PubMed DOI

Nakagawa H, Fujita M, Fujimoto A. Genome sequencing analysis of liver cancer for precision medicine. Semin Cancer Biol. (2018) 55:120–7. 10.1016/j.semcancer.2018.03.004 PubMed DOI

Baciu C, Pasini E, Angeli M, Schwenger K, Afrin J, Humar A, et al. . Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis. PLoS ONE. (2017) 12:e0189223. 10.1371/journal.pone.0189223 PubMed DOI PMC

Luo WJ, Cheng TY, Wong KI, Fang WH, Liao KM, Hsieh YT, et al. . Novel therapeutic drug identification and gene correlation for fatty liver disease using high-content screening: proof of concept. Eur J Pharm Sci. (2018) 121:106–17. 10.1016/j.ejps.2018.05.018 PubMed DOI

Shubham K, Vinay L, Vinod PK. Systems-level organization of non-alcoholic fatty liver disease progression network. Mol Biosyst. (2017) 13:1898–911. 10.1039/c7mb00013h PubMed DOI

Kleiner DE, Brunt EM, Van Natta M, Behling C, Contos MJ, Cummings OW, et al. . Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology. (2005) 41:1313–21. 10.1002/hep.20701 PubMed DOI

Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. (2001) 25:402–8. 10.1006/meth.2001.1262 PubMed DOI

R Core Team . R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; (2017).

Ryaboshapkina M, Hammar M. Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. Sci Rep. (2017) 7:12361. 10.1038/s41598-017-10930-w PubMed DOI PMC

Wruck W, Graffmann N, Kawala MA, Adjaye J. Concise review: current status and future directions on research related to nonalcoholic fatty liver disease. Stem Cells. (2017) 35:89–96. 10.1002/stem.2454 PubMed DOI

Ahrens M, Ammerpohl O, von Schonfels W, Kolarova J, Bens S, Itzel T, et al. . DNA methylation analysis in nonalcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after bariatric surgery. Cell Metab. (2013) 18:296–302. 10.1016/j.cmet.2013.07.004 PubMed DOI

du Plessis J, van Pelt J, Korf H, Mathieu C, van der Schueren B, Lannoo M, et al. . Association of adipose tissue inflammation with histologic severity of nonalcoholic fatty liver disease. Gastroenterology. (2015) 149:635–48.e14. 10.1053/j.gastro.2015.05.044 PubMed DOI

Horvath S, Erhart W, Brosch M, Ammerpohl O, von Schonfels W, Ahrens M, et al. . Obesity accelerates epigenetic aging of human liver. Proc Natl Acad Sci USA. (2014) 111:15538–43. 10.1073/pnas.1412759111 PubMed DOI PMC

Wruck W, Kashofer K, Rehman S, Daskalaki A, Berg D, Gralka E, et al. . Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes. Sci Data. (2015) 2:150068. 10.1038/sdata.2015.68 PubMed DOI PMC

Musso G, Gambino R, Cassader M. Cholesterol metabolism and the pathogenesis of non-alcoholic steatohepatitis. Prog Lipid Res. (2013) 52:175–91. 10.1016/j.plipres.2012.11.002 PubMed DOI

Makishima M, Okamoto AY, Repa JJ, Tu H, Learned RM, Luk A, et al. . Identification of a nuclear receptor for bile acids. Science. (1999) 284:1362–5. PubMed

Han CY. Update on FXR biology: promising therapeutic target? Int J Mol Sci. (2018) 19:2069. 10.3390/ijms19072069 PubMed DOI PMC

Abenavoli L, Falalyeyeva T, Boccuto L, Tsyryuk O, Kobyliak N. Obeticholic acid: a new era in the treatment of nonalcoholic fatty liver disease. Pharmaceuticals. (2018) 11:E104. 10.3390/ph11040104 PubMed DOI PMC

Paradies G, Paradies V, Ruggiero FM, Petrosillo G. Oxidative stress, cardiolipin and mitochondrial dysfunction in nonalcoholic fatty liver disease. World J Gastroenterol. (2014) 20:14205–18. 10.3748/wjg.v20.i39.14205 PubMed DOI PMC

Del Campo JA, Gallego P, Grande L. Role of inflammatory response in liver diseases: therapeutic strategies. World J Hepatol. (2018) 10:1–7. 10.4254/wjh.v10.i1.1 PubMed DOI PMC

Moylan CA, Pang H, Dellinger A, Suzuki A, Garrett ME, Guy CD, et al. . Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease. Hepatology. (2014) 59:471–82. 10.1055/s-0035-1568035 PubMed DOI PMC

Caballero F, Fernandez A, Matias N, Martinez L, Fucho R, Elena M, et al. . Specific contribution of methionine and choline in nutritional nonalcoholic steatohepatitis: impact on mitochondrial S-adenosyl-L-methionine and glutathione. J Biol Chem. (2010) 285:18528–36. 10.1074/jbc.m109.099333 PubMed DOI PMC

Frades I, Andreasson E, Mato JM, Alexandersson E, Matthiesen R, Martinez-Chantar ML. Integrative genomic signatures of hepatocellular carcinoma derived from nonalcoholic Fatty liver disease. PLoS ONE. (2015) 10:e0124544. 10.1371/journal.pone.0124544 PubMed DOI PMC

Lu SC, Mato JM. S-adenosylmethionine in liver health, injury, and cancer. Physiol Rev. (2012) 92:1515–42. 10.1152/physrev.00047.2011 PubMed DOI PMC

Anstee QM, Day CP. S-adenosylmethionine (SAMe) therapy in liver disease: a review of current evidence and clinical utility. J Hepatol. (2012) 57:1097–109. 10.1016/j.jhep.2012.04.041 PubMed DOI

Puri P, Baillie RA, Wiest MM, Mirshahi F, Choudhury J, Cheung O, et al. . A lipidomic analysis of nonalcoholic fatty liver disease. Hepatology. (2007) 46:1081–90. 10.1002/hep.21763 PubMed DOI

Walker AK, Jacobs RL, Watts JL, Rottiers V, Jiang K, Finnegan DM, et al. . A conserved SREBP-1/phosphatidylcholine feedback circuit regulates lipogenesis in metazoans. Cell. (2011) 147:840–52. 10.1016/j.cell.2011.09.045 PubMed DOI PMC

Murphy SK, Yang H, Moylan CA, Pang H, Dellinger A, Abdelmalek MF, et al. . Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease. Gastroenterology. (2013) 145:1076–87. 10.1053/j.gastro.2013.07.047 PubMed DOI PMC

Targher G, Byrne CD. Diagnosis and management of nonalcoholic fatty liver disease and its hemostatic/thrombotic and vascular complications. Semin Thromb Hemost. (2013) 39:214–28. 10.1055/s-0033-1334866 PubMed DOI

Costa RH, Kalinichenko VV, Holterman AX, Wang X. Transcription factors in liver development, differentiation, and regeneration. Hepatology. (2003) 38:1331–47. 10.1016/j.hep.2003.09.034 PubMed DOI