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Transcriptional network analysis implicates altered hepatic immune function in NASH development and resolution

Nature Metabolism volume 1, pages 604–614 (2019)Cite this article

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Abstract

Progression of fatty liver to non-alcoholic steatohepatitis (NASH) is a rapidly growing health problem. The presence of inflammatory infiltrates in the liver and hepatocyte damage distinguish NASH from simple steatosis. However, the underlying molecular mechanisms involved in the development of NASH remain to be fully understood. Here we perform transcriptional and immune profiling of patients with NASH before and after lifestyle intervention (LSI). Analysis of liver microarray data from a cohort of patients with histologically assessed non-alcoholic fatty liver disease (NAFLD) reveals a hepatic gene signature, which is associated with NASH and is sensitive to regression of NASH activity on LSI independently of body weight loss. Enrichment analysis reveals the presence of immune-associated genes linked to inflammatory responses, antigen presentation and cytotoxic cells in the NASH-linked gene signature. In an independent cohort, NASH is also associated with alterations in blood immune cell populations, including conventional dendritic cells (cDC) type 1 and 2, and cytotoxic CD8 T cells. Lobular inflammation and ballooning are associated with the accumulation of CD8 T cells in the liver. Progression from simple steatosis to NASH in a mouse model of diet-driven NASH results in a comparable immune-related hepatic expression signature and the accumulation of intrahepatic cDC and CD8 T cells. These results show that NASH, compared to normal liver or simple steatosis, is associated with a distinct hepatic immune-related gene signature, elevated hepatic CD8 T cells, and altered antigen-presenting and cytotoxic cells in blood. These findings expand our understanding of NASH and may identify potential targets for NASH therapy.

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Fig. 1: Identification of hepatic transcriptomic signature of NASH.
Fig. 2: Correlations between blood immune cell populations, disease activity in NASH and genes in module ‘blue’.
Fig. 3: A diet-induced NASH model alters cDC and CD8 T cells and inflammation in the liver.
Fig. 4: NASH and T2D alter activity of cytotoxic CD8 T cells.
Fig. 5: Hepatic CD8 T lymphocytes correlate with lobular inflammation, ballooning and transcriptomic signature of NASH.

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Data availability

Microarray data used in this study were from the Gene Expression Omnibus repository under accession number GSE106737 and GSE83452. Requests for other data should be made to the corresponding author.

Change history

  • 24 June 2019

    In the version of this article initially published, ANR grant ANR-16-RHUS-0006 to author Joel T. Haas was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Haas, J. T., Francque, S. & Staels, B. Pathophysiology and mechanisms of nonalcoholic fatty liver disease. Annu. Rev. Physiol. 78, 181–205 (2016).

    Article  CAS  Google Scholar 

  2. Luyckx, F. H., Lefebvre, P. J. & Scheen, A. J. Non-alcoholic steatohepatitis: association with obesity and insulin resistance, and influence of weight loss. Diabetes Metab. 26, 98–106 (2000).

    CAS  PubMed  Google Scholar 

  3. Brunt, E. M. Pathology of nonalcoholic fatty liver disease. Nat. Rev. Gastroenterol. Hepatol. 7, 195–203 (2010).

    Article  Google Scholar 

  4. Brunt, E. M. et al. Nonalcoholic fatty liver disease (NAFLD) activity score and the histopathologic diagnosis in NAFLD: distinct clinicopathologic meanings. Hepatology 53, 810–820 (2011).

    Article  CAS  Google Scholar 

  5. Bedossa, P. et al. Histopathological algorithm and scoring system for evaluation of liver lesions in morbidly obese patients. Hepatology 56, 1751–1759 (2012).

    Article  Google Scholar 

  6. Hirsova, P. & Gores, G. J. Ballooned hepatocytes, undead cells, sonic hedgehog, and vitamin E: therapeutic implications for nonalcoholic steatohepatitis. Hepatology 61, 15–17 (2015).

    Article  Google Scholar 

  7. Vonghia, L., Michielsen, P. & Francque, S. Immunological mechanisms in the pathophysiology of non-alcoholic steatohepatitis. Int. J. Mol. Sci. 14, 19867–19890 (2013).

    Article  Google Scholar 

  8. Liaskou, E. et al. Monocyte subsets in human liver disease show distinct phenotypic and functional characteristics. Hepatology 57, 385–398 (2013).

    Article  CAS  Google Scholar 

  9. Rau, M. et al. Progression from nonalcoholic fatty liver to nonalcoholic steatohepatitis is marked by a higher frequency of Th17 cells in the liver and an increased Th17/resting regulatory T cell ratio in peripheral blood and in the liver. J. Immunol. 196, 97–105 (2016).

    Article  CAS  Google Scholar 

  10. Wolf, M. J. et al. Metabolic activation of intrahepatic CD8+ T cells and NKT cells causes nonalcoholic steatohepatitis and liver cancer via cross-talk with hepatocytes. Cancer Cell 26, 549–564 (2014).

    Article  CAS  Google Scholar 

  11. Kleiner, D. E. & Bedossa, P. Liver histology and clinical trials for nonalcoholic steatohepatitis-perspectives from 2 pathologists. Gastroenterology 149, 1305–1308 (2015).

    Article  Google Scholar 

  12. Ryaboshapkina, M. & Hammar, M. Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. Sci. Rep. 7, 12361 (2017).

    Article  Google Scholar 

  13. Moylan, C. A. et al. Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease. Hepatology 59, 471–482 (2014).

    Article  CAS  Google Scholar 

  14. Vilar-Gomez, E. et al. Weight loss through lifestyle modification significantly reduces features of nonalcoholic steatohepatitis. Gastroenterology 149, 367–378 e365 (2015).

    Article  Google Scholar 

  15. Lassailly, G. et al. Bariatric surgery reduces features of nonalcoholic steatohepatitis in morbidly obese patients. Gastroenterology 149, 379–388 (2015).

    Article  Google Scholar 

  16. Lefebvre, P. et al. Interspecies NASH disease activity whole-genome profiling identifies a fibrogenic role of PPARalpha-regulated dermatopontin. JCI Insight 2, e92264 (2017).

    Article  Google Scholar 

  17. Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).

    Article  Google Scholar 

  18. Vonghia, L. et al. CD4+ROR gamma t++ and tregs in a mouse model of diet-induced nonalcoholic steatohepatitis. Mediators Inflamm. 2015, 239623 (2015).

    Article  Google Scholar 

  19. Bhattacharjee, J. et al. Hepatic natural killer T-cell and CD8+ T-cell signatures in mice with nonalcoholic steatohepatitis. Hepatol. Commun. 1, 299–310 (2017).

    Article  CAS  Google Scholar 

  20. Sutti, S. et al. Adaptive immune responses triggered by oxidative stress contribute to hepatic inflammation in NASH. Hepatology 59, 886–897 (2014).

    Article  CAS  Google Scholar 

  21. Clapper, J. R. et al. Diet-induced mouse model of fatty liver disease and nonalcoholic steatohepatitis reflecting clinical disease progression and methods of assessment. Am. J. Physiol. Gastrointest. Liver Physiol. 305, G483–G495 (2013).

    Article  CAS  Google Scholar 

  22. Asgharpour, A. et al. A diet-induced animal model of non-alcoholic fatty liver disease and hepatocellular cancer. J. Hepatol. 65, 579–588 (2016).

    Article  CAS  Google Scholar 

  23. Jensen, T. et al. Fructose and sugar: a major mediator of non-alcoholic fatty liver disease. J. Hepatol. 68, 1063–1075 (2018).

    Article  CAS  Google Scholar 

  24. Ioannou, G. N. The role of cholesterol in the pathogenesis of NASH. Trends Endocrinol. Metab. 27, 84–95 (2016).

    Article  CAS  Google Scholar 

  25. Bottini, N. & Peterson, E. J. Tyrosine phosphatase PTPN22: multifunctional regulator of immune signaling, development, and disease. Annu. Rev. Immunol. 32, 83–119 (2014).

    Article  CAS  Google Scholar 

  26. Froylich, D. et al. Effect of Roux-en-Y gastric bypass and sleeve gastrectomy on nonalcoholic fatty liver disease: a comparative study. Surg. Obes. Relat. Dis. 12, 127–131 (2016).

    Article  Google Scholar 

  27. Patouraux, S. et al. CD44 is a key player in non-alcoholic steatohepatitis. J. Hepatol. 67, 328–338 (2017).

    Article  CAS  Google Scholar 

  28. Zhang, X. et al. CXCL10 plays a key role as an inflammatory mediator and a non-invasive biomarker of non-alcoholic steatohepatitis. J. Hepatol. 61, 1365–1375 (2014).

    Article  CAS  Google Scholar 

  29. Tilg, H., Moschen, A. R. & Roden, M. NAFLD and diabetes mellitus. Nat. Rev. Gastroenterol. Hepatol. 14, 32–42 (2017).

    Article  CAS  Google Scholar 

  30. Syn, W. K. et al. Accumulation of natural killer T cells in progressive nonalcoholic fatty liver disease. Hepatology 51, 1998–2007 (2010).

    Article  CAS  Google Scholar 

  31. Miura, K., Yang, L., van Rooijen, N., Ohnishi, H. & Seki, E. Hepatic recruitment of macrophages promotes nonalcoholic steatohepatitis through CCR2. Am. J. Physiol. Gastrointest. Liver Physiol. 302, G1310–G1321 (2012).

    Article  CAS  Google Scholar 

  32. Durai, V. & Murphy, K. M. Functions of murine dendritic cells. Immunity 45, 719–736 (2016).

    Article  CAS  Google Scholar 

  33. Vu Manh, T. P., Bertho, N., Hosmalin, A., Schwartz-Cornil, I. & Dalod, M. Investigating evolutionary conservation of dendritic cell subset identity and functions. Front. Immunol. 6, 260 (2015).

    Google Scholar 

  34. Henning, J. R. et al. Dendritic cells limit fibroinflammatory injury in nonalcoholic steatohepatitis in mice. Hepatology 58, 589–602 (2013).

    Article  CAS  Google Scholar 

  35. Worbs, T., Hammerschmidt, S. I. & Forster, R. Dendritic cell migration in health and disease. Nat. Rev. Immunol. 17, 30–48 (2017).

    Article  CAS  Google Scholar 

  36. Kelly, A. et al. CD141(+) myeloid dendritic cells are enriched in healthy human liver. J. Hepatol. 60, 135–142 (2014).

    Article  CAS  Google Scholar 

  37. Doganay, L. et al. HLA DQB1 alleles are related with nonalcoholic fatty liver disease. Mol. Biol. Rep. 41, 7937–7943 (2014).

    Article  CAS  Google Scholar 

  38. Nishimura, S. et al. CD8+ effector T cells contribute to macrophage recruitment and adipose tissue inflammation in obesity. Nat. Med. 15, 914–920 (2009).

    Article  CAS  Google Scholar 

  39. Wieser, V. et al. Adipose type I interferon signalling protects against metabolic dysfunction. Gut 67, 157–165 (2018).

    Article  CAS  Google Scholar 

  40. Ghazarian, M. et al. Type I interferon responses drive intrahepatic T cells to promote metabolic syndrome. Sci. Immunol. 2, eaai7616 (2017).

    Article  Google Scholar 

  41. Luo, J. L., Kamata, H. & Karin, M. IKK/NF-kappaB signaling: balancing life and death—a new approach to cancer therapy. J. Clin. Invest. 115, 2625–2632 (2005).

    Article  CAS  Google Scholar 

  42. du Plessis, J. et al. Association of adipose tissue inflammation with histologic severity of nonalcoholic fatty liver disease. Gastroenterology 149, 635–648 e614 (2015).

    Article  Google Scholar 

  43. Bijnen, M. et al. Adipose tissue macrophages induce hepatic neutrophil recruitment and macrophage accumulation in mice. Gut 67, 1317–1327 (2018).

    Article  CAS  Google Scholar 

  44. Francque, S. et al. PPARalpha gene expression correlates with severity and histological treatment response in patients with non-alcoholic steatohepatitis. J. Hepatol. 63, 164–173 (2015).

    Article  CAS  Google Scholar 

  45. Matthews, D. R. et al. Homeostasis model assessment: insulin resistance and beta-cell function from fasting plasma glucose and insulin concentrations in man. Diabetologia 28, 412–419 (1985).

    Article  CAS  Google Scholar 

  46. Verrijken, A. et al. A gene variant of PNPLA3, but not of APOC3, is associated with histological parameters of NAFLD in an obese population. Obesity (Silver Spring) 21, 2138–2145 (2013).

    Article  CAS  Google Scholar 

  47. Kleiner, D. E. et al. Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology 41, 1313–1321 (2005).

    Article  Google Scholar 

  48. Rubtsov, Y. P. et al. Regulatory T cell-derived interleukin-10 limits inflammation at environmental interfaces. Immunity 28, 546–558 (2008).

    Article  CAS  Google Scholar 

  49. Pawlak, M. et al. The transrepressive activity of peroxisome proliferator-activated receptor alpha is necessary and sufficient to prevent liver fibrosis. Hepatology 60, 1593–1606 (2014).

    Article  CAS  Google Scholar 

  50. Irizarry, R. A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249–264 (2003).

    Article  Google Scholar 

  51. Leek, J. T. & Storey, J. D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 3, 1724–1735 (2007).

    Article  CAS  Google Scholar 

  52. Smyth, G. K., Michaud, J. & Scott, H. S. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21, 2067–2075 (2005).

    Article  CAS  Google Scholar 

  53. Goeman, J. J. & Buhlmann, P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23, 980–987 (2007).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by grants from the ANR and the European Union: nos. EGID ANR-10-LABX-46 and Fondation Leducq LEAN 16CVD01 (to B.S., D.D. and P.L.), no. ANR-18 NASHILCCD8 (to B.S. and D.D.) no. FP6 HEPADIP LSHM-CT-2005-018734 (to B.S., A.V., L.V.G. and S. Francque) and no. FP7-HEALTH RESOLVE 305707 (to B.S., A.V., L.V.G. and S. Francque). S. Francque is a recipient of the Flanders Fund for Scientific Research (FWO klinisch mandaat no. 1802154N). B.S. is a recipient of an Advanced European Research Council grant (no. 694717). J.T.H. was supported by an EMBO Long Term Fellowship (no. ALTF277-2014) and by ANR grant ANR-16-RHUS-0006.

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Author notes

  1. These authors contributed equally: Joel T. Haas, Luisa Vonghia, Denis A. Mogilenko.

  2. These authors jointly supervised this work: Bart Staels, Sven Francque, David Dombrowicz.

Authors and Affiliations

  1. University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France

    Joel T. Haas, Denis A. Mogilenko, Olivier Molendi-Coste, Sébastien Fleury, Audrey Deprince, Artemii Nikitin, Eloïse Woitrain, Lucie Ducrocq-Geoffroy, Samuel Pic, Bruno Derudas, Hélène Dehondt, Céline Gheeraert, Philippe Lefebvre, Bart Staels & David Dombrowicz

  2. Department of Gastroenterology and Hepatology, Antwerp University Hospital, Antwerp, Belgium

    Luisa Vonghia & Sven Francque

  3. Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium

    Luisa Vonghia, An Verrijken, Luc Van Gaal & Sven Francque

  4. Department of Endocrinology, Diabetology and Metabolism, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium

    An Verrijken & Luc Van Gaal

  5. Department of Pathology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium

    Ann Driessen

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Contributions

L.V. and S. Francque collected human biopsies, histological and biochemical data. L.V., S. Francque, L.V.G. and A.V. supervised the human biopsies collection and analysis. A. Driessen performed the histology of the liver biopsies. J.T.H. and D.A.M. performed mouse experiments, flow cytometry, immunological and transcriptomic analysis, and WGCNA. S. Fleury performed immunohistochemistry. B.D., H.D., C.G. and P.L. performed microarray analysis. O.M.-C., A. Deprince, A.N., E.W., L.D.G. and S.P. performed mouse experiments and flow cytometry. D.A.M., L.V., J.T.H., S. Francque, B.S. and D.D. conceived the study, interpreted data and wrote the manuscript.

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Correspondence to Luisa Vonghia or David Dombrowicz.

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Competing interests

B.S. and S. Francque are consultants for Genfit S.A. S. Francque and LV are consultants for Inventiva. All other authors have nothing to declare.

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Haas, J.T., Vonghia, L., Mogilenko, D.A. et al. Transcriptional network analysis implicates altered hepatic immune function in NASH development and resolution. Nat Metab 1, 604–614 (2019). https://doi.org/10.1038/s42255-019-0076-1

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