Decoding liver fibrogenesis with single-cell technologies

Tingting Zhou, Musunuru Kiran, Kathy O. Lui, Qiurong Ding

PDF(632 KB)
PDF(632 KB)
Life Medicine ›› 2022, Vol. 1 ›› Issue (3) : 333-344. DOI: 10.1093/lifemedi/lnac040
Review
Review

Decoding liver fibrogenesis with single-cell technologies

Author information +
History +

Abstract

Liver fibrogenesis is a highly dynamic and complex process that drives the progression of chronic liver disease toward liver failure and end-stage liver diseases. Despite decades of intense studies, the cellular and molecular mechanisms underlying liver fibrogenesis remain elusive, and no approved therapies to treat liver fibrosis are currently available. The rapid development of single-cell RNA sequencing (scRNA-seq) technologies allows the characterization of cellular alterations under healthy and diseased conditions at an unprecedented resolution. In this Review, we discuss how the scRNA-seq studies are transforming our understanding of the regulatory mechanisms of liver fibrosis. We specifically emphasize discoveries on disease-relevant cell subpopulations, molecular events, and cell interactions on cell types including hepatocytes, liver sinusoidal endothelial cells, myofibroblasts, and macrophages. These discoveries have uncovered critical pathophysiological changes during liver fibrogenesis. Further efforts are urged to fully understand the functional contributions of these changes to liver fibrogenesis, and to translate the new knowledge into effective therapeutic approaches.

Keywords

fibrotic niche / non-parenchymal cells / zonation / stellakines / lipid-associated macrophage (LAM)

Cite this article

Download citation ▾
Tingting Zhou, Musunuru Kiran, Kathy O. Lui, Qiurong Ding. Decoding liver fibrogenesis with single-cell technologies. Life Medicine, 2022, 1(3): 333‒344 https://doi.org/10.1093/lifemedi/lnac040

References

[1]
Marcellin P, Kutala BK. Liver diseases: a major, neglected global public health problem requiring urgent actions and large-scale screening. Liver Int 2018;38:2–6.
CrossRef Google scholar
[2]
Wang FS, Fan JG, Zhang Z, et al. The global burden of liver disease: the major impact of China. Hepatology 2014;60:2099–108.
CrossRef Google scholar
[3]
Friedman SL, Neuschwander-Tetri BA, Rinella M, et al. Mechanisms of NAFLD development and therapeutic strategies. Nat Med 2018;24:908–22.
CrossRef Google scholar
[4]
Kisseleva T, Brenner D. Molecular and cellular mechanisms of liver fibrosis and its regression. Nat Rev Gastroenterol Hepatol 2021;18:151–66.
CrossRef Google scholar
[5]
Schuppan D, Ashfaq-Khan M, Yang AT, et al. Liver fibrosis: direct antifibrotic agents and targeted therapies. Matrix Biol 2018;68–69:435–51.
CrossRef Google scholar
[6]
Tsuchida T, Friedman SL. Mechanisms of hepatic stellate cell activation. Nat Rev Gastroenterol Hepatol 2017;14:397–411.
CrossRef Google scholar
[7]
Bataller R, Brenner DA. Liver fibrosis. J Clin Invest 2005;115:209–18.
CrossRef Google scholar
[8]
Dobie R, Wilson-Kanamori JR, Henderson BEP, et al. Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis. Cell Rep 2019;29:1832–1847.e8.
CrossRef Google scholar
[9]
Krenkel O, Hundertmark J, Ritz TP, et al. Single cell RNA sequencing identifies subsets of hepatic stellate cells and myofibroblasts in liver fibrosis. Cells 2019;8:503.
CrossRef Google scholar
[10]
Ramachandran P, Dobie R, Wilson-Kanamori JR, et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 2019;575:512–8.
CrossRef Google scholar
[11]
Tamburini BAJ, Finlon JM, Gillen AE, et al. Chronic liver disease in humans causes expansion and differentiation of liver lymphatic endothelial cells. Front Immunol 2019;10:1036.
CrossRef Google scholar
[12]
Xiong X, Kuang H, Ansari S, et al. Landscape of intercellular cross-talk in healthy and NASH liver revealed by single-cell secretome gene analysis. Mol Cell 2019;75:644–660.e5.
CrossRef Google scholar
[13]
Krenkel O, Hundertmark J, Abdallah AT, et al. Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis. Gut 2020;69:551–63.
CrossRef Google scholar
[14]
Remmerie A, Martens L, Thone T, et al. Osteopontin expression identifies a subset of recruited macrophages distinct from kupffer cells in the fatty liver. Immunity 2020;53:641–657.e14.
CrossRef Google scholar
[15]
Tran S, Baba I, Poupel L, et al. Impaired kupffer cell self-renewal alters the liver response to lipid overload during non-alcoholic steatohepatitis. Immunity 2020;53:627–640.e5.
CrossRef Google scholar
[16]
Terkelsen MK, Bendixen SM, Hansen D, et al. Transcriptional dynamics of hepatic sinusoid-associated cells after liver injury. Hepatology 2020;72:2119–33.
CrossRef Google scholar
[17]
Bleriot C, Barreby E, Dunsmore G, et al. A subset of Kupffer cells regulates metabolism through the expression of CD36. Immunity 2021;54:2101–2116.e6.
CrossRef Google scholar
[18]
Daemen S, Gainullina A, Kalugotla G, et al. Dynamic shifts in the composition of resident and recruited macrophages influence tissue remodeling in NASH. Cell Rep 2021;34:108626.
CrossRef Google scholar
[19]
Guilliams M, Bonnardel J, Haest B, et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell 2022;185:379–396.e38.
CrossRef Google scholar
[20]
Park SR, Cho CS, Xi J, et al. Holistic characterization of single-hepatocyte transcriptome responses to high-fat diet. Am J Physiol Endocrinol Metab 2021;320:E244–58.
CrossRef Google scholar
[21]
Qing J, Ren Y, Zhang Y, et al. Dopamine receptor D2 antagonism normalizes profibrotic macrophage-endothelial crosstalk in non-alcoholic steatohepatitis. J Hepatol 2022;76:394–406.
CrossRef Google scholar
[22]
Richter ML, Deligiannis IK, Yin K, et al. Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy. Nat Commun 2021;12:4264.
CrossRef Google scholar
[23]
Wang J, Hu W, Shen Z, et al. Dissecting the single-cell transcriptome underlying chronic liver injury. Mol Ther Nucleic Acids 2021;26:1364–73.
CrossRef Google scholar
[24]
Ye X, Wei J, Yue M, et al. Leveraging single-cell RNA-seq data to uncover the association between cell type and chronic liver diseases. Front Genet 2021;12:637322.
CrossRef Google scholar
[25]
Yuan Z, Zhou Q, Cai L, et al. SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nat Methods 2021;18:1223–32.
CrossRef Google scholar
[26]
Ramachandran P, Matchett KP, Dobie R, et al. Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis. Nat Rev Gastroenterol Hepatol 2020;17:457–72.
CrossRef Google scholar
[27]
Lan T, Kisseleva T, Brenner DA. Deficiency of NOX1 or NOX4 prevents liver inflammation and fibrosis in mice through inhibition of hepatic stellate cell activation. PLoS One 2015;10:e0129743.
CrossRef Google scholar
[28]
Wang X, Zheng Z, Caviglia JM, et al. Hepatocyte TAZ/WWTR1 promotes inflammation and fibrosis in nonalcoholic steatohepatitis. Cell Metab 2016;24:848–62.
CrossRef Google scholar
[29]
Xie G, Karaca G, Swiderska-Syn M, et al. Cross-talk between Notch and Hedgehog regulates hepatic stellate cell fate in mice. Hepatology 2013;58:1801–13.
CrossRef Google scholar
[30]
Zhu C, Kim K, Wang X, et al. Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis. Sci Transl Med 2018;10:eaat0344.
CrossRef Google scholar
[31]
Aizarani N, Saviano A, Sagar , et al. A human liver cell atlas reveals heterogeneity and epithelial progenitors. Nature 2019;572:199–204.
CrossRef Google scholar
[32]
Ben-Moshe S, Shapira Y, Moor AE, et al. Spatial sorting enables comprehensive characterization of liver zonation. Nat Metab 2019;1:899–911.
CrossRef Google scholar
[33]
Halpern KB, Shenhav R, Matcovitch-Natan O, et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature 2017;542:352–6.
CrossRef Google scholar
[34]
Ben-Moshe S, Itzkovitz S. Spatial heterogeneity in the mammalian liver. Nat Rev Gastroenterol Hepatol 2019;16:395–410.
CrossRef Google scholar
[35]
Chalasani N, Wilson L, Kleiner DE, et al. Relationship of steatosis grade and zonal location to histological features of steatohepatitis in adult patients with non-alcoholic fatty liver disease. J Hepatol 2008;48:829–34.
CrossRef Google scholar
[36]
Hall Z, Bond NJ, Ashmore T, et al. Lipid zonation and phospholipid remodeling in nonalcoholic fatty liver disease. Hepatology 2017;65:1165–80.
CrossRef Google scholar
[37]
Hijmans BS, Grefhorst A, Oosterveer MH, et al. Zonation of glucose and fatty acid metabolism in the liver: mechanism and metabolic consequences. Biochimie 2014;96:121–9.
CrossRef Google scholar
[38]
Font-Burgada J, Shalapour S, Ramaswamy S, et al. Hybrid periportal hepatocytes regenerate the injured liver without giving rise to cancer. Cell 2015;162:766–79.
CrossRef Google scholar
[39]
Lin S, Nascimento EM, Gajera CR, et al. Distributed hepatocytes expressing telomerase repopulate the liver in homeostasis and injury. Nature 2018;556:244–8.
CrossRef Google scholar
[40]
MacParland SA, Liu JC, Ma XZ, et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun 2018;9:4383.
CrossRef Google scholar
[41]
Wang B, Zhao L, Fish M, et al. Self-renewing diploid Axin2(+) cells fuel homeostatic renewal of the liver. Nature 2015;524:180–5.
CrossRef Google scholar
[42]
He L, Pu W, Liu X, et al. Proliferation tracing reveals regional hepatocyte generation in liver homeostasis and repair. Science 2021;371:eabc4346.
CrossRef Google scholar
[43]
Wei Y, Wang YG, Jia Y, et al. Liver homeostasis is maintained by midlobular zone 2 hepatocytes. Science 2021;371:eabb1625.
CrossRef Google scholar
[44]
Chen F, Jimenez RJ, Sharma K, et al. Broad distribution of hepatocyte proliferation in liver homeostasis and regeneration. Cell Stem Cell 2020;26:27–33.e4.
CrossRef Google scholar
[45]
Matsumoto T, Wakefield L, Tarlow BD, et al. In vivo lineage tracing of polyploid hepatocytes reveals extensive proliferation during liver regeneration. Cell Stem Cell 2020;26:34–47.e33.
CrossRef Google scholar
[46]
Sun T, Pikiolek M, Orsini V, et al. AXIN2(+) pericentral hepatocytes have limited contributions to liver homeostasis and regeneration. Cell Stem Cell 2020;26:97–107.e6.
CrossRef Google scholar
[47]
Dai Z, Ott M, Sharma AD. Equal opportunity offer for all hepatocytes. J Hepatol 2020;73:6–8.
CrossRef Google scholar
[48]
Monga SP. No zones left behind: democratic hepatocytes contribute to liver homeostasis and repair. Cell Stem Cell 2020;26:2–3.
CrossRef Google scholar
[49]
Li W, Li L, Hui L. Cell plasticity in liver regeneration. Trends Cell Biol 2020;30:329–38.
CrossRef Google scholar
[50]
Michalopoulos GK. Liver regeneration. J Cell Physiol 2007;213:286–300.
CrossRef Google scholar
[51]
Miyajima A, Tanaka M, Itoh T. Stem/progenitor cells in liver development, homeostasis, regeneration, and reprogramming. Cell Stem Cell 2014;14:561–74.
CrossRef Google scholar
[52]
Poisson J, Lemoinne S, Boulanger C, et al. Liver sinusoidal endothelial cells: physiology and role in liver diseases. J Hepatol 2017;66:212–27.
CrossRef Google scholar
[53]
Shetty S, Lalor PF, Adams DH. Liver sinusoidal endothelial cells - gatekeepers of hepatic immunity. Nat Rev Gastroenterol Hepatol 2018;15:555–67.
CrossRef Google scholar
[54]
DeLeve LD, Wang X, Hu L, et al. Rat liver sinusoidal endothelial cell phenotype is maintained by paracrine and autocrine regulation. Am J Physiol Gastrointest Liver Physiol 2004;287:G757–63.
CrossRef Google scholar
[55]
Ding BS, Cao Z, Lis R, et al. Divergent angiocrine signals from vascular niche balance liver regeneration and fibrosis. Nature 2014;505:97–102.
CrossRef Google scholar
[56]
Xie G, Wang X, Wang L, et al. Role of differentiation of liver sinusoidal endothelial cells in progression and regression of hepatic fibrosis in rats. Gastroenterology 2012;142:918–927.e6.
CrossRef Google scholar
[57]
Kisseleva T, Brenner DA. Mechanisms of fibrogenesis. Exp Biol Med (Maywood) 2008;233:109–22.
CrossRef Google scholar
[58]
Schmitt-Graff A, Kruger S, Bochard F, et al. Modulation of alpha smooth muscle actin and desmin expression in perisinusoidal cells of normal and diseased human livers. Am J Pathol 1991;138:1233–42.
[59]
Nishio T, Hu R, Koyama Y, et al. Activated hepatic stellate cells and portal fibroblasts contribute to cholestatic liver fibrosis in MDR2 knockout mice. J Hepatol 2019;71:573–85.
CrossRef Google scholar
[60]
Herrnberger L, Hennig R, Kremer W, et al. Formation of fenestrae in murine liver sinusoids depends on plasmalemma vesicle-associated protein and is required for lipoprotein passage. PLoS One 2014;9:e115005.
CrossRef Google scholar
[61]
Rantakari P, Jappinen N, Lokka E, et al. Fetal liver endothelium regulates the seeding of tissue-resident macrophages. Nature 2016;538:392–6.
CrossRef Google scholar
[62]
Heymann F, Tacke F. Immunology in the liver—from homeostasis to disease. Nat Rev Gastroenterol Hepatol 2016;13:88–110.
CrossRef Google scholar
[63]
Robinson MW, Harmon C, O’Farrelly C. Liver immunology and its role in inflammation and homeostasis. Cell Mol Immunol 2016;13:267–276.
CrossRef Google scholar
[64]
Krenkel O, Tacke F. Liver macrophages in tissue homeostasis and disease. Nat Rev Immunol 2017;17:306–21.
CrossRef Google scholar
[65]
Liu Z, Gu Y, Chakarov S, et al. Fate Mapping via Ms4a3-expression history traces monocyte-derived cells. Cell 2019;178:1509–1525. e19.
CrossRef Google scholar
[66]
Seidman JS, Troutman TD, Sakai M, et al. Niche-specific reprogramming of epigenetic landscapes drives myeloid cell diversity in nonalcoholic steatohepatitis. Immunity 2020;52:1057–1074.e7.
CrossRef Google scholar
[67]
David BA, Rezende RM, Antunes MM, et al. Combination of mass cytometry and imaging analysis reveals origin, location, and functional repopulation of liver myeloid cells in mice. Gastroenterology 2016;151:1176–91.
CrossRef Google scholar
[68]
Scott CL, Zheng F, De Baetselier P, et al. Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells. Nat Commun 2016;7:10321.
CrossRef Google scholar
[69]
Karlmark KR, Weiskirchen R, Zimmermann HW, et al. Hepatic recruitment of the inflammatory Gr1+ monocyte subset upon liver injury promotes hepatic fibrosis. Hepatology 2009;50:261–74.
CrossRef Google scholar
[70]
De Simone G, Andreata F, Bleriot C, et al. Identification of a Kupffer cell subset capable of reverting the T cell dysfunction induced by hepatocellular priming. Immunity 2021;54:2089–2100.e8.
CrossRef Google scholar
[71]
Liang Y, Kaneko K, Xin B, et al. Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics. Dev Cell 2022;57:398–414.e5.
CrossRef Google scholar
[72]
Hume DA, Offermanns S, Bonnavion R. Contamination of isolated mouse Kupffer cells with liver sinusoidal endothelial cells. Immunity 2022;55:1139–40.
CrossRef Google scholar
[73]
Iannacone M, Bleriot C, Andreata F, et al. Response to contamination of isolated mouse Kupffer cells with liver sinusoidal endothelial cells. Immunity 2022;55:1141–2.
CrossRef Google scholar
[74]
Bonnardel J, T’Jonck W, Gaublomme D, et al. Stellate cells, hepatocytes, and endothelial cells imprint the kupffer cell identity on monocytes colonizing the liver macrophage niche. Immunity 2019;51:638–654.e9.
CrossRef Google scholar
[75]
Gola A, Dorrington MG, Speranza E, et al. Commensal-driven immune zonation of the liver promotes host defence. Nature 2021;589:131–6.
CrossRef Google scholar
[76]
Seki E, de Minicis S, Inokuchi S, et al. CCR2 promotes hepatic fibrosis in mice. Hepatology 2009;50:185–97.
CrossRef Google scholar
[77]
Zimmermann HW, Seidler S, Nattermann J, et al. Functional contribution of elevated circulating and hepatic non-classical CD14CD16 monocytes to inflammation and human liver fibrosis. PLoS One 2010;5:e11049.
CrossRef Google scholar
[78]
Barreby E, Chen P, Aouadi M. Macrophage functional diversity in NAFLD - more than inflammation. Nat Rev Endocrinol 2022;18:461–72.
CrossRef Google scholar
[79]
Bleriot C, Dupuis T, Jouvion G, et al. Liver-resident macrophage necroptosis orchestrates type 1 microbicidal inflammation and type-2-mediated tissue repair during bacterial infection. Immunity 2015;42:145–58.
CrossRef Google scholar
[80]
Jaitin DA, Adlung L, Thaiss CA, et al. Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner. Cell 2019;178:686–698.e14.
CrossRef Google scholar
[81]
Seth D, Duly A, Kuo PC, et al. Osteopontin is an important mediator of alcoholic liver disease via hepatic stellate cell activation. World J Gastroenterol 2014;20:13088–104.
CrossRef Google scholar
[82]
Arriazu E, Ge X, Leung TM, et al. Signalling via the osteopontin and high mobility group box-1 axis drives the fibrogenic response to liver injury. Gut 2017;66:1123–37.
CrossRef Google scholar
[83]
Coombes JD, Choi SS, Swiderska-Syn M, et al. Osteopontin is a proximal effector of leptin-mediated non-alcoholic steatohepatitis (NASH) fibrosis. Biochim Biophys Acta 2016;1862:135–44.
CrossRef Google scholar
[84]
Honda M, Kimura C, Uede T, et al. Neutralizing antibody against osteopontin attenuates non-alcoholic steatohepatitis in mice. J Cell Commun Signal 2020;14:223–32.
CrossRef Google scholar
[85]
Kiefer FW, Zeyda M, Gollinger K, et al. Neutralization of osteopontin inhibits obesity-induced inflammation and insulin resistance. Diabetes 2010;59:935–46.
CrossRef Google scholar
[86]
Keren-Shaul H, Spinrad A, Weiner A, et al. A Unique microglia type associated with restricting development of Alzheimer’s disease. Cell 2017;169:1276–1290.e17.
CrossRef Google scholar
[87]
Liao M, Liu Y, Yuan J, et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat Med 2020;26:842–4.
CrossRef Google scholar
[88]
Baran-Gale J, Chandra T, Kirschner K. Experimental design for single-cell RNA sequencing. Brief Funct Genomics 2018;17:233–9.
CrossRef Google scholar
[89]
Lafzi A, Moutinho C, Picelli S, et al. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. Nat Protoc 2018;13:2742–57.
CrossRef Google scholar
[90]
Eng CL, Lawson M, Zhu Q, et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature 2019;568:235–9.
CrossRef Google scholar
[91]
Rodriques SG, Stickels RR, Goeva A, et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 2019;363:1463–7.
CrossRef Google scholar
[92]
Vickovic S, Eraslan G, Salmen F, et al. High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods 2019;16:987–90.
CrossRef Google scholar
[93]
Shema E, Bernstein BE, Buenrostro JD. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat Genet 2019;51:19–25.
CrossRef Google scholar
[94]
Wen L, Tang F. Recent advances in single-cell sequencing technologies. Precis Clin Med 2022;5:pbac002.
CrossRef Google scholar
[95]
Peterson VM, Zhang KX, Kumar N, et al. Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol 2017;35:936–9.
CrossRef Google scholar
[96]
Stoeckius M, Hafemeister C, Stephenson W, et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 2017;14:865–8.
CrossRef Google scholar

RIGHTS & PERMISSIONS

2022 The Author(s) 2022. Published by Oxford University Press on behalf of Higher Education Press.
AI Summary AI Mindmap
PDF(632 KB)

Accesses

Citations

Detail

Sections
Recommended

/