Table Info

Table 1.

LncRNAs modulated in NASH mice in comparison with healthy mice. Fold regulation expression of each lncRNA with respect to healthy mice was calculated using the ΔΔCt method

Symbol	Fold regulation
Gm5602	6.59
5830432E09Rik^#	5.75
4921504A21Rik	4.07
Meg3^#	3.43
Gm16754^#	3.37
A430108G06Rik	3.08
Gm14379	3.05
1810019N24Rik^#	2.58
C230088H06Rik	2.57
4933427G23Rik^#	2.53
D930015M05Rik^#	2.35
Neat1^#	2.3
Gm15050^#	2.25
Gm4117^#	2.15
9430037G07Rik	2.14
A930024N18Rik^#	2.13
Chd3os	2.03
Dleu2	–2.05
2310001H17Rik	–2.29
Gm6410	–2.98

^# LncRNAs modulated both in NASH mice compared with healthy mice, and in HLSC-EV treated NASH mice compared with NASH mice

Supplementary materials

The supplementary material for this article is available at: https://www.explorationpub.com/uploads/Article/file/100525_sup_1.pdf.

Declarations

Author contributions

G Chiabotto: Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing—original draft. EC: Formal analysis, Investigation, Methodology, Validation, Visualization. CP: Investigation. MBHS: Investigation, Methodology, Formal Analysis. MC: Methodology. G Camussi: Funding acquisition, Resources, Writing—review & editing. SB: Conceptualization, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Visualization, Writing—review & editing. All authors have read and agreed to the published version of the manuscript.

Conflicts of interest

G Camussi is a component of the scientific advisory board of Unicyte and is named inventor in a related patent (WO2006126219-A1). The other authors declare that they have no conflict of interest.

Ethical approval

HLSCs were generated from one donor liver. The permission was obtained by the National Transplant Center in accordance with Italian legislation. The animal study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Italian Health Ministry (authorization number: 419/2016-PR, 26/04/2016).

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

All datasets generated for this study are included in the manuscript and the supplementary files.

Funding

This research was funded by grant “Terapie avanzate per processi fibrotici cronici” [Progetto EVER, codice domanda 320-39], by grant RiLo-2020, and by Unicyte AG (Oberdorf, NW, Switzerland). The funders had no role in the study design, data collection, analysis and interpretation of the data, the decision to publish, or the preparation of the manuscript.

Copyright

References

Argo CK, Caldwell SH. Epidemiology and natural history of non-alcoholic steatohepatitis. Clin Liver Dis. 2009;13:511–31. [DOI] [PubMed]

Younossi ZM, Koenig AB, Abdelatif D, Fazel Y, Henry L, Wymer M. Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes. Hepatology. 2016;64:73–84. [DOI] [PubMed]

Wong RJ, Aguilar M, Cheung R, Perumpail RB, Harrison SA, Younossi ZM, et al. Nonalcoholic steatohepatitis is the second leading etiology of liver disease among adults awaiting liver transplantation in the United States. Gastroenterology. 2015;148:547–55. [DOI] [PubMed]

Bruno S, Herrera Sanchez MB, Pasquino C, Tapparo M, Cedrino M, Tetta C, et al. Human liver-derived stem cells improve fibrosis and inflammation associated with nonalcoholic steatohepatitis. Stem Cells Int. 2019;2019:6351091. [DOI] [PubMed] [PMC]

Bruno S, Pasquino C, Herrera Sanchez MB, Tapparo M, Figliolini F, Grange C, et al. HLSC-derived extracellular vesicles attenuate liver fibrosis and inflammation in a murine model of non-alcoholic steatohepatitis. Mol Ther. 2020;28:479–89. [DOI] [PubMed] [PMC]

Quesenberry PJ, Aliotta J, Deregibus MC, Camussi G. Role of extracellular RNA-carrying vesicles in cell differentiation and reprogramming. Stem Cell Res Ther. 2015;6:153. [DOI] [PubMed] [PMC]

Derkus B, Emregul KC, Emregul E. A new approach in stem cell research-exosomes: their mechanism of action via cellular pathways. Cell Biol Int. 2017;41:466–75. [DOI] [PubMed]

Mederacke I, Hsu CC, Troeger JS, Huebener P, Mu X, Dapito DH, et al. Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology. Nat Commun. 2013;4:2823. [DOI] [PubMed] [PMC]

Chiabotto G, Ceccotti E, Tapparo M, Camussi G, Bruno S. Human liver stem cell-derived extracellular vesicles target hepatic stellate cells and attenuate their pro-fibrotic phenotype. Front Cell Dev Biol. 2021;9:777462. [DOI] [PubMed] [PMC]

10.

Wang Z, Yang X, Gui S, Yang F, Cao Z, Cheng R, et al. The roles and mechanisms of lncRNAs in liver fibrosis. Front Pharmacol. 2021;12:779606. [DOI] [PubMed] [PMC]

11.

Marchese FP, Raimondi I, Huarte M. The multidimensional mechanisms of long noncoding RNA function. Genome Biol. 2017;18:206. [DOI] [PubMed] [PMC]

12.

Zhang K, Shi ZM, Chang YN, Hu ZM, Qi HX, Hong W. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene. 2014;547:1–9. [DOI] [PubMed]

13.

Statello L, Guo CJ, Chen LL, Huarte M. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol. 2021;22:96–118. [DOI] [PubMed] [PMC]

14.

Zha F, Qu X, Tang B, Li J, Wang Y, Zheng P, et al. Long non-coding RNA MEG3 promotes fibrosis and inflammatory response in diabetic nephropathy via miR-181a/Egr-1/TLR4 axis. Aging (Albany NY). 2019;11:3716–30. [DOI] [PubMed] [PMC]

15.

Xue R, Li Y, Li X, Ma J, An C, Ma Z. MiR-185 affected the EMT, cell viability, and proliferation via DNMT1/MEG3 pathway in TGF-β1-induced renal fibrosis. Cell Biol Int. 2019;43:1152–62. [DOI] [PubMed]

16.

Piccoli MT, Gupta SK, Viereck J, Foinquinos A, Samolovac S, Kramer FL, et al. Inhibition of the cardiac fibroblast-enriched lncRNA Meg3 prevents cardiac fibrosis and diastolic dysfunction. Circ Res. 2017;121:575–83. [DOI] [PubMed]

17.

Li W, Li Y, Cui S, Liu J, Tan L, Xia H, et al. Se alleviates homocysteine-induced fibrosis in cardiac fibroblasts via downregulation of lncRNA MEG3. Exp Ther Med. 2021;22:1269. [DOI] [PubMed] [PMC]

18.

Gokey JJ, Snowball J, Sridharan A, Speth JP, Black KE, Hariri LP, et al. MEG3 is increased in idiopathic pulmonary fibrosis and regulates epithelial cell differentiation. JCI Insight. 2018;3:e122490. [DOI] [PubMed] [PMC]

19.

Zhan H, Chang X, Wang X, Yang M, Gao Q, Liu H, et al. LncRNA MEG3 mediates nickel oxide nanoparticles-induced pulmonary fibrosis via suppressing TGF-β1 expression and epithelial-mesenchymal transition process. Environ Toxicol. 2021;36:1099–110. [DOI] [PubMed]

20.

Spada M, Porta F, Righi D, Gazzera C, Tandoi F, Ferrero I, et al. Intrahepatic administration of human liver stem cells in infants with inherited neonatal-onset hyperammonemia: a phase I study. Stem Cell Rev Rep. 2020;16:186–97. [DOI] [PubMed] [PMC]

21.

Koliha N, Wiencek Y, Heider U, Jüngst C, Kladt N, Krauthäuser S, et al. A novel multiplex bead-based platform highlights the diversity of extracellular vesicles. J Extracell Vesicles. 2016;5:29975. [DOI] [PubMed] [PMC]

22.

Deregibus MC, Figliolini F, D'Antico S, Manzini PM, Pasquino C, De Lena M, et al. Charge-based precipitation of extracellular vesicles. Int J Mol Med. 2016;38:1359–66. [DOI] [PubMed] [PMC]

23.

Pelz S, Stock P, Brückner S, Christ B. A methionine-choline-deficient diet elicits NASH in the immunodeficient mouse featuring a model for hepatic cell transplantation. Exp Cell Res. 2012;318:276–87. [DOI] [PubMed]

24.

Winkler S, Borkham-Kamphorst E, Stock P, Brückner S, Dollinger M, Weiskirchen R, et al. Human mesenchymal stem cells towards non-alcoholic steatohepatitis in an immunodeficient mouse model. Exp Cell Res. 2014;326:230–9. [DOI] [PubMed]

25.

Machado MV, Michelotti GA, Xie G, de Almeida TP, Boursier J, Bohnic B, et al. Mouse models of diet-induced nonalcoholic steatohepatitis reproduce the heterogeneity of the human disease. PLoS One. 2015;10:e0132315. [DOI] [PubMed] [PMC]

26.

Chien Y, Huang CS, Lin HC, Lu KH, Tsai PH, Lai YH, et al. Improvement of non-alcoholic steatohepatitis by hepatocyte-like cells generated from iPSCs with Oct4/Sox2/Klf4/Parp1. Oncotarget. 2018;9:18594–606. [DOI] [PubMed] [PMC]

27.

Xu L, Hui AY, Albanis E, Arthur MJ, O'Byrne SM, Blaner WS, et al. Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut. 2005;54:142–51. [DOI] [PubMed] [PMC]

28.

Zheng Q, Lin Z, Xu J, Lu Y, Meng Q, Wang C, et al. Long noncoding RNA MEG3 suppresses liver cancer cells growth through inhibiting β-catenin by activating PKM2 and inactivating PTEN. Cell Death Dis. 2018;9:253. [DOI] [PubMed] [PMC]

29.

Théry C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, et al. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles. 2018;7:1535750. [DOI] [PubMed] [PMC]

30.

Herrera MB, Bruno S, Buttiglieri S, Tetta C, Gatti S, Deregibus MC, et al. Isolation and characterization of a stem cell population from adult human liver. Stem Cells. 2006;24:2840–50. [DOI] [PubMed]

31.

Bruno S, Herrera Sanchez MB, Chiabotto G, Fonsato V, Navarro-Tableros V, Pasquino C, et al. Human liver stem cells: a liver-derived mesenchymal stromal cell-like population with pro-regenerative properties. Front Cell Dev Biol. 2021;9:644088. [DOI] [PubMed] [PMC]

32.

Li J, Tian H, Yang J, Gong Z. Long noncoding RNAs regulate cell growth, proliferation, and apoptosis. DNA Cell Biol. 2016;35:459–70. [DOI] [PubMed]

33.

Hu G, Niu F, Humburg BA, Liao K, Bendi S, Callen S, et al. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget. 2018;9:18648–63. [DOI] [PubMed] [PMC]

34.

Sun C, Liu X, Yi Z, Xiao X, Yang M, Hu G, et al. Genome-wide analysis of long noncoding RNA expression profiles in patients with non-alcoholic fatty liver disease. IUBMB Life. 2015;67:847–52. [DOI] [PubMed]

35.

Leti F, Legendre C, Still CD, Chu X, Petrick A, Gerhard GS, et al. Altered expression of MALAT1 lncRNA in nonalcoholic steatohepatitis fibrosis regulates CXCL5 in hepatic stellate cells. Transl Res. 2017;190:25–39.E21. [DOI] [PubMed] [PMC]

36.

Sookoian S, Flichman D, Garaycoechea ME, San Martino J, Castaño GO, Pirola CJ. Metastasis-associated lung adenocarcinoma transcript 1 as a common molecular driver in the pathogenesis of nonalcoholic steatohepatitis and chronic immune-mediated liver damage. Hepatol Commun. 2018;2:654–65. [DOI] [PubMed] [PMC]

37.

Hanson A, Wilhelmsen D, DiStefano JK. The role of long non-coding RNAs (lncRNAs) in the development and progression of fibrosis associated with nonalcoholic fatty liver disease (NAFLD). Noncoding RNA. 2018;4:18. [DOI] [PubMed] [PMC]

38.

Shabgah AG, Norouzi F, Hedayati-Moghadam M, Soleimani D, Pahlavani N, Navashenaq JG. A comprehensive review of long non-coding RNAs in the pathogenesis and development of non-alcoholic fatty liver disease. Nutr Metab (Lond). 2021;18:22. [DOI] [PubMed] [PMC]

39.

Rohilla S, Awasthi A, Kaur S, Puria R. Evolutionary conservation of long non-coding RNAs in non-alcoholic fatty liver disease. Life Sci. 2021;264:118560. [DOI] [PubMed]

40.

Xiang J, Deng YY, Liu HX, Pu Y. LncRNA MALAT1 promotes PPARα/CD36-mediated hepatic lipogenesis in nonalcoholic fatty liver disease by modulating miR-206/ARNT axis. Front Bioeng Biotechnol. 2022;10:858558. [DOI] [PubMed] [PMC]

41.

Liu J, Tang T, Wang GD, Liu B. LncRNA-H19 promotes hepatic lipogenesis by directly regulating miR-130a/PPARγ axis in non-alcoholic fatty liver disease. Biosci Rep. 2019;39:BSR20181722. [DOI] [PubMed] [PMC]

42.

Wang H, Cao Y, Shu L, Zhu Y, Peng Q, Ran L, et al. Long non-coding RNA (lncRNA) H19 induces hepatic steatosis through activating MLXIPL and mTORC1 networks in hepatocytes. J Cell Mol Med. 2020;24:1399–412. [DOI] [PubMed] [PMC]

43.

Di Mauro S, Salomone F, Scamporrino A, Filippello A, Morisco F, Guido M, et al. Coffee restores expression of lncRNAs involved in steatosis and fibrosis in a mouse model of NAFLD. Nutrients. 2021;13:2952. [DOI] [PubMed] [PMC]

44.

Wang Y, Tai YL, Way G, Zeng J, Zhao D, Su L, et al. RNA binding protein HuR protects against NAFLD by suppressing long noncoding RNA H19 expression. Cell Biosci. 2022;12:172. [DOI] [PubMed] [PMC]

45.

Guo B, Cheng Y, Yao L, Zhang J, Lu J, Qi H, et al. LncRNA HOTAIR regulates the lipid accumulation in non-alcoholic fatty liver disease via miR-130b-3p/ROCK1 axis. Cell Signal. 2022;90:110190. [DOI] [PubMed]

46.

Cui J, Wang Y, Xue H. Long non-coding RNA GAS5 contributes to the progression of nonalcoholic fatty liver disease by targeting the microRNA-29a-3p/NOTCH2 axis. Bioengineered. 2022;13:8370–81. [DOI] [PubMed] [PMC]

47.

Xu S, Wang Y, Li Z, Hua Q, Jiang M, Fan X. LncRNA GAS5 knockdown mitigates hepatic lipid accumulation via regulating miR-26a-5p/PDE4B to activate cAMP/CREB pathway. Front Endocrinol (Lausanne). 2022;13:889858. [DOI] [PubMed] [PMC]

48.

Wang X. Down-regulation of lncRNA-NEAT1 alleviated the non-alcoholic fatty liver disease via mTOR/S6K1 signaling pathway. J Cell Biochem. 2018;119:1567–74. [DOI] [PubMed]

49.

Sun Y, Song Y, Liu C, Geng J. LncRNA NEAT1-MicroRNA-140 axis exacerbates nonalcoholic fatty liver through interrupting AMPK/SREBP-1 signaling. Biochem Biophys Res Commun. 2019;516:584–90. [DOI] [PubMed]

50.

Chen X, Tan XR, Li SJ, Zhang XX. LncRNA NEAT1 promotes hepatic lipid accumulation via regulating miR-146a-5p/ROCK1 in nonalcoholic fatty liver disease. Life Sci. 2019;235:116829. [DOI] [PubMed]

51.

Guo CJ, Xiao X, Sheng L, Chen L, Zhong W, Li H, et al. RNA sequencing and bioinformatics analysis implicate the regulatory role of a long noncoding RNA-mRNA network in hepatic stellate cell activation. Cell Physiol Biochem. 2017;42:2030–42. [DOI] [PubMed]

52.

Gerhard GS, Davis B, Wu X, Hanson A, Wilhelmsen D, Piras IS, et al. Differentially expressed mRNAs and lncRNAs shared between activated human hepatic stellate cells and nash fibrosis. Biochem Biophys Rep. 2020;22:100753. [DOI] [PubMed] [PMC]

53.

Zhang L, Yang Z, Trottier J, Barbier O, Wang L. Long noncoding RNA MEG3 induces cholestatic liver injury by interaction with PTBP1 to facilitate shp mRNA decay. Hepatology. 2017;65:604–15. [DOI] [PubMed] [PMC]

54.

Cheng X, Shihabudeen Haider Ali MS, Moran M, Viana MP, Schlichte SL, Zimmerman MC, et al. Long non-coding RNA Meg3 deficiency impairs glucose homeostasis and insulin signaling by inducing cellular senescence of hepatic endothelium in obesity. Redox Biol. 2021;40:101863. [DOI] [PubMed] [PMC]

55.

Zhu X, Wu YB, Zhou J, Kang DM. Upregulation of lncRNA MEG3 promotes hepatic insulin resistance via increasing FoxO1 expression. Biochem Biophys Res Commun. 2016;469:319–25. [DOI] [PubMed]

56.

Zhu X, Li H, Wu Y, Zhou J, Yang G, Wang W. lncRNA MEG3 promotes hepatic insulin resistance by serving as a competing endogenous RNA of miR-214 to regulate ATF4 expression. Int J Mol Med. 2019;43:345–57. [DOI] [PubMed] [PMC]

57.

Chen DL, Shen DY, Han CK, Tian Y. LncRNA MEG3 aggravates palmitate-induced insulin resistance by regulating miR-185-5p/Egr2 axis in hepatic cells. Eur Rev Med Pharmacol Sci. 2019;23:5456–67. [DOI] [PubMed]

58.

Wang X, Wang J. High-content hydrogen water-induced downregulation of miR-136 alleviates non-alcoholic fatty liver disease by regulating Nrf2 via targeting MEG3. Biol Chem. 2018;399:397–406. [DOI] [PubMed]

59.

Huang P, Huang FZ, Liu HZ, Zhang TY, Yang MS, Sun CZ. LncRNA MEG3 functions as a ceRNA in regulating hepatic lipogenesis by competitively binding to miR-21 with LRP6. Metabolism. 2019;94:1–8. [DOI] [PubMed]

60.

Zou D, Liu L, Zeng Y, Wang H, Dai D, Xu M. LncRNA MEG3 up-regulates SIRT6 by ubiquitinating EZH2 and alleviates nonalcoholic fatty liver disease. Cell Death Discov. 2022;8:103. [DOI] [PubMed] [PMC]

61.

Zhang W, Conway SJ, Liu Y, Snider P, Chen H, Gao H, et al. Heterogeneity of hepatic stellate cells in fibrogenesis of the liver: insights from single-cell transcriptomic analysis in liver injury. Cells. 2021;10:2129. [DOI] [PubMed] [PMC]

62.

He Y, Wu YT, Huang C, Meng XM, Ma TT, Wu BM, et al. Inhibitory effects of long noncoding RNA MEG3 on hepatic stellate cells activation and liver fibrogenesis. Biochim Biophys Acta. 2014;1842:2204–15. [DOI] [PubMed]

63.

Qin R, Huang W, Huang Y, Zhang Z, Su Y, Chen S, et al. lncRNA MEG3 modulates hepatic stellate cell activation by sponging miR145 to regulate PPARγ. Mol Med Rep. 2022;25:3. [DOI] [PubMed] [PMC]

64.

Schinagl M, Tomin T, Gindlhuber J, Honeder S, Pfleger R, Schittmayer M, et al. Proteomic changes of activated hepatic stellate cells. Int J Mol Sci. 2021;22:12782. [DOI] [PubMed] [PMC]

65.

Chiabotto G, Ceccotti E, Bruno S. Narrative review of in vitro experimental models of hepatic fibrogenesis. Dig Med Res. 2022;5:33. [DOI]