An Integrative Transcriptome Subtraction Strategy to Identify Human LncRNAs That Specifically Play a Role in Activation of Human Hepatic Stellate Cells

Overview

Journal Noncoding RNA

Date 2024 Jun 26

PMID 38921831

Authors

Yonghe Ma

Jamie Harris

Ping Li

Chengfei Jiang

Hang Sun

Haiming Cao

Affiliations

Soon will be listed here.

Abstract

Fibrotic liver features excessive deposition of extracellular matrix (ECM), primarily produced from "activated" hepatic stellate cells (HSCs). While targeting human HSCs (hHSCs) in fibrosis therapeutics shows promise, the overall understanding of hHSC activation remains limited, in part because it is very challenging to define the role of human long non-coding RNAs (lncRNAs) in hHSC activation. To address this challenge, we identified another cell type that acts via a diverse gene network to promote fibrogenesis. Then, we identified the lncRNAs that were differentially regulated in activated hHSCs and the other profibrotic cell. Next, we conducted concurrent analysis to identify those lncRNAs that were specifically involved in fibrogenesis. We tested and confirmed that transdifferentiation of vascular smooth muscle cells (VSMCs) represents such a process. By overlapping TGFβ-regulated lncRNAs in multiple sets of hHSCs and VSMCs, we identified a highly selected list of lncRNA candidates that could specifically play a role in hHSC activation. We experimentally characterized one human lncRNA, named CARMN, which was significantly regulated by TGFβ in all conditions above. CARMN knockdown significantly reduced the expression levels of a panel of marker genes for hHSC activation, as well as the levels of ECM deposition and hHSC migration. Conversely, gain of function of CARMN using CRISPR activation (CRISPR-a) yielded the completely opposite effects. Taken together, our work addresses a bottleneck in identifying human lncRNAs that specifically play a role in hHSC activation and provides a framework to effectively select human lncRNAs with significant pathophysiological role.

References

Sato M, Suzuki S, Senoo H . Hepatic stellate cells: unique characteristics in cell biology and phenotype. Cell Struct Funct. 2003; 28(2):105-12. DOI: 10.1247/csf.28.105. View

Seifuddin F, Singh K, Suresh A, Judy J, Chen Y, Chaitankar V . lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. Sci Data. 2020; 7(1):326. PMC: 7536183. DOI: 10.1038/s41597-020-00659-z. View

Ruan X, Li P, Ma Y, Jiang C, Chen Y, Shi Y . Identification of human long noncoding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis. J Clin Invest. 2020; 131(1). PMC: 7773374. DOI: 10.1172/JCI136336. View

Ni H, Haemmig S, Deng Y, Chen J, Simion V, Yang D . A Smooth Muscle Cell-Enriched Long Noncoding RNA Regulates Cell Plasticity and Atherosclerosis by Interacting With Serum Response Factor. Arterioscler Thromb Vasc Biol. 2021; 41(9):2399-2416. PMC: 8387455. DOI: 10.1161/ATVBAHA.120.315911. View

Tsuchida T, Friedman S . Mechanisms of hepatic stellate cell activation. Nat Rev Gastroenterol Hepatol. 2017; 14(7):397-411. DOI: 10.1038/nrgastro.2017.38. View

Dong K, Shen J, He X, Hu G, Wang L, Osman I . Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin. Circulation. 2021; 144(23):1856-1875. PMC: 8726016. DOI: 10.1161/CIRCULATIONAHA.121.055949. View

Deng K, Huang X, Lei F, Zhang X, Zhang P, She Z . Role of hepatic lipid species in the progression of nonalcoholic fatty liver disease. Am J Physiol Cell Physiol. 2022; 323(2):C630-C639. DOI: 10.1152/ajpcell.00123.2022. View

Friedman S, Roll F . Isolation and culture of hepatic lipocytes, Kupffer cells, and sinusoidal endothelial cells by density gradient centrifugation with Stractan. Anal Biochem. 1987; 161(1):207-18. DOI: 10.1016/0003-2697(87)90673-7. View

Ruan X, Li P, Chen Y, Shi Y, Pirooznia M, Seifuddin F . In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits. Nat Commun. 2020; 11(1):45. PMC: 6940387. DOI: 10.1038/s41467-019-13688-z. View

10.

Bao L, Chu Y, Kang H . SNAI1-activated long non-coding RNA LINC01711 promotes hepatic fibrosis cell proliferation and migration by regulating XYLT1. Genomics. 2023; 115(3):110597. DOI: 10.1016/j.ygeno.2023.110597. View

11.

Hautekeete M, Geerts A . The hepatic stellate (Ito) cell: its role in human liver disease. Virchows Arch. 1997; 430(3):195-207. DOI: 10.1007/BF01324802. View

12.

Jaffe M, Sesti C, Washington I, Du L, Dronadula N, Chin M . Transforming growth factor-β signaling in myogenic cells regulates vascular morphogenesis, differentiation, and matrix synthesis. Arterioscler Thromb Vasc Biol. 2011; 32(1):e1-11. DOI: 10.1161/ATVBAHA.111.238410. View

13.

Chen C, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C . Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science. 2016; 354(6311):468-472. DOI: 10.1126/science.aae0047. View

14.

Diederichs S . The four dimensions of noncoding RNA conservation. Trends Genet. 2014; 30(4):121-3. DOI: 10.1016/j.tig.2014.01.004. View

15.

Wirz W, Antoine M, Tag C, Gressner A, Korff T, Hellerbrand C . Hepatic stellate cells display a functional vascular smooth muscle cell phenotype in a three-dimensional co-culture model with endothelial cells. Differentiation. 2008; 76(7):784-94. DOI: 10.1111/j.1432-0436.2007.00260.x. View

16.

Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U . The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature. 2014; 505(7485):635-40. DOI: 10.1038/nature12943. View

17.

Mann D, Marra F . Fibrogenic signalling in hepatic stellate cells. J Hepatol. 2010; 52(6):949-50. DOI: 10.1016/j.jhep.2010.02.005. View

18.

Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B . CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis. J Mol Cell Cardiol. 2015; 89(Pt A):98-112. DOI: 10.1016/j.yjmcc.2015.09.016. View

19.

Tacke F, Puengel T, Loomba R, Friedman S . An integrated view of anti-inflammatory and antifibrotic targets for the treatment of NASH. J Hepatol. 2023; 79(2):552-566. DOI: 10.1016/j.jhep.2023.03.038. View

20.

Sallam T, Jones M, Gilliland T, Zhang L, Wu X, Eskin A . Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis. Nature. 2016; 534(7605):124-8. PMC: 4896091. DOI: 10.1038/nature17674. View