The role of long noncoding RNAs in hepatocellu.pdf

REVIEWOpen AccessThe role of long noncoding RNAs inhepatocellular carcinomaZhao Huang1,Jian-Kang Zhou1,Yong Peng1,Weifeng He2*and Canhua Huang1*AbstractHepatocellular carcinoma(HCC)is the most frequent subtype of primary liver cancer and one of the leading causesof cancer-related death worldwide.However,the molecular mechanisms underlying HCC pathogenesis have notbeen fully understood.Emerging evidences have recently suggested the crucial role of long noncoding RNAs(lncRNAs)in the tumorigenesis and progression of HCC.Various HCC-related lncRNAs have been shown to possessaberrant expression and participate in cancerous phenotypes(e.g.persistent proliferation,evading apoptosis,accelerated vessel formation and gain of invasive capability)through their binding with DNA,RNA or proteins,orencoding small peptides.Thus,a deeper understanding of lncRNA dysregulation would provide new insights intoHCC pathogenesis and novel tools for the early diagnosis and treatment of HCC.In this review,we summarize thedysregulation of lncRNAs expression in HCC and their tumor suppressive or oncogenic roles during HCCtumorigenesis.Moreover,we discuss the diagnostic and therapeutic potentials of lncRNAs in HCC.Keywords:Long noncoding RNA,Hepatocellular carcinoma,Biomarker,Targeted therapyIntroductionHepatocellular carcinoma(HCC)is one of the mostcommon malignancies worldwide and ranks as the thirdmost common cause of cancer-related death,especiallyin Africa and Eastern Asia due to the lack of surveillanceand treatment options 1.The risk factors underlyingHCC pathogenesis are highly variable,including chronichepatitis B(HBV)and hepatitis C virus(HCV)infection,alcohol consumption,non-alcoholic fatty liver disease(NAFLD),and aflatoxin B1 intake 2.These factors mayinduce DNA damage,epigenetic alterations and cancer-related mutations,leading to the silencing of tumor sup-pressors(e.g.TP53,CDH1,RASSF1)and the activation ofoncogenes(e.g.MYC,VEGFA,MAPK7),which eventuallycontribute to HCC progression 36.To date,severalpreventive and therapeutic strategies have been implicatedin the management of HCC,as exampled by the adminis-tration of anti-hepatitis vaccine,specific kinase inhibitors(e.g.Sorafenib and Regorafenib),surgical resection andliver transplantation 710.These treatments,togetherwith biomarker screening(e.g.a-fetoprotein),have mini-mized HCC-related death to a certain extent,but theirperformance is far from acceptable therapeutic effect,thusnovel diagnostic/therapeutic approaches are still urgentlyneeded to improve the clinic outcomes of HCC.EarlyHCC-relatedstudiesmainlyfocusedontheprotein-coding genes due to their central roles in the regu-lation of biological processes.However,less than 2%ofgenome DNA encodes proteins,whereas the remaining98%noncoding sequences and their RNA transcripts(ncRNAs)have been functionally uncharacterized andthought to be“noise”in the past 11.Recently,increasingevidences indicate that these evolutionarily conservedncRNAs,such as microRNA(miRNA),circular RNA(cir-cRNA)and PIWI-interacting RNA(piRNA),particularly The Author(s).2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,which permits use,sharing,adaptation,distribution and reproduction in any medium or format,as long as you giveappropriate credit to the original author(s)and the source,provide a link to the Creative Commons licence,and indicate ifchanges were made.The images or other third party material in this article are included in the articles Creative Commonslicence,unless indicated otherwise in a credit line to the material.If material is not included in the articles Creative Commonslicence and your intended use is not permitted by statutory regulation or exceeds the permitted use,you will need to obtainpermission directly from the copyright holder.To view a copy of this licence,visit http:/creativecommons.org/licenses/by/4.0/.The Creative Commons Public Domain Dedication waiver(http:/creativecommons.org/publicdomain/zero/1.0/)applies to thedata made available in this article,unless otherwise stated in a credit line to the data.*Correspondence:;Zhao Huang and Jian-Kang Zhou contributed equally to this work.2Institute of Burn Research,Southwest Hospital;State Key Laboratory ofTrauma,Burn and Combined Injury,Chongqing Key Laboratory for DiseaseProteomics,Army Military Medical University,Chongqing 400038,China1State Key Laboratory of Biotherapy and Cancer Center,West China Hospital,and West China School of Basic Medical Sciences&Forensic Medicine,Sichuan University,and Collaborative Innovation Center for Biotherapy,Chengdu 610041,ChinaHuang et al.Molecular Cancer (2020)19:77 https:/doi.org/10.1186/s12943-020-01188-4long noncoding RNA(lncRNA),play an important role indiverse physiological and pathological processes.In 1990,the first lncRNA H19,which restricts organ growth viadecreasing IGF2 expression,was identified in fetal livertissue 12,13.Next year,the lncRNA XIST mediating Xchromosome inactivation was found 14.To date,over 50,000 genes have been found to transcribe lncRNAs andtheir number is still rapidly growing 15.These lncRNAsare differentially expressed in different tissues and cancers,including HCC 16.Currently,the roles of most lncRNAsin HCC remain elusive,while a small part of which hasbeen extensively investigated.For instance,lncRNA HULCis upregulated in HCC and has been shown to promoteHCC growth,metastasis and drug resistance 1719.Intri-guingly,some HCC-related lncRNAs are present in bodyfluids,which are easy to detect and analyze,making themhave the potential to be attractive biomarkers in liquid bi-opsy of HCC.For instance,lncRNA-WRAP53 in serum isan independent prognostic marker to predict high relapserate of HCC patients 20.These vital roles and uniqueproperties of lncRNAs suggest their potential clinical valuein the HCC diagnosis and treatment.In this review,webriefly introduce dysregulation of lncRNAs expression inHCC,and summarize how lncRNAs regulate HCC pro-gression by acting as tumor suppressor or oncogene.Inaddition,we discuss the diagnostic and therapeutic poten-tial of lncRNAs in HCC.LncRNA as a modulator of liver microenvironmentand chronic liver diseasesLiver cancer is distinguished from other cancer types byseveral unique features,including viral infection,regenera-tive signals and hypoxic microenvironment.These factorsprovide both opportunities and challenges for HCC cellproliferation and survival.Importantly,lncRNA modulatesimmune response,liver regeneration and redox signal-ing,which play critical roles in the regulation of livermicroenvironment and chronic liver diseases.Dysreg-ulation of lncRNA in these processes leads to chronichepatitis,liver outgrowth and oxidative stress,whicheventually result in the initiation and progression ofHCC(Fig.1).Fig.1 LncRNAs modulate liver microenvironment and chronic liver diseases.LncRNAs are involved in physiological and pathological processes,including(a)Viral infection and immune repression.Virus-induced lncRNAs are capable of promoting cell proliferation or suppressing hostimmune response,resulting in chronic infection and HCC formation.b Liver regeneration and outgrowth.In response to hepatectomy,liver isregenerated via activating proliferative signalings.These signalings can also be stimulated by certain lncRNAs independent of tissue loss,leadingto liver overgrowth and HCC.c Hypoxic liver injury and oxidative stress.Drug detoxification induces ROS accumulation in liver,which upregulatesHIF-1 to facilitate blood vessel formation therefore relief oxidative stress.To some similarities,several lncRNAs also activate HIF-1 to supportHCC survival under hypoxic condition.ISGs,IFN-stimulated genes.ROS,reactive oxygen speciesHuang et al.Molecular Cancer (2020)19:77 Page 2 of 18Viral infectionHepatitis B virus(HBV)and hepatitis C virus(HCV)aretwo major viruses invading liver and causing chronicinflammation.More than 240 and 70 million people areinfected respectively with HBV and HCV worldwide,apart of who tend to develop HCC if untreated 21,22.Hepatitis viruses hijack host cells to facilitate their repli-cation or production via multiple mechanisms,one ofwhich is regulating the transcription of certain lncRNAs.For instance,the HBV X protein(HBx)upregulatesoncogenic lncRNA HUR1,which binds and blocks p53to promote HCC growth 23.Besides,HBx can alsodownregulate tumor suppressive lncRNA Dreh,leadingto re-expression of vimentin and promoting HCC metas-tasis 24.During infection,the host immune is activatedto restrict viral replication.However,the invaded hepa-titis viruses are able to alter Toll-like receptor(TLR)signaling,resulting in a defective immune response thatis inadequate for virus clearance.It allows the virus toescape from immune surveillance,in which lncRNAsplay crucial roles.It has been shown that infection ofHCV upregulates the level of a series of lncRNAs suchas IFI6,CMPK2 and EGOT that inhibit the expressionof IFN-stimulated genes(ISGs),leading to immune sup-pression and chronic inflammation 2527.These find-ings indicate that viruses modulate antiviral responsethrough lncRNAs encoded by host or itself genome.Intri-guingly,lncRNA can also be generated from an integratedgenome.Lau et al.reported a viral-human gene fusionthat produces a chimeric lncRNA HBx-LINE1,which pro-motes HCC through activating Wnt signaling 28.Thischimeric lncRNA can be detected in 23.3%HBV bearingHCC samples and decrease the survival of HCC patients,suggesting HBV/HCV associated lncRNAs might be po-tential biomarkers in HCC risk evaluation and diagnosis.Liver regenerationLiver is the only visceral organ capable of regeneration afterpartial hepatectomy or chemical injury.After a hepatec-tomy,hepatic growth factor(HGF)is released due to ele-vated urokinase activity,which potently activates EGFR andc-Met 29,30.EGFR and c-Met promote hepatocyte pro-liferation through activating multiple signalings,such asWnt 31,32.Once regeneration is completed,TGF-re-presses the function of urokinase and HGF thus brings livercells back to the quiescent state 33.Several lncRNAs areinvolved in this process.For example,lncRNA-LALR1 hasbeen found to suppress Axin1 thus activating Wnt signal-ing,which stimulates hepatocyte proliferation during liverregeneration 34.Besides,lncHand2 is capable of upregu-lating the expression of Nkx12,thereby activating c-Metin hepatocyte to facilitate liver regeneration 35.However,persistentproliferativesignalinginducedbylncRNAdysregulation frequently leads to liver tumorigenesis.Forinstance,lncRNA DSCR8 36 and SNHG5 37 have beenshown to upregulate Wnt and result in liver tumor growth,whereas lnc-EGFR 38 and lncRNA NEAT1 39 are cap-able of activating EGFR and c-Met respectively,leading toHCC development.These lncRNAs are probably activatedin the absence of liver tissue loss or failed to be silenced byquiescent signal TGF-.Indeed,TGF-may upregulatecertain lncRNAs such as ATB to promote HCC metastasis40,and the key regulatory mechanisms to determinewhether an oncogenic or tumor suppressive role of TGF-in this context remains unclear.Oxidative stressLiver accounts for approximately 2%of body weight butreceives about 25%of cardiac output.Sufficient bloodsupply is indispensable for its oxygen demand,whereaspoor oxygen delivery or inadequate antioxidant machin-ery frequently results in hypoxic liver injury,an oxidativestress-associated liver disease 41.In addition,variousrisk factors such as alcohol consumption,viral infection,drug detoxification and metabolism also markedly in-duce accumulation of reactive oxygen species(ROS),leading to oxidative stress in liver.To adapt to this hyp-oxic microenvironment,HCC cells develop survivalstrategies such as promoting angiogenesis,thereby re-ceiving additional oxygen supply from the bloodstream42.This process involves HIF-1,a master transcrip-tion factor that facilitates angiogenesis.Recent studiesrevealed that several lncRNAs are sensitive to hypoxiaand might function through HIF-1.One of hypoxia-responsive lncRNAs is linc-RoR,which is induced byoxidative stress and upregulates HIF-1 to support HCCcell survival 43.In contrast,lncRNAs that negativelyregulate HIF-1,including lncRNA LET,are downregu-lated during HCC progression 44.Mechanistically,lncRNA-LET interacts with a RNA-binding protein NF90and promotes its degradation,leading to destabilization ofHIF-1 mRNA.In response to hypoxia,HDAC3 is in-duced and represses the transcription of lncRNA-LET,resulting in expression of HIF-1 and HCC metastasis44.For protecting liver from oxidative damage,naturalantioxidant supplies including green tea,jujube honey andvirgin olive oil are encouraged 45,but the roles oflncRNAs in this process is yet to be determined.Aberrant expression of lncRNA in HCCThe biogenesis of lncRNAs shows high similarities withthat of protein-coding transcripts.Epigenetic modifica-tion,transcription complex recruitment and RNA pro-cessing are major events regulating lncRNA biogenesis.Before transcription,active chromatin marks are com-monly present within lncRNA promoter,including theacetylation of H3K9 and H3K27,as well as the dimethy-lation or trimethylation of H3K4 46.In contrast,theHuang et al.Molecular Cancer (2020)19:77 Page 3 of 18trimethylation of H3K27 is recognized as a repressivechromatin mark.For example,knockdown of EZH2,amethyltransferase responsible for H3K27me3 modifica-tion,has been shown to reactivate the transcription oflncRNAs in embryonic stem cells 47.These evidencesindicate that the epigenetic modification of lncRNA genesmay follow nearly the same regulatory rules as protein-coding genes.Interestingly,another transcriptional repres-sion mark H3K9me3 is more enriched in the promoter re-gion of lncRNAs compared with mRNAs,suggestingsome unique features of lncRNAs in their histone modifi-cation patterns 48.The detailed mechanisms underlyingthese epigenetic modifications remain elusive,whereassome chromatin remodeling complex such as Isw2,Swr1,Ino80 and Rsc are probably involved 49.Next,in the presence of active chromatin marks or theabsence of repressive marks,RNA polymerase II is re-cruited to initiate the transcription of lncRNAs,sometimesin a bidirectional way to yield divergent transcripts.Gener-ally,lncRNA genes tend to share the same promoter withtheir neighbor protein-coding genes 50.Besides,someother transcription patterns have been extensively reviewedelsewhere 51.Then,the majority of nascent transcriptsare processed into mature lncRNAs through canonical wayslike mRNAs,including methylguanosine capping at 5 end,polyadenylation to form a poly-A tail at 3 end,and splicingto remove introns.Alternatively,some lncRNAs have beenshown to undergo non-canonical processing ways.For in-stance,the lncRNA MALAT1 and MEN are cleaved bytRNA processing enzymes RNase P and RNase Z to formtriple-helical structures at their 3 end,which protects themfrom degradation and facilitates their cellular accumulationin the absence of poly(A)t