RNA-based therapies in hepatocellular carcinoma: state of the art and clinical perspectives

Abstract

Liver cancer is a heterogeneous disease and is one of the leading causes of cancer deaths worldwide. Hepatocellular carcinoma, comprising approximately 90% of cases, presents a formidable challenge with a less than 20% 5-year survival rate despite recent treatment advancements. The impediments of drug resistance and off-target effects underscore the critical need for innovative and efficacious therapies. Harnessing the growing understanding of RNA function offers a promising avenue to address previously "undruggable" proteins, transcripts, and genes. Various RNAs demonstrate the potential to selectively act on these targets, expanding the scope of therapeutic interventions. With diverse regulatory roles in cancer pathways, RNAs emerge as valuable targets and tools for anticancer therapy development. This article provides an in-depth exploration of current RNA-based therapies, elucidates their mechanisms of action, and discusses their combinations with chemo-/immunotherapies in clinical trials for hepatocellular carcinoma.

Keywords

RNA-based therapies / drug resistance / mRNA vaccines

References

[1] Sung H,Siegel RL.Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.CA Cancer J Clin2021;71:209-49

[2] Llovet JM,Villanueva A.Hepatocellular carcinoma.Nat Rev Dis Primers2021;7:6

[3] Kudo M,Qin S.Lenvatinib versus sorafenib in first-line treatment of patients with unresectable hepatocellular carcinoma: a randomised phase 3 non-inferiority trial.Lancet2018;391:1163-73

[4] Greten TF,Cheng AL.Society for immunotherapy of cancer (SITC) clinical practice guideline on immunotherapy for the treatment of hepatocellular carcinoma.J Immunother Cancer2021;9:e002794 PMCID:PMC8438858

[5] Gallage S,Szydlowska M.The therapeutic landscape of hepatocellular carcinoma.Med2021;2:505-52

[6] Lee MS,Hsu CH.GO30140 investigatorsAtezolizumab with or without bevacizumab in unresectable hepatocellular carcinoma (GO30140): an open-label, multicentre, phase 1b study.Lancet Oncol2020;21:808-20

[7] Finn RS,Merle P.KEYNOTE-240 investigatorsPembrolizumab As second-line therapy in patients with advanced hepatocellular carcinoma in KEYNOTE-240: a randomized, double-blind, phase III trial.J Clin Oncol2020;38:193-202

[8] Finn RS,Ikeda M.IMbrave150 InvestigatorsAtezolizumab plus bevacizumab in unresectable hepatocellular carcinoma.N Engl J Med2020;382:1894-905

[9] Wang F,Watts JK.RNA therapeutics on the rise.Nat Rev Drug Discov2020;19:441-2

[10] Kim YK.RNA therapy: rich history, various applications and unlimited future prospects.Exp Mol Med2022;54:455-65 PMCID:PMC9016686

[11] Kim YK.RNA therapy.Exp Mol Med2023;55:1281-2 PMCID:PMC10393985

[12] Crooke ST,Bennett CF.RNA-targeted therapeutics.Cell Metab2018;27:714-39

[13] Wilson RC.Molecular mechanisms of RNA interference.Annu Rev Biophys2013;42:217-39 PMCID:PMC5895182

[14] Han X,Li T.Beyond blocking: engineering RNAi-mediated targeted immune checkpoint nanoblocker enables T-cell-independent cancer treatment.ACS Nano2020;14:17524-34

[15] Zhang C,Yang Y.RNAi mediated silencing of Nanog expression suppresses the growth of human colorectal cancer stem cells.Biochem Biophys Res Commun2021;534:254-60

[16] Pardi N,Porter FW.mRNA vaccines - a new era in vaccinology.Nat Rev Drug Discov2018;17:261-79 PMCID:PMC5906799

[17] Rosenblum D,Kedmi R.CRISPR-Cas9 genome editing using targeted lipid nanoparticles for cancer therapy.Sci Adv2020;6 PMCID:PMC7673804

[18] Adachi T.Aptamers: a review of their chemical properties and modifications for therapeutic application.Molecules2019;24:4229 PMCID:PMC6930564

[19] Fire A,Montgomery MK,Driver SE.Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.Nature1998;391:806-11

[20] Martinez J,Urlaub H,Tuschl T.Single-stranded antisense siRNAs guide target RNA cleavage in RNAi.Cell2002;110:563-74

[21] Bernstein E,Hammond SM.Role for a bidentate ribonuclease in the initiation step of RNA interference.Nature2001;409:363-6

[22] Meister G.Mechanisms of gene silencing by double-stranded RNA.Nature2004;431:343-9

[23] Robb T,Blenkiron C.Exploiting microRNAs as cancer therapeutics.Target Oncol2017;12:163-78

[24] Roberts TC,Wood MJA.Advances in oligonucleotide drug delivery.Nat Rev Drug Discov2020;19:673-94 PMCID:PMC7419031

[25] Oura K,Masaki T.Molecular and functional roles of microRNAs in the progression of hepatocellular carcinoma-A review.Int J Mol Sci2020;21:8362 PMCID:PMC7664704

[26] To KKW,Tong CWS,Yan W.Advances in the discovery of microRNA-based anticancer therapeutics: latest tools and developments.Expert Opin Drug Discov2020;15:63-83

[27] Barata P,Hong DS.RNA-targeted therapeutics in cancer clinical trials: Current status and future directions.Cancer Treat Rev2016;50:35-47

[28] Dolgin E.The tangled history of mRNA vaccines.Nature2021;597:318-24

[29] Miao L,Huang L.mRNA vaccine for cancer immunotherapy.Mol Cancer2021;20:41 PMCID:PMC7905014

[30] Mockey M,Dupuy FP,Pichon C.mRNA transfection of dendritic cells: synergistic effect of ARCA mRNA capping with poly(A) chains in cis and in trans for a high protein expression level.Biochem Biophys Res Commun2006;340:1062-8

[31] Muttach F,Rentmeister A.Synthetic mRNA capping.Beilstein J Org Chem2017;13:2819-32 PMCID:PMC5753152

[32] Shanmugasundaram M,Kore AR.Recent advances in modified cap analogs: synthesis, biochemical properties, and mRNA based vaccines.Chem Rec2022;22:e202200005 PMCID:PMC9111249

[33] Orlandini von Niessen AG,Rechner C.Improving mRNA-based therapeutic gene delivery by expression-augmenting 3' UTRs identified by cellular library screening.Mol Ther2019;27:824-36 PMCID:PMC6453560

[34] Jia L,Ji Q,Yewdell JW.Decoding mRNA translatability and stability from the 5' UTR.Nat Struct Mol Biol2020;27:814-21

[35] Alexaki A,Athey JC.Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.Sci Rep2019;9:15449 PMCID:PMC6820528

[36] Karikó K.Naturally occurring nucleoside modifications suppress the immunostimulatory activity of RNA: implication for therapeutic RNA development.Curr Opin Drug Discov Devel2007;10:523-32.

[37] Holtkamp S,Selmi A.Modification of antigen-encoding RNA increases stability, translational efficacy, and T-cell stimulatory capacity of dendritic cells.Blood2006;108:4009-17

[38] Willis E,Parkhouse K.Nucleoside-modified mRNA vaccination partially overcomes maternal antibody inhibition of de novo immune responses in mice.Sci Transl Med2020;12 PMCID:PMC7339908

[39] Sharifnia Z,Kazemi B.Design and development of modified mRNA encoding core antigen of hepatitis C virus: a possible application in vaccine production.Iran Biomed J2019;23:57-67 PMCID:PMC6305823

[40] Karikó K,Welsh FA.Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability.Mol Ther2008;16:1833-40 PMCID:PMC2775451

[41] Oberli MA,Dorkin JR.Lipid nanoparticle assisted mRNA delivery for potent cancer immunotherapy.Nano Lett2017;17:1326-35 PMCID:PMC5523404

[42] Chen J,Huang C.Lipid nanoparticle-mediated lymph node-targeting delivery of mRNA cancer vaccine elicits robust CD8⁺ T cell response.Proc Natl Acad Sci U S A2022;119:e2207841119 PMCID:PMC9407666

[43] Kreiter S,van de Roemer N.Mutant MHC class II epitopes drive therapeutic immune responses to cancer.Nature2015;520:692-6 PMCID:PMC4838069

[44] Kranz LM,Haas H.Systemic RNA delivery to dendritic cells exploits antiviral defence for cancer immunotherapy.Nature2016;534:396-401

[45] Linares-Fernández S,Exposito JY.Tailoring mRNA vaccine to balance innate/adaptive immune response.Trends Mol Med2020;26:311-23

[46] Esprit A,Bahadur Shahi R,Franceschini L.Neo-antigen mRNA vaccines.Vaccines2020;8:776 PMCID:PMC7766040

[47] Peng M,Wang Y.Neoantigen vaccine: an emerging tumor immunotherapy.Mol Cancer2019;18:128 PMCID:PMC6708248

[48] Keskin DB,Sun J.Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.Nature2019;565:234-9 PMCID:PMC6546179

[49] Lang F,Löwer M,Sahin U.Identification of neoantigens for individualized therapeutic cancer vaccines.Nat Rev Drug Discov2022;21:261-82 PMCID:PMC7612664

[50] Liu JQ,Zhang X.Intratumoral delivery of IL-12 and IL-27 mRNA using lipid nanoparticles for cancer immunotherapy.J Control Release2022;345:306-13 PMCID:PMC9133152

[51] Tan AT,Jin J.Immunological alterations after immunotherapy with short lived HBV-TCR T cells associates with long-term treatment response in HBV-HCC.Hepatol Commun2022;6:841-54 PMCID:PMC8948543

[52] Rajan T, Gugliandolo A, Bramanti P, Mazzon E. In vitro-transcribed mRNA chimeric antigen receptor T cell (IVT mRNA CAR T) therapy in hematologic and solid tumor management: a preclinical update.Int J Mol Sci2020;21:6514 PMCID:PMC7556036

[53] Crooke ST.Molecular mechanisms of antisense oligonucleotides.Nucleic Acid Ther2017;27:70-7 PMCID:PMC5372764

[54] Wu H,Zhang H,Sun H.Determination of the role of the human RNase H1 in the pharmacology of DNA-like antisense drugs.J Biol Chem2004;279:17181-9

[55] Liang XH,Nichols JG.RNase H1-dependent antisense oligonucleotides are robustly active in directing rna cleavage in both the cytoplasm and the nucleus.Mol Ther2017;25:2075-92 PMCID:PMC5589097

[56] Ruhanen H,Yasukawa T.Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells.Biochim Biophys Acta2011;1813:2000-7 PMCID:PMC3223524

[57] Lima WF,Damle SS.Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function.Nucleic Acids Res2016;44:5299-312 PMCID:PMC4914116

[58] Hyjek M,Nowotny M.RNases H: Structure and mechanism.DNA Repair2019;84:102672

[59] Cerritelli SM.RNases H: multiple roles in maintaining genome integrity.DNA Repair2019;84:102742 PMCID:PMC7498118

[60] Lai F,Ling KK.Directed RNase H cleavage of nascent transcripts causes transcription termination.Mol Cell2020;77:1032-1043.e4

[61] Khan P,Lakshmanan I.RNA-based therapies: a cog in the wheel of lung cancer defense.Mol Cancer2021;20:54 PMCID:PMC7977189

[62] Crooke ST,Crooke RM.Antisense technology: an overview and prospectus.Nat Rev Drug Discov2021;20:427-53

[63] Ramasamy T,Munusamy S,Kim JO.Nano drug delivery systems for antisense oligonucleotides (ASO) therapeutics..J Control Release2022;352:861-78

[64] Desterro J,Carmo-Fonseca M.Targeting mRNA processing as an anticancer strategy.Nat Rev Drug Discov2020;19:112-29

[65] Li D,Fletcher S.Precision medicine through antisense oligonucleotide-mediated exon skipping.trends Pharmacol Sci2018;39:982-94

[66] Morse DE.Polarity and the degradation of mRNA.Nature1969;224:329-31

[67] Dowdy SF.Overcoming cellular barriers for RNA therapeutics.Nat Biotechnol2017;35:222-9

[68] Chen X,Rodriguez-Aguayo C,Lopez-Berestein G.RNA interference-based therapy and its delivery systems.Cancer Metastasis Rev2018;37:107-24 PMCID:PMC5898634

[69] Meng C,Li G,Shen H.Nanoplatforms for mRNA therapeutics.Adv Ther2021;4:2000099

[70] Byun MJ,Kim SN.Advances in nanoparticles for effective delivery of RNA therapeutics.Biochip J2022;16:128-45 PMCID:PMC8891745

[71] Li Y,Zhang T.Lipid-mRNA nanoparticles landscape for cancer therapy.Front Bioeng Biotechnol2022;10:1053197 PMCID:PMC9659646

[72] Witzigmann D,Leung J,Cullis PR.Lipid nanoparticle technology for therapeutic gene regulation in the liver.Adv Drug Deliv Rev2020;159:344-63 PMCID:PMC7329694

[73] Hou X,Langer R.Lipid nanoparticles for mRNA delivery.Nat Rev Mater2021;6:1078-94 PMCID:PMC8353930

[74] Gilleron J,Zeigerer A.Image-based analysis of lipid nanoparticle-mediated siRNA delivery, intracellular trafficking and endosomal escape.Nat Biotechnol2013;31:638-46

[75] Sato Y,Hashiba K.Different kinetics for the hepatic uptake of lipid nanoparticles between the apolipoprotein E/low density lipoprotein receptor and the N-acetyl-d-galactosamine/asialoglycoprotein receptor pathway.J Control Release2020;322:217-26

[76] Kamaly N,Valencia PM,Farokhzad OC.Targeted polymeric therapeutic nanoparticles: design, development and clinical translation.Chem Soc Rev2012;41:2971-3010 PMCID:PMC3684255

[77] Rai R,Badea I.Polymeric nanoparticles in gene therapy: new avenues of design and optimization for delivery applications.Polymers2019;11:745 PMCID:PMC6523186

[78] Sung YK.Recent advances in polymeric drug delivery systems.Biomater Res2020;24:12 PMCID:PMC7285724

[79] Ke L,Wu Y.Polymeric nonviral gene delivery systems for cancer immunotherapy.Adv Ther2020;3:1900213

[80] Aqil F,Jeyabalan J.Milk exosomes - natural nanoparticles for siRNA delivery.Cancer Lett2019;449:186-95

[81] Liang Y,Wang L.Self-crosslinkable chitosan-hyaluronic acid dialdehyde nanoparticles for CD44-targeted siRNA delivery to treat bladder cancer.Bioact Mater2021;6:433-46 PMCID:PMC7490593

[82] Höbel S,Gaillard PJ.Targeted CRM197-PEG-PEI/siRNA complexes for therapeutic RNAi in glioblastoma.Pharmaceuticals2011;4:1591-606 PMCID:PMC4060103

[83] Pandey AP.Polyethylenimine: a versatile, multifunctional non-viral vector for nucleic acid delivery.Mater Sci Eng C Mater Biol Appl2016;68:904-18

[84] Shi YC,Yin C.C/EBPα inhibits hepatocellular carcinoma by reducing Notch3/Hes1/p27 cascades.Dig Liver Dis2013;45:844-51

[85] Voutila J,Roberts TC.Development and mechanism of small activating RNA targeting CEBPA, a novel therapeutic in clinical trials for liver cancer.Mol Ther2017;25:2705-14 PMCID:PMC5768526

[86] Sarker D,Meyer T.MTL-CEBPA, a small activating RNA therapeutic upregulating C/EBP-α, in patients with advanced liver cancer: a first-in-human, multicenter, open-label, phase I trial.Clin Cancer Res2020;26:3936-46

[87] Schaub FX,Berger AC.Cancer Genome Atlas NetworkPan-cancer alterations of the MYC oncogene and its proximal network across the cancer genome atlas.Cell Syst2018;6:282-300.e2 PMCID:PMC5892207

[88] Liu F,Zhang Z.MYC in liver cancer: mechanisms and targeted therapy opportunities.Oncogene2023;42:3303-18

[89] Liu X.Targeting polo-like kinases: a promising therapeutic approach for cancer treatment.Transl Oncol2015;8:185-95 PMCID:PMC4486469

[90] Semple SC,Robbins M.Abstract 2829: preclinical characterization of TKM-080301, a lipid nanoparticle formulation of a small interfering RNA directed against polo-like kinase 1.Cancer Res2011;71:2829-2829

[91] El Dika I,Yong WP.An open-label, multicenter, Phase I, dose escalation study with phase ii expansion cohort to determine the safety, pharmacokinetics, and preliminary antitumor activity of intravenous TKM-080301 in subjects with advanced hepatocellular carcinoma.Oncologist2019;24:747-e218 PMCID:PMC6656521

[92] Cervantes A,Tabernero J.Phase I dose-escalation study of ALN-VSP02, a novel RNAi therapeutic for solid tumors with liver involvement.JCO2011;29:3025

[93] Zhang L,Tang L.MicroRNA-34 family: a potential tumor suppressor and therapeutic candidate in cancer.J Exp Clin Cancer Res2019;38:53 PMCID:PMC6360685

[94] Hong DS,Borad M.Phase 1 study of MRX34, a liposomal miR-34a mimic, in patients with advanced solid tumours.Br J Cancer2020;122:1630-7 PMCID:PMC7251107

[95] Hu Z,Allesøe RL.Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma.Nat Med2021;27:515-25 PMCID:PMC8273876

[96] Weber JS,Khattak A.Individualised neoantigen therapy mRNA-4157 (V940) plus pembrolizumab versus pembrolizumab monotherapy in resected melanoma (KEYNOTE-942): a randomised, phase 2b study.Lancet2024;403:632-44

[97] Rodriguez-rivera II,Ciotti R.A phase 1/2 open-label study to evaluate the safety, tolerability, pharmacokinetics, pharmacodynamics, and preliminary antitumor activity of OTX-2002 as a single agent and in combination with standard of care in patients with hepatocellular carcinoma and other solid tumor types known for association with the MYC oncogene (MYCHELANGELO I).JCO2023;41:TPS627-TPS627

[98] Oliver SE,Marin M.The advisory committee on immunization practices' interim recommendation for use of Pfizer-BioNTech COVID-19 vaccine - United States, December 2020.MMWR Morb Mortal Wkly Rep2020;69:1922-4 PMCID:PMC7745957

[99] Ledford H.Moderna COVID vaccine becomes second to get US authorization.Nature2020;Online ahead of print

[100] Childs-Disney JL,Gibaut QMR,Batey RT.Targeting RNA structures with small molecules.Nat Rev Drug Discov2022;21:736-62 PMCID:PMC9360655

[101] Falese JP,Hargrove AE.Targeting RNA with small molecules: from fundamental principles towards the clinic.Chem Soc Rev2021;50:2224-43 PMCID:PMC8018613

[102] Winkle M,Fabbri M.Noncoding RNA therapeutics - challenges and potential solutions.Nat Rev Drug Discov2021;20:629-51 PMCID:PMC8212082

[103] Chi X,Papoian T.Safety of antisense oligonucleotide and siRNA-based therapeutics.Drug Discov Today2017;22:823-33