N6-Methyladenine-Related Signature for Immune Microenvironment and Response to Immunotherapy in Hepatocellular Carcinoma

References

• Sung H, Ferlay J, Siegel RL, et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin. 2021;71(3):209–249.
   PubMed Web of Science ®Google Scholar
• El-Khoueiry AB, Sangro B, Yau T, et al. Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, Phase 1/2 dose escalation and expansion trial. Lancet. 2017;389(10088):2492–2502.
   PubMed Web of Science ®Google Scholar
• Pitt JM, Vetizou M, Daillere R, et al. Resistance Mechanisms to Immune-Checkpoint Blockade in Cancer: tumor-Intrinsic and -Extrinsic Factors. Immunity. 2016;44(6):1255–1269.
   PubMed Web of Science ®Google Scholar
• Llovet JM, Castet F, Heikenwalder M, et al. Immunotherapies for hepatocellular carcinoma. Nat Rev Clin Oncol. 2021.
   PubMed Web of Science ®Google Scholar
• Marin JJG, Romero MR, Herraez E, et al. Mechanisms of Pharmacoresistance in Hepatocellular Carcinoma: new Drugs but Old Problems. Semin Liver Dis. 2021;1:374.
   Google Scholar
• Tumeh PC, Harview CL, Yearley JH, et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014;515(7528):568–571.
   PubMed Web of Science ®Google Scholar
• Dong ZY, Wu SP, Liao RQ, Huang SM, Wu YL. Potential biomarker for checkpoint blockade immunotherapy and treatment strategy. Tumour Biol. 2016;37(4):4251–4261.
   PubMedGoogle Scholar
• Desrosiers R, Friderici K, Rottman F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc Natl Acad Sci U S A. 1974;71(10):3971–3975.
   PubMed Web of Science ®Google Scholar
• Wang S, Chai P, Jia R, Jia R. Novel insights on m(6)A RNA methylation in tumorigenesis: a double-edged sword. Mol Cancer. 2018;17(1):101.
   PubMed Web of Science ®Google Scholar
• Liu ZX, Li LM, Sun HL, Liu SM. Link Between m6A Modification and Cancers. Front Bioeng Biotechnol. 2018;6:89.
   PubMed Web of Science ®Google Scholar
• Davalos V, Blanco S, Esteller M. SnapShot: messenger RNA Modifications. Cell. 2018;174(2):498–498 e491.
   PubMed Web of Science ®Google Scholar
• He L, Li H, Wu A, Peng Y, Shu G, Yin G. Functions of N6-methyladenosine and its role in cancer. Mol Cancer. 2019;18(1):176.
   PubMed Web of Science ®Google Scholar
• Li H, Su Q, Li B, et al. High expression of WTAP leads to poor prognosis of gastric cancer by influencing tumour-associated T lymphocyte infiltration. J Cell Mol Med. 2020;24(8):4452–4465.
   PubMed Web of Science ®Google Scholar
• Xu F, Chen JX, Yang XB, et al. Analysis of Lung Adenocarcinoma Subtypes Based on Immune Signatures Identifies Clinical Implications for Cancer Therapy. Mol Ther Oncolytics. 2020;17:241–249.
   PubMed Web of Science ®Google Scholar
• Zhang B, Wu Q, Li B, Wang D, Wang L, Zhou YL. m(6)A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer. Mol Cancer. 2020;19(1):53.
   PubMed Web of Science ®Google Scholar
• Fang Q, Chen H. The significance of m6A RNA methylation regulators in predicting the prognosis and clinical course of HBV-related hepatocellular carcinoma. Molecular med. 2020;26(1):60.
   PubMed Web of Science ®Google Scholar
• Fu Y, Dominissini D, Rechavi G, He C. Gene expression regulation mediated through reversible m(6)A RNA methylation. Nat Rev Genet. 2014;15(5):293–306.
   PubMed Web of Science ®Google Scholar
• Dai D, Wang H, Zhu L, Jin H, Wang X. N6-methyladenosine links RNA metabolism to cancer progression. Cell Death Dis. 2018;9(2):124.
   PubMed Web of Science ®Google Scholar
• Chen XY, Zhang J, Zhu JS. The role of m(6)A RNA methylation in human cancer. Mol Cancer. 2019;18(1):103.
   PubMed Web of Science ®Google Scholar
• Lan Q, Liu PY, Haase J, Bell JL, Huttelmaier S, Liu T. The Critical Role of RNA m(6)A Methylation in Cancer. Cancer Res. 2019;79(7):1285–1292.
   PubMed Web of Science ®Google Scholar
• Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573.
   PubMed Web of Science ®Google Scholar
• Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Charoentong P, Finotello F, Angelova M, et al. Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Rep. 2017;18(1):248–262.
   PubMed Web of Science ®Google Scholar
• Newman AM, Steen CB, Liu CL, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37(7):773–782.
   PubMed Web of Science ®Google Scholar
• Shankavaram UT, Varma S, Kane D, et al. CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics. 2009;10:277.
   PubMed Web of Science ®Google Scholar
• Reinhold WC, Sunshine M, Liu H, et al. CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res. 2012;72(14):3499–3511.
   PubMed Web of Science ®Google Scholar
• Angell H, Galon J. From the immune contexture to the Immunoscore: the role of prognostic and predictive immune markers in cancer. Curr Opin Immunol. 2013;25(2):261–267.
   PubMed Web of Science ®Google Scholar
• Tang X, Shu Z, Zhang W, et al. Clinical significance of the immune cell landscape in hepatocellular carcinoma patients with different degrees of fibrosis. Ann Transl Med. 2019;7(20):528.
   PubMed Web of Science ®Google Scholar
• Zhang F, Ruan X, Ma J, et al. DGCR8/ZFAT-AS1 Promotes CDX2 Transcription in a PRC2 Complex-Dependent Manner to Facilitate the Malignant Biological Behavior of Glioma Cells. Mol Ther. 2020;28(2):613–630.
   PubMed Web of Science ®Google Scholar
• Sun L, Yu S, Xu H, et al. FHL2 interacts with EGFR to promote glioblastoma growth. Oncogene. 2018;37(10):1386–1398.
   PubMed Web of Science ®Google Scholar
• Zhou Z, Zhang J, Xu C, et al. An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer. EBioMedicine. 2021;65:103271.
   PubMed Web of Science ®Google Scholar
• Khan FS, Ali I, Afridi UK, Ishtiaq M, Mehmood R. Epigenetic mechanisms regulating the development of hepatocellular carcinoma and their promise for therapeutics. Hepatol Int. 2017;11(1):45–53.
   PubMed Web of Science ®Google Scholar
• Li Z, Li F, Peng Y, Fang J, Zhou J. Identification of three m6A-related mRNAs signature and risk score for the prognostication of hepatocellular carcinoma. Cancer Med. 2020;9(5):1877–1889.
   PubMed Web of Science ®Google Scholar
• Zhu B, Gong Y, Shen L, et al. Total Panax notoginseng saponin inhibits vascular smooth muscle cell proliferation and migration and intimal hyperplasia by regulating WTAP/p16 signals via m(6)A modulation. Biomed Pharmacother. 2020;124:109935.
   PubMed Web of Science ®Google Scholar
• Zhu ZM, Huo FC, Pei DS. Function and evolution of RNA N6-methyladenosine modification. Int J Biol Sci. 2020;16(11):1929–1940.
   PubMed Web of Science ®Google Scholar
• Lin Y, Wei X, Jian Z, Zhang X. METTL3 expression is associated with glycolysis metabolism and sensitivity to glycolytic stress in hepatocellular carcinoma. Cancer Med. 2020;9(8):2859–2867.
   PubMed Web of Science ®Google Scholar
• Zhong L, Liao D, Zhang M, et al. YTHDF2 suppresses cell proliferation and growth via destabilizing the EGFR mRNA in hepatocellular carcinoma. Cancer Lett. 2019;442:252–261.
   PubMed Web of Science ®Google Scholar
• Han D, Liu J, Chen C, et al. Anti-tumour immunity controlled through mRNA m(6)A methylation and YTHDF1 in dendritic cells. Nature. 2019;566(7743):270–274.
   PubMed Web of Science ®Google Scholar
• Wang H, Hu X, Huang M, et al. Mettl3-mediated mRNA m(6)A methylation promotes dendritic cell activation. Nat Commun. 2019;10(1):1898.
   PubMed Web of Science ®Google Scholar
• Altorki NK, Markowitz GJ, Gao D, et al. The lung microenvironment: an important regulator of tumour growth and metastasis. Nat Rev Cancer. 2019;19(1):9–31.
   PubMed Web of Science ®Google Scholar
• Cacho-Diaz B, Garcia-Botello DR, Wegman-Ostrosky T, Reyes-Soto G, Ortiz-Sanchez E, Herrera-Montalvo LA. Tumor microenvironment differences between primary tumor and brain metastases. J Transl Med. 2020;18(1):1.
   PubMed Web of Science ®Google Scholar
• Finkin S, Yuan D, Stein I, et al. Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma. Nat Immunol. 2015;16(12):1235–1244.
   PubMed Web of Science ®Google Scholar
• Hackl H, Charoentong P, Finotello F, Trajanoski Z. Computational genomics tools for dissecting tumour-immune cell interactions. Nat Rev Genet. 2016;17(8):441–458.
   PubMed Web of Science ®Google Scholar
• Ding W, Xu X, Qian Y, et al. Prognostic value of tumor-infiltrating lymphocytes in hepatocellular carcinoma: a meta-analysis. Medicine. 2018;97(50):e13301.
   PubMed Web of Science ®Google Scholar
• Jiang P, Gu S, Pan D, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018;24(10):1550–1558.
   PubMed Web of Science ®Google Scholar
• Qu S, Chen Z, Liu B, Liu J, Wang H. N6-methyladenine-related genes affect biological behavior and the prognosis of glioma. Cancer Med. 2021;10(1):98–108.
   PubMed Web of Science ®Google Scholar
• Herbst RS, Soria JC, Kowanetz M, et al. Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature. 2014;515(7528):563–567.
   PubMed Web of Science ®Google Scholar
• Ji RR, Chasalow SD, Wang L, et al. An immune-active tumor microenvironment favors clinical response to ipilimumab. Cancer Immunol Immunother. 2012;61(7):1019–1031.
   PubMed Web of Science ®Google Scholar
• Shi F, Shi M, Zeng Z, et al. PD-1 and PD-L1 upregulation promotes CD8(+) T-cell apoptosis and postoperative recurrence in hepatocellular carcinoma patients. Int J Cancer. 2011;128(4):887–896.
   PubMed Web of Science ®Google Scholar
• Gao Q, Wang XY, Qiu SJ, et al. Overexpression of PD-L1 significantly associates with tumor aggressiveness and postoperative recurrence in human hepatocellular carcinoma. Clin Cancer Res. 2009;15(3):971–979.
   PubMed Web of Science ®Google Scholar
• Cariani E, Missale G. Immune landscape of hepatocellular carcinoma microenvironment: implications for prognosis and therapeutic applications. Liver Int. 2019;39(9):1608–1621.
   PubMed Web of Science ®Google Scholar
• Mantovani A, Marchesi F, Malesci A, Laghi L, Allavena P. Tumour-associated macrophages as treatment targets in oncology. Nat Rev Clin Oncol. 2017;14(7):399–416.
   PubMed Web of Science ®Google Scholar
• Xu Q, Hu Y, Chen S, et al. Immunological Significance of Prognostic DNA Methylation Sites in Hepatocellular Carcinoma. Front Mol Biosci. 2021;8:683240.
   PubMed Web of Science ®Google Scholar
• Shen S, Yan J, Zhang Y, Dong Z, Xing J, He Y. N6-methyladenosine (m6A)-mediated messenger RNA signatures and the tumor immune microenvironment can predict the prognosis of hepatocellular carcinoma. Ann Transl Med. 2021;9(1):59.
   PubMed Web of Science ®Google Scholar
• Mantovani A, Allavena P, Sica A, Balkwill F. Cancer-related inflammation. Nature. 2008;454(7203):436–444.
   PubMed Web of Science ®Google Scholar
• Salvagno C, Ciampricotti M, Tuit S, et al. Therapeutic targeting of macrophages enhances chemotherapy efficacy by unleashing type I interferon response. Nat Cell Biol. 2019;21(4):511–521.
   PubMed Web of Science ®Google Scholar
• Mok S, Koya RC, Tsui C, et al. Inhibition of CSF-1 receptor improves the antitumor efficacy of adoptive cell transfer immunotherapy. Cancer Res. 2014;74(1):153–161.
   PubMed Web of Science ®Google Scholar
• Rodriguez CP, Wu QV, Voutsinas J, et al. A Phase II Trial of Pembrolizumab and Vorinostat in Recurrent Metastatic Head and Neck Squamous Cell Carcinomas and Salivary Gland Cancer. Clin Cancer Res. 2020;26(4):837–845.
   PubMed Web of Science ®Google Scholar
• Liu X, Jiang J, Liao YP, et al. Combination Chemo-Immunotherapy for Pancreatic Cancer Using the Immunogenic Effects of an Irinotecan Silicasome Nanocarrier Plus Anti-PD-1. Adv Sci. 2021;8(6):2002147.
   Web of Science ®Google Scholar