The sorafenib resistance-related gene signature predicts prognosis and indicates immune activity in hepatocellular carcinoma

References

• Sayiner M, Golabi P, Younossi ZM. Disease burden of hepatocellular carcinoma: A global perspective. Dig Dis Sci. 2019;64(4):910–917. doi: 10.1007/s10620-019-05537-2
   PubMed Web of Science ®Google Scholar
• Riquelme E, Zhang Y, Zhang L, et al. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell. 2019;178(4):795–806.e12. doi: 10.1016/j.cell.2019.07.008
   PubMed Web of Science ®Google Scholar
• Huang A, Yang XR, Chung WY, et al. Targeted therapy for hepatocellular carcinoma. Signal Transduct Target Ther. 2020;5(1):146. doi: 10.1038/s41392-020-00264-x
   PubMed Web of Science ®Google Scholar
• Adhikari S, Bhattacharya A, Adhikary S, et al. The paradigm of drug resistance in cancer: an epigenetic perspective. Biosci Rep. 2022;42(4):BSR20211812. doi: 10.1042/BSR20211812
   PubMed Web of Science ®Google Scholar
• Ikeda M, Shimizu S, Sato T, et al. Sorafenib plus hepatic arterial infusion chemotherapy with cisplatin versus sorafenib for advanced hepatocellular carcinoma: randomized phase II trial. Ann Oncol. 2016;27(11):2090–2096. doi: 10.1093/annonc/mdw323
   PubMed Web of Science ®Google Scholar
• Bruix J, Gores GJ, Mazzaferro V. Hepatocellular carcinoma: clinical frontiers and perspectives. Gut. 2014;63(5):844–855. doi: 10.1136/gutjnl-2013-306627
   PubMed Web of Science ®Google Scholar
• Pinter M, Peck-Radosavljevic M. Review article: systemic treatment of hepatocellular carcinoma. Aliment Pharmacol Ther. 2018;48(6):598–609. doi: 10.1111/apt.14913
   PubMed Web of Science ®Google Scholar
• Liu L, Cao Y, Chen C, et al. Sorafenib blocks the RAF/MEK/ERK pathway, inhibits tumor angiogenesis, and induces tumor cell apoptosis in hepatocellular carcinoma model PLC/PRF/5. Cancer Res. 2006;66(24):11851–11858. doi: 10.1158/0008-5472.CAN-06-1377
   PubMed Web of Science ®Google Scholar
• Wei L, Lee D, Law CT, et al. Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for sorafenib resistance in HCC. Nat Commun. 2019;10(1):4681. doi: 10.1038/s41467-019-12606-7
   PubMed Web of Science ®Google Scholar
• Peng L, Chen Y, Ou Q, et al. LncRNA MIAT correlates with immune infiltrates and drug reactions in hepatocellular carcinoma. Int Immunopharmacol. 2020;89(A):107071. doi: 10.1016/j.intimp.2020.107071
   PubMedGoogle Scholar
• Shrestha R, Prithviraj P, Bridle KR, et al. Combined inhibition of TGF-β1-induced EMT and PD-L1 silencing resensitizes hepatocellular carcinoma to sorafenib treatment. J Clin Med. 2021;10(9):1889. doi: 10.3390/jcm10091889
   PubMed Web of Science ®Google Scholar
• Tian X, Yan T, Liu F, et al. Link of sorafenib resistance with the tumor microenvironment in hepatocellular carcinoma: mechanistic insights. Front Pharmacol. 2022;13:991052. doi: 10.3389/fphar.2022.991052
   PubMed Web of Science ®Google Scholar
• Hinshaw DC, Shevde LA. The tumor microenvironment innately modulates cancer progression. Cancer Res. 2019;79(18):4557–4566. doi: 10.1158/0008-5472.CAN-18-3962
   PubMed Web of Science ®Google Scholar
• Binnewies M, Roberts EW, Kersten K, et al. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med. 2018;24(5):541–550. doi: 10.1038/s41591-018-0014-x
   PubMed Web of Science ®Google Scholar
• Rowshanravan B, Halliday N, Sansom DM. CTLA-4: a moving target in immunotherapy. Blood. 2018;131(1):58–67. doi: 10.1182/blood-2017-06-741033
   PubMed Web of Science ®Google Scholar
• Han Y, Liu D, Li L. PD-1/PD-L1 pathway: current researches in cancer. Am J Cancer Res. 2020;10(3):727–742.
   PubMed Web of Science ®Google Scholar
• Xu M, Zhao Z, Song J, et al. Interactions between interleukin-6 and myeloid-derived suppressor cells drive the chemoresistant phenotype of hepatocellular cancer. Exp Cell Res. 2017;351(2):142–149. doi: 10.1016/j.yexcr.2017.01.008
   PubMed Web of Science ®Google Scholar
• Zhou SL, Zhou ZJ, Hu ZQ, et al. Tumor-associated neutrophils recruit macrophages and T-regulatory cells to promote progression of hepatocellular carcinoma and resistance to sorafenib. Gastroenterology. 2016;150(7):1646–1658.e17. doi: 10.1053/j.gastro.2016.02.040
   PubMed Web of Science ®Google Scholar
• Kao KJ, Chang K, Hsu H, et al. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization. BMC Cancer. 2011;11(1): (143. doi: 10.1186/1471-2407-11-143
   PubMedGoogle Scholar
• Pinyol R, Montal R, Bassaganyas L, et al. Molecular predictors of prevention of recurrence in HCC with sorafenib as adjuvant treatment and prognostic factors in the phase 3 STORM trial. Gut. 2019;68(6):1065–1075. doi: 10.1136/gutjnl-2018-316408
   PubMed Web of Science ®Google Scholar
• Regan-Fendt K, Li D, Reyes R, et al. Transcriptomics-based drug repurposing approach identifies novel drugs against sorafenib-resistant hepatocellular carcinoma. Cancers (Basel). 2020;12(10):2730. doi: 10.3390/cancers12102730
   PubMed Web of Science ®Google Scholar
• Engebretsen S, Bohlin J. Statistical predictions with glmnet. Clin Epigenetics. 2019;11(1):123. doi: 10.1186/s13148-019-0730-1
   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. doi: 10.1093/bioinformatics/btq170
   PubMed Web of Science ®Google Scholar
• Hänzelmann S, Castelo R, Guinney J, et al. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinf. 2013;14(1):7. doi: 10.1186/1471-2105-14-7
   PubMed Web of Science ®Google Scholar
• Liberzon A, Birger C, Thorvaldsdóttir H, et al. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi: 10.1016/j.cels.2015.12.004
   PubMed Web of Science ®Google Scholar
• Yu G. Gene ontology semantic similarity analysis using GOSemSim. Methods Mol Biol. 2020;2117:207–215.
   PubMedGoogle Scholar
• Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30. doi: 10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS A J Integr Biol. 2012;16(5):284–287. doi: 10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Liang L, Yu J, Li J, et al. Integration of scRNA-seq and bulk RNA-seq to analyse the heterogeneity of ovarian cancer immune cells and establish a molecular risk model. Front Oncol Model [J]. 2021;11:711020. doi: 10.3389/fonc.2021.711020
   PubMed Web of Science ®Google Scholar
• Geeleher P, Cox N, Huang RS. pRrophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One. 2014;9(9):e107468. doi: 10.1371/journal.pone.0107468
   PubMed Web of Science ®Google Scholar
• Lu J, Yu C, Bao Q, et al. Identification and analysis of necroptosis-associated signatures for prognostic and immune microenvironment evaluation in hepatocellular carcinoma. Front Immunol. 2022;13:973649. doi: 10.3389/fimmu.2022.973649
   PubMed Web of Science ®Google Scholar
• Mikami D, Kobayashi M, Uwada J, et al. AR420626, a selective agonist of GPR41/FFA3, suppresses growth of hepatocellular carcinoma cells by inducing apoptosis via HDAC inhibition. Ther Adv Med Oncol. 2020;12:Ar.420626. doi: 10.1177/1758835920913432
   PubMed Web of Science ®Google Scholar
• Shen X, Hu B, Xu J, et al. The m6A methylation landscape stratifies hepatocellular carcinoma into 3 subtypes with distinct metabolic characteristics. Cancer Biol Med. 2020;17(4):937–952. doi: 10.20892/j.issn.2095-3941.2020.0402
   PubMed Web of Science ®Google Scholar
• He Q, Yang J, Jin Y. Immune infiltration and clinical significance analyses of the coagulation-related genes in hepatocellular carcinoma. Brief Bioinform. 2022;23(4). doi: 10.1093/bib/bbac291
   Web of Science ®Google Scholar
• Dong W, Xie Y, Huang H. Prognostic value of cancer-associated fibroblast-related gene signatures in hepatocellular carcinoma. Front Endocrinol. 2022;13:884777. doi: 10.3389/fendo.2022.884777
   PubMed Web of Science ®Google Scholar
• Min J, Feng Q, Liao W, et al. Retracted: IFITM3 promotes hepatocellular carcinoma invasion and metastasis by regulating MMP9 through p38/MAPK signaling. FEBS Open Bio. 2018;8(8):1299–1311. doi: 10.1002/2211-5463.12479
   PubMed Web of Science ®Google Scholar
• Min J, Hu J, Luo C, et al. IFITM3 upregulates c-myc expression to promote hepatocellular carcinoma proliferation via the ERK1/2 signalling pathway. Biosci Trends. 2020;13(6):523–529. doi: 10.5582/bst.2019.01289
   PubMed Web of Science ®Google Scholar
• Liu L, Liu Z, Gao J, et al. CD8+ T cell trajectory subtypes decode tumor heterogeneity and provide treatment recommendations for hepatocellular carcinoma. Front Immunol. 2022;13:964190. doi: 10.3389/fimmu.2022.964190
   PubMed Web of Science ®Google Scholar
• Peng S, Du T, Wu W, et al. Decreased expression of serine protease inhibitor family G1 (SERPING1) in prostate cancer can help distinguish high-risk prostate cancer and predicts malignant progression. Urol Oncol. 2018;36(8):.e366.1–.e3699. doi: 10.1016/j.urolonc.2018.05.021
   Web of Science ®Google Scholar
• Yan L, Gong YZ, Shao MN, et al. Distinct diagnostic and prognostic values of γ-aminobutyric acid type a receptor family genes in patients with colon adenocarcinoma. Oncol Lett. 2020;20(1):275–291. doi: 10.3892/ol.2020.11573
   PubMed Web of Science ®Google Scholar
• Ibrahim AA, Schmithals C, Kowarz E, et al. Hypoxia causes downregulation of dicer in hepatocellular carcinoma, which is required for upregulation of hypoxia-inducible factor 1α and epithelial-mesenchymal transition. Clin Cancer Res. 2017;23(14):3896–3905. doi: 10.1158/1078-0432.CCR-16-1762
   PubMed Web of Science ®Google Scholar
• Wei T, Lin R, Fu X, et al. Epigenetic regulation of the DNMT1/MT1G/KLF4/CA9 axis synergises the anticancer effects of sorafenib in hepatocellular carcinoma. Pharmacol Res. 2022;180:106244. doi: 10.1016/j.phrs.2022.106244
   PubMed Web of Science ®Google Scholar
• Carbajo-Pescador S, Martín-Renedo J, García-Palomo A, et al. Changes in the expression of melatonin receptors induced by melatonin treatment in hepatocarcinoma HepG2 cells. J Pineal Res. 2009;47(4):330–338. doi: 10.1111/j.1600-079X.2009.00719.x
   PubMed Web of Science ®Google Scholar
• García-Irigoyen O, Latasa MU, Carotti S, et al. Matrix metalloproteinase 10 contributes to hepatocarcinogenesis in a novel crosstalk with the stromal derived factor 1/C-X-C chemokine receptor 4 axis. Hepatology. 2015;62(1):166–178. doi: 10.1002/hep.27798
   PubMed Web of Science ®Google Scholar
• Luo YD, Zhang J, Fang L, et al. FBXW10 promotes hepatocarcinogenesis in male patients and mice. Carcinogenesis. 2020;41(5):689–698. doi: 10.1093/carcin/bgz138
   PubMed Web of Science ®Google Scholar
• Beck M, Schirmacher P, Singer S. Alterations of the nuclear transport system in hepatocellular carcinoma – new basis for therapeutic strategies. J Hepatol. 2017;67(5):1051–1061. doi: 10.1016/j.jhep.2017.06.021
   PubMed Web of Science ®Google Scholar
• Lee HL, Chien YC, Wang HL, et al. Analysis of MUC6 genetic variants on the clinicopathologic characteristics of patients with hepatocellular carcinoma. J Cancer. 2022;13(11):3251–3257. doi: 10.7150/jca.75754
   PubMed Web of Science ®Google Scholar
• Gabrilovich DI, Nagaraj S. Myeloid-derived suppressor cells as regulators of the immune system. Nat Rev Immunol. 2009;9(3):162–174. doi: 10.1038/nri2506
   PubMed Web of Science ®Google Scholar
• Highfill SL, Cui Y, Giles AJ, et al. Disruption of CXCR2-mediated MDSC tumor trafficking enhances anti-PD1 efficacy. Sci Transl Med. 2014;6(237):237ra67. doi: 10.1126/scitranslmed.3007974
   PubMed Web of Science ®Google Scholar
• Liu S, Tang Q, Huang J, et al. Prognostic analysis of tumor mutation burden and immune infiltration in hepatocellular carcinoma based on TCGA data. Aging. 2021;13(8):11257–11280. doi: 10.18632/aging.202811
   PubMedGoogle Scholar
• Guo CL, Yang HC, Yang XH, et al. Associations between infiltrating lymphocyte subsets and hepatocellular carcinoma. Asian Pac J Cancer Prev. 2012;13(11):5909–5913. doi: 10.7314/APJCP.2012.13.11.5909
   PubMedGoogle Scholar
• Schaller J, Agudo J. Metastatic colonization: escaping immune surveillance. Cancers (Basel). 2020;12(11):3385. doi: 10.3390/cancers12113385
   PubMed Web of Science ®Google Scholar
• Jiménez-Sánchez A, Memon D, Pourpe S, et al. Heterogeneous tumor-immune microenvironments among differentially growing metastases in an ovarian cancer patient. JIMéNEZ-Sánchez A Cell. 2017;170(5):927–38.e20. doi: 10.1016/j.cell.2017.07.025
   Google Scholar