A programmed cell death-related gene signature to predict prognosis and therapeutic responses in liver hepatocellular carcinoma

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer J Clin. 2021;71(3):209–49.

Google Scholar 

Chidambaranathan-Reghupaty S, Fisher PB, Sarkar D. Hepatocellular carcinoma (HCC): epidemiology, etiology and molecular classification. Adv Cancer Res. 2021;149:1–61.

Article  PubMed  Google Scholar 

Yang S, Zhou Y, Zhang X, Wang L, Fu J, Zhao X, et al. The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma. BMC Bioinform. 2021;22(1):217.

Article  Google Scholar 

Shu X, Wang Q, Wu Q. The Eph/Ephrin system in hepatocellular carcinoma: functional roles and potential therapeutic targets. Oncologie. 2022;24(3):427–39.

Article  Google Scholar 

Song Y, Zhou B, Du X, Wang Y, Zhang J, Ai Y, et al. Folic acid (FA)-conjugated mesoporous silica nanoparticles combined with MRP-1 siRNA improves the suppressive effects of myricetin on non-small cell lung cancer (NSCLC). Biomed Pharmacother. 2020;125:109561.

Article  PubMed  Google Scholar 

Xie D-Y, Ren Z-G, Zhou J, Fan J, Gao Q. 2019 Chinese clinical guidelines for the management of hepatocellular carcinoma: updates and insights. Hepatobiliary Surg Nutr. 2020;9(4):452.

Article  PubMed  PubMed Central  Google Scholar 

Strasser A, Vaux DL. Cell death in the origin and treatment of cancer. Mol Cell. 2020;78(6):1045–54.

Article  PubMed  Google Scholar 

Wang Y, Zhang L, Zhou F. Cuproptosis: a new form of programmed cell death. Cell Mol Immunol. 2022;19(8):867–8.

Article  PubMed  PubMed Central  Google Scholar 

Djulbegovic MB, Uversky VN. Ferroptosis–an iron-and disorder-dependent programmed cell death. Int J Biol Macromol. 2019;135:1052–69.

Article  PubMed  Google Scholar 

Wang Y, Kanneganti T-D. From pyroptosis, apoptosis and necroptosis to PANoptosis: a mechanistic compendium of programmed cell death pathways. Comput Struct Biotechnol J. 2021;19:4641–57.

Article  PubMed  PubMed Central  Google Scholar 

Denton D, Kumar S. Autophagy-dependent cell death. Cell Death Differ. 2019;26(4):605–16.

Article  PubMed  Google Scholar 

Mishra AP, Salehi B, Sharifi-Rad M, Pezzani R, Kobarfard F, Sharifi-Rad J, et al. Programmed cell death, from a cancer perspective: an overview. Mol Diagn Ther. 2018;22:281–95.

Article  PubMed  Google Scholar 

Liu J, Hong M, Li Y, Chen D, Wu Y, Hu Y. Programmed cell death tunes tumor immunity. Front Immunol. 2022;13:847345.

Article  PubMed  PubMed Central  Google Scholar 

Pan S, Meng H, Fan T, Hao B, Song C, Li D, et al. Comprehensive analysis of programmed cell death signature in the prognosis, tumor microenvironment and drug sensitivity in lung adenocarcinoma. Front Genet. 2022. https://doi.org/10.3389/fgene.2022.900159.

Article  PubMed  PubMed Central  Google Scholar 

Zhang Y, He R, Lei X, Mao L, Jiang P, Ni C, et al. A novel pyroptosis-related signature for predicting prognosis and indicating immune microenvironment features in osteosarcoma. Front Genet. 2021;12:780780.

Article  PubMed  PubMed Central  Google Scholar 

Li Y, Song K, Zheng W. The cuproptosis-related long noncoding RNA signature predicts prognosis and immune cell infiltration in hepatocellular carcinoma. J Oncol. 2023. https://doi.org/10.1155/2023/9557690.

Article  PubMed  PubMed Central  Google Scholar 

Wang T, Yang Y, Sun T, Qiu H, Wang J, Ding C, et al. The pyroptosis-related long noncoding RNA signature predicts prognosis and indicates immunotherapeutic efficiency in hepatocellular carcinoma. Front Cell Dev Biol. 2022. https://doi.org/10.3389/fcell.2022.779269.

Article  PubMed  PubMed Central  Google Scholar 

Zou Y, Xie J, Zheng S, Liu W, Tang Y, Tian W, et al. Leveraging diverse cell-death patterns to predict the prognosis and drug sensitivity of triple-negative breast cancer patients after surgery. Int J Surg. 2022;107:106936.

Article  PubMed  Google Scholar 

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Yang T-HO, et al. The immune landscape of cancer. Immunity. 2018;48(4):812–30.

Article  PubMed  PubMed Central  Google Scholar 

Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–3.

Article  PubMed  PubMed Central  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl Acids Res. 2015;43(7):e47.

Article  PubMed  PubMed Central  Google Scholar 

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database hallmark gene set collection. Cell Syst. 2015;1(6):417–25.

Article  PubMed  PubMed Central  Google Scholar 

Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics A J Integr Biol. 2012;16(5):284–7.

Article  Google Scholar 

Engebretsen S, Bohlin J. Statistical predictions with glmnet. Clin Epigenet. 2019;11(1):123.

Article  Google Scholar 

Blanche P. TimeROC: Time-dependent ROC curve and AUC for censored survival data. R package version. 2015;2.

Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating immune cells with CIBERSORT. In: von Stechow Louise, editor. Cancer systems biology. New York: Springer; 2018. p. 243–59.

Chapter  Google Scholar 

Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17(1):218.

Article  PubMed  PubMed Central  Google Scholar 

Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, et al. TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells. Cancer Res. 2017;77(21):e108–10.

Article  PubMed  PubMed Central  Google Scholar 

Yeo JG, Wasser M, Kumar P, Pan L, Poh SL, Ally F, et al. The extended polydimensional immunome characterization (EPIC) web-based reference and discovery tool for cytometry data. Nat Biotechnol. 2020;38(6):679–84.

Article  PubMed  Google Scholar 

Hu F-F, Liu C-J, Liu L-L, Zhang Q, Guo A-Y. Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response. Brief Bioinform. 2021;22(3):176.

Article  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.

Article  ADS  PubMed  PubMed Central  Google Scholar 

Tomiyama T, Itoh S, Iseda N, Toshida K, Morinaga A, Yugawa K, et al. Myeloid-derived suppressor cell infiltration is associated with a poor prognosis in patients with hepatocellular carcinoma. Oncol Lett. 2022;23(3):1–9.

Article  Google Scholar 

Hu C-E, Gan J, Zhang R-D, Cheng Y-R, Huang G-J. Up-regulated myeloid-derived suppressor cell contributes to hepatocellular carcinoma development by impairing dendritic cell function. Scand J Gastroenterol. 2011;46(2):156–64.

Article  PubMed  Google Scholar 

He Q, Liu M, Huang W, Chen X, Zhang B, Zhang T, et al. IL-1β-Induced elevation of solute carrier family 7 member 11 promotes hepatocellular carcinoma metastasis through Up-regulating programmed death ligand 1 and colony-stimulating factor 1. Hepatology. 2021;74(6):3174–93.

Article  PubMed  Google Scholar 

Nishida N, Kudo M. Immune checkpoint blockade for the treatment of human hepatocellular carcinoma. Hepatol Res. 2018;48(8):622–34.

Article  PubMed  Google Scholar 

Fan Y, Mao R, Yang J. NF-kappaB and STAT3 signaling pathways collaboratively link inflammation to cancer. Protein Cell. 2013;4(3):176–85.

Article  PubMed  PubMed Central  Google Scholar 

Nunnery SE, Mayer IA. Targeting the PI3K/AKT/mTOR pathway in hormone-positive breast cancer. Drugs. 2020;80(16):1685–97.

Article  PubMed  PubMed Central  Google Scholar 

Chen X, Cubillos-Ruiz JR. Endoplasmic reticulum stress signals in the tumour and its microenvironment. Nat Rev Cancer. 2021;21(2):71–88.

Article  PubMed  Google Scholar 

Colombo M, Mirandola L, Chiriva-Internati M, Basile A, Locati M, Lesma E, et al. Cancer cells exploit notch signaling to redefine a supportive cytokine milieu. Front Immunol. 2018;9:1823.

Article  PubMed  PubMed Central  Google Scholar 

Jung HI, Jeong D, Ji S, Ahn TS, Bae SH, Chin S, et al. Overexpression of PD-L1 and PD-L2 is associated with poor prognosis in patients with hepatocellular carcinoma. Cancer Res Treat. 2017;49(1):246–54.

Article  PubMed  Google Scholar 

Hu J, Cao J, Topatana W, Juengpanich S, Li S, Zhang B, et al. Targeting mutant p53 for cancer therapy: direct and indirect strategies. J Hematol Oncol. 2021;14(1):157.

Article  PubMed  PubMed Central 

Comments (0)

No login
gif