Construction of a Prognostic Model for Hepatocellular Carcinoma Based on Immunoautophagy-Related Genes and Tumor Microenvironment

References

• Schmidt N, Thimme R. Role of immunity in pathogenesis and treatment of hepatocellular carcinoma. Dig Dis. 2016;34(4):429–437. doi:10.1159/000444558
   PubMed Web of Science ®Google Scholar
• Lei X, Lei Y, Li J-K, et al. Immune cells within the tumor microenvironment: biological functions and roles in cancer immunotherapy. Cancer Lett. 2020;470:126–133. doi:10.1016/j.canlet.2019.11.009
   PubMed Web of Science ®Google Scholar
• Li Z, Chen G, Cai Z, et al. Profiling of hepatocellular carcinoma neoantigens reveals immune microenvironment and clonal evolution related patterns. Chin J Cancer Res. 2021;33(3):364–378. doi:10.21147/j.issn.1000-9604.2021.03.08
   PubMed Web of Science ®Google Scholar
• Hilmi M, Neuzillet C, Calderaro J, Lafdil F, Pawlotsky J-M, Rousseau B. Angiogenesis and immune checkpoint inhibitors as therapies for hepatocellular carcinoma: current knowledge and future research directions. J Immunother Cancer. 2019;7(1):333. doi:10.1186/s40425-019-0824-5
   PubMed Web of Science ®Google Scholar
• Liu Y, Zhang X, Zhang J, Tan J, Li J, Song Z. Development and validation of a combined ferroptosis and immune prognostic classifier for hepatocellular carcinoma. Front Cell Dev Biol. 2020;8:1716. doi:10.3389/fcell.2020.596679
   Web of Science ®Google Scholar
• Jiang X, Overholtzer M, Thompson CB. Autophagy in cellular metabolism and cancer. J Clin Invest. 2015;125(1):47–54. doi:10.1172/JCI73942
   PubMed Web of Science ®Google Scholar
• Yorimitsu T, Klionsky DJ. Autophagy: molecular machinery for self-eating. Cell Death Differ. 2005;12(Suppl 2):1542–1552. doi:10.1038/sj.cdd.4401765
   PubMed Web of Science ®Google Scholar
• Wu Y-X, Jin S-H, Cui J. Autophagy and Immune Tolerance. Adv Exp Med Biol. 2019;1206:635–665. doi:10.1007/978-981-15-0602-4_28
   PubMed Web of Science ®Google Scholar
• Zhong Z, Sanchez-Lopez E, Karin M. Autophagy, inflammation, and immunity: a troika governing cancer and its treatment. Cell. 2016;166(2):288–298. doi:10.1016/j.cell.2016.05.051
   PubMed Web of Science ®Google Scholar
• Jiao S, Li G, Zhang D, Xu Y, Liu J, Li G. Anatomic versus non-anatomic resection for hepatocellular carcinoma, do we have an answer? A meta-analysis. Int J Surg. 2020;80:243–255. doi:10.1016/j.ijsu.2020.05.008
   PubMed Web of Science ®Google Scholar
• Wang Z, Zhu J, Liu Y, et al. Development and validation of a novel immune-related prognostic model in hepatocellular carcinoma. J Transl Med. 2020;18(1):67. doi:10.1186/s12967-020-02255-6
   PubMed Web of Science ®Google Scholar
• Xu D, Wang Y, Zhou K, et al. Development and validation of a novel 8 immune gene prognostic signature based on the immune expression profile for hepatocellular carcinoma. Onco Targets Ther. 2020;13:8125–8140. doi:10.2147/OTT.S263047
   PubMed Web of Science ®Google Scholar
• Fang Q, Chen H. Development of a novel autophagy-related prognostic signature and nomogram for hepatocellular carcinoma. Front Oncol. 2020;10:591356. doi:10.3389/fonc.2020.591356
   PubMed Web of Science ®Google Scholar
• Yang W, Niu L, Zhao X, et al. Development and validation of a survival model based on autophagy-associated genes for predicting prognosis of hepatocellular carcinoma. Am J Transl Res. 2020;12(10):6705–6722.
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Andorf S, Gomes L, et al. ImmPort: disseminating data to the public for the future of immunology. Immunol Res. 2014;58(2–3):234–239. doi:10.1007/s12026-014-8516-1
   PubMed Web of Science ®Google Scholar
• Xu J, Dai S, Yuan Y, Xiao Q, Ding K, Prognostic A. Model for colon cancer patients based on eight signature autophagy genes. Front Cell Dev Biol. 2020;8:602174. doi:10.3389/fcell.2020.602174
   PubMed Web of Science ®Google Scholar
• Tian Z, Meng L, Long X, et al. Identification and validation of an immune-related gene-based prognostic index for bladder cancer. Am J Transl Res. 2020;12(9):5188–5204.
   PubMed Web of Science ®Google Scholar
• Jia Y, Chen Y, Liu J. Prognosis-predictive signature and nomogram based on autophagy-related long non-coding RNAs for hepatocellular carcinoma. Front Genet. 2020;11:608668. doi:10.3389/fgene.2020.608668
   PubMed Web of Science ®Google Scholar
• Meng L, Tian Z, Long X, et al. Prognostic autophagy model based on and expression in patients with renal cancer: independent datasets-based study. Am J Transl Res. 2020;12(11):7475–7489.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Miao T, Si Q, Wei Y, Fan R, Wang J, An X. Identification and validation of seven prognostic long non-coding RNAs in oral squamous cell carcinoma. Oncol Lett. 2020;20(1):939–946. doi:10.3892/ol.2020.11603
   PubMed Web of Science ®Google Scholar
• Yao Y, Zhang T, Qi L, et al. Identification of four genes as prognosis signatures in lung adenocarcinoma microenvironment. Pharmgenomics Pers Med. 2021;14:15–26. doi:10.2147/PGPM.S283414
   PubMed Web of Science ®Google Scholar
• Huang R, Liao X, Li Q. Identification and validation of potential prognostic gene biomarkers for predicting survival in patients with acute myeloid leukemia. Onco Targets Ther. 2017;10:5243–5254. doi:10.2147/OTT.S147717
   PubMed Web of Science ®Google Scholar
• Ma X, Zhang L, Huang D, et al. Quantitative radiomic biomarkers for discrimination between neuromyelitis optica spectrum disorder and multiple sclerosis. J Magn Reson Imaging. 2019;49(4):1113–1121. doi:10.1002/jmri.26287
   PubMed Web of Science ®Google Scholar
• Ma B, Shi R, Yang S, et al. DUSP4/MKP2 overexpression is associated with BRAF(V600E) mutation and aggressive behavior of papillary thyroid cancer. Onco Targets Ther. 2016;9:2255–2263. doi:10.2147/OTT.S103554
   PubMed Web of Science ®Google Scholar
• Wang Y, Zou Y, Zhang Y, Li C. Developing a risk scoring system based on immune-related lncRNAs for patients with gastric cancer. Biosci Rep. 2020;41(1):BSR20202203. doi:10.1042/BSR20202203
   Web of Science ®Google Scholar
• Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 2020;48(W1):W509–W514. doi:10.1093/nar/gkaa407
   PubMed Web of Science ®Google Scholar
• Rhodes DR, Kalyana-Sundaram S, Mahavisno V, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007;9(2):166–180. doi:10.1593/neo.07112
   PubMed Web of Science ®Google Scholar
• Wu Z, Zhang Y, Chen X, Tan W, He L, Peng L. Characterization of the prognostic values of the CXCR1-7 in clear cell renal cell carcinoma (ccRCC) microenvironment. Front Mol Biosci. 2020;7:601206. doi:10.3389/fmolb.2020.601206
   PubMed Web of Science ®Google Scholar
• White E, Mehnert JM, Chan CS. Autophagy, metabolism, and cancer. Clin Cancer Res. 2015;21(22):5037–5046. doi:10.1158/1078-0432.CCR-15-0490
   PubMed Web of Science ®Google Scholar
• Degenhardt K, Mathew R, Beaudoin B, et al. Autophagy promotes tumor cell survival and restricts necrosis, inflammation, and tumorigenesis. Cancer Cell. 2006;10(1):51–64. doi:10.1016/j.ccr.2006.06.001
   PubMed Web of Science ®Google Scholar
• Cui J, Shen H-M, Lim LHK. The role of autophagy in liver cancer: crosstalk in signaling pathways and potential therapeutic targets. Pharmaceuticals (Basel). 2020;13(12):432. doi:10.3390/ph13120432
   PubMedGoogle Scholar
• Yu S, Wang Y, Jing L, et al. Autophagy in the “inflammation-carcinogenesis” pathway of liver and HCC immunotherapy. Cancer Lett. 2017;411:82–89. doi:10.1016/j.canlet.2017.09.049
   PubMed Web of Science ®Google Scholar
• D’Alesio C, Bellese G, Gagliani MC, et al. The chromodomain helicase CHD4 regulates ERBB2 signaling pathway and autophagy in ERBB2 breast cancer cells. Biol Open. 2019;8(4):bio038323. doi:10.1242/bio.038323
   PubMed Web of Science ®Google Scholar
• Hanyu X, Lanyue L, Miao D, Wentao F, Cangran C, Hui S. Effect of ganoderma applanatum polysaccharides on MAPK/ERK pathway affecting autophagy in breast cancer MCF-7 cells. Int J Biol Macromol. 2020;146:353–362. doi:10.1016/j.ijbiomac.2020.01.010
   PubMed Web of Science ®Google Scholar
• Liu F, Chang L, Hu J. Activating transcription factor 6 regulated cell growth, migration and inhibited cell apoptosis and autophagy via MAPK pathway in cervical cancer. J Reprod Immunol. 2020;139:103120. doi:10.1016/j.jri.2020.103120
   PubMed Web of Science ®Google Scholar
• Song M, Zhang H, Chen Z, et al. Shikonin reduces hepatic fibrosis by inducing apoptosis and inhibiting autophagy via the platelet-activating factor-mitogen-activated protein kinase axis. Exp Ther Med. 2021;21(1):28. doi:10.3892/etm.2020.9460
   PubMed Web of Science ®Google Scholar
• Llovet JM, Zucman-Rossi J, Pikarsky E, et al. Hepatocellular carcinoma. Nat Rev Dis Primers. 2016;2:16018. doi:10.1038/nrdp.2016.18
   PubMed Web of Science ®Google Scholar
• Tang B, Zhu J, Li J, et al. The ferroptosis and iron-metabolism signature robustly predicts clinical diagnosis, prognosis and immune microenvironment for hepatocellular carcinoma. Cell Commun Signal. 2020;18(1):174. doi:10.1186/s12964-020-00663-1
   PubMed Web of Science ®Google Scholar
• Vogiatzi F, Brandt DT, Schneikert J, et al. Mutant p53 promotes tumor progression and metastasis by the endoplasmic reticulum UDPase ENTPD5. Proc Natl Acad Sci U S A. 2016;113(52):E8433–E8442. doi:10.1073/pnas.1612711114
   PubMed Web of Science ®Google Scholar
• Chen Y, Ma D, Wang X, et al. Calnexin impairs the antitumor immunity of CD4 and CD8 T cells. Cancer Immunol Res. 2019;7(1):123–135. doi:10.1158/2326-6066.CIR-18-0124
   PubMed Web of Science ®Google Scholar
• Okayama A, Miyagi Y, Oshita F, et al. Proteomic analysis of proteins related to prognosis of lung adenocarcinoma. J Proteome Res. 2014;13(11):4686–4694. doi:10.1021/pr4012969
   PubMed Web of Science ®Google Scholar
• Kobayashi M, Nagashio R, Jiang S-X, et al. Calnexin is a novel sero-diagnostic marker for lung cancer. Lung Cancer. 2015;90(2):342–345. doi:10.1016/j.lungcan.2015.08.015
   PubMed Web of Science ®Google Scholar
• Ryan D, Carberry S, Murphy ÁC, et al. Calnexin, an ER stress-induced protein, is a prognostic marker and potential therapeutic target in colorectal cancer. J Transl Med. 2016;14(1):196. doi:10.1186/s12967-016-0948-z
   PubMed Web of Science ®Google Scholar
• Ros M, Nguyen AT, Chia J, et al. ER-resident oxidoreductases are glycosylated and trafficked to the cell surface to promote matrix degradation by tumour cells. Nat Cell Biol. 2020;22(11):1371–1381. doi:10.1038/s41556-020-00590-w
   PubMed Web of Science ®Google Scholar
• Wang X-Q, Bai H-M, Li S-T, et al. Knockdown of HDAC1 expression suppresses invasion and induces apoptosis in glioma cells. Oncotarget. 2017;8(29):48027–48040. doi:10.18632/oncotarget.18227
   PubMedGoogle Scholar
• Fritzsche FR, Weichert W, Röske A, et al. Class I histone deacetylases 1, 2 and 3 are highly expressed in renal cell cancer. BMC Cancer. 2008;8(1):381. doi:10.1186/1471-2407-8-381
   PubMed Web of Science ®Google Scholar
• Weichert W, Röske A, Gekeler V, et al. Histone deacetylases 1, 2 and 3 are highly expressed in prostate cancer and HDAC2 expression is associated with shorter PSA relapse time after radical prostatectomy. Br J Cancer. 2008;98(3):604–610. doi:10.1038/sj.bjc.6604199
   PubMed Web of Science ®Google Scholar
• Weichert W, Röske A, Niesporek S, et al. Class I histone deacetylase expression has independent prognostic impact in human colorectal cancer: specific role of class I histone deacetylases in vitro and in vivo. Clin Cancer Res. 2008;14(6):1669–1677. doi:10.1158/1078-0432.CCR-07-0990
   PubMed Web of Science ®Google Scholar
• Weichert W, Röske A, Gekeler V, et al. Association of patterns of class I histone deacetylase expression with patient prognosis in gastric cancer: a retrospective analysis. Lancet Oncol. 2008;9(2):139–148. doi:10.1016/S1470-2045(08)70004-4
   PubMed Web of Science ®Google Scholar
• Carew JS, Giles FJ, Nawrocki ST. Histone deacetylase inhibitors: mechanisms of cell death and promise in combination cancer therapy. Cancer Lett. 2008;269(1):7–17. doi:10.1016/j.canlet.2008.03.037
   PubMed Web of Science ®Google Scholar
• Thurn KT, Thomas S, Raha P, Qureshi I, Munster PN. Histone deacetylase regulation of ATM-mediated DNA damage signaling. Mol Cancer Ther. 2013;12(10):2078–2087. doi:10.1158/1535-7163.MCT-12-1242
   PubMed Web of Science ®Google Scholar
• Zhang L, Bu L, Hu J, et al. HDAC1 knockdown inhibits invasion and induces apoptosis in non-small cell lung cancer cells. Biol Chem. 2018;399(6):603–610. doi:10.1515/hsz-2017-0306
   PubMed Web of Science ®Google Scholar
• Yoo YG, Na TY, Seo HW, et al. Hepatitis B virus X protein induces the expression of MTA1 and HDAC1, which enhances hypoxia signaling in hepatocellular carcinoma cells. Oncogene. 2008;27(24):3405–3413. doi:10.1038/sj.onc.1211000
   PubMed Web of Science ®Google Scholar
• Ler SY, Leung CHW, Khin LW, et al. HDAC1 and HDAC2 independently predict mortality in hepatocellular carcinoma by a competing risk regression model in a Southeast Asian population. Oncol Rep. 2015;34(5):2238–2250. doi:10.3892/or.2015.4263
   PubMed Web of Science ®Google Scholar