Identifying Potential Gene Defect Patterns Related to COVID-19 Based on Pharmacological and Bioinformatics Analysis for Lung Adenocarcinoma

References

• Addeo A, Friedlaender A. Cancer and COVID-19: unmasking their ties. Cancer Treat Rev. 2020;88:102041. doi:10.1016/j.ctrv.2020.102041
   PubMed Web of Science ®Google Scholar
• Bakouny Z, Hawley JE, Choueiri TK, et al. COVID-19 and cancer: current challenges and perspectives. Cancer Cell. 2020;38(5):629–646. doi:10.1016/j.ccell.2020.09.018
   PubMed Web of Science ®Google Scholar
• Giannakoulis VG, Papoutsi E, Siempos II. Effect of cancer on clinical outcomes of patients with COVID-19: a meta-analysis of patient data. JCO Glob Oncol. 2020;6:799–808. doi:10.1200/GO.20.00225
   PubMedGoogle Scholar
• Kuderer NM, Choueiri TK, Shah DP, et al. Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study. Lancet. 2020;395(10241):1907–1918. doi:10.1016/S0140-6736(20)31187-9
   PubMed Web of Science ®Google Scholar
• Saini KS, Tagliamento M, Lambertini M, et al. Mortality in patients with cancer and coronavirus disease 2019: a systematic review and pooled analysis of 52 studies. Eur J Cancer. 2020;139:43–50. doi:10.1016/j.ejca.2020.08.011
   PubMed Web of Science ®Google Scholar
• Zhang H, Han H, He T, et al. Clinical characteristics and outcomes of COVID-19-infected cancer patients: a systematic review and meta-analysis. J Natl Cancer Inst. 2021;113(4):371–380. doi:10.1093/jnci/djaa168
   PubMedGoogle Scholar
• Liang W, Guan W, Chen R, et al. Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China. Lancet Oncol. 2020;21(3):335–337. doi:10.1016/S1470-2045(20)30096-6
   PubMed Web of Science ®Google Scholar
• Bade BC, Dela Cruz CS. Lung cancer 2020: epidemiology, etiology, and prevention. Clin Chest Med. 2020;41(1):1–24. doi:10.1016/j.ccm.2019.10.001
   PubMed Web of Science ®Google Scholar
• Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2021. CA Cancer J Clin. 2021;71(1):7–33. doi:10.3322/caac.21654
   PubMed Web of Science ®Google Scholar
• Passaro A, Bestvina C, Velez Velez M, Garassino MC, Garon E, Peters S. Severity of COVID-19 in patients with lung cancer: evidence and challenges. J Immunother Cancer. 2021;9(3):e002266. doi:10.1136/jitc-2020-002266
   PubMed Web of Science ®Google Scholar
• Dai M, Liu D, Liu M, et al. Patients with cancer appear more vulnerable to SARS-CoV-2: a multicenter study during the COVID-19 outbreak. Cancer Discov. 2020;10(6):783–791. doi:10.1158/2159-8290.CD-20-0422
   PubMed Web of Science ®Google Scholar
• Li Q, Wang H, Li X, et al. The role played by traditional Chinese medicine in preventing and treating COVID-19 in China. Front Med. 2020;14(5):681–688. doi:10.1007/s11684-020-0801-x
   PubMed Web of Science ®Google Scholar
• Ren JL, Zhang AH, Wang XJ. Traditional Chinese medicine for COVID-19 treatment. Pharmacol Res. 2020;155:104743. doi:10.1016/j.phrs.2020.104743
   PubMed Web of Science ®Google Scholar
• Zhao Z, Li Y, Zhou L, et al. Prevention and treatment of COVID-19 using traditional Chinese medicine: a review. Phytomedicine. 2021;85:153308. doi:10.1016/j.phymed.2020.153308
   PubMed Web of Science ®Google Scholar
• National Health Commission in China. TCM protocol in diagnosis and treatment protocol for COVID-19 (trial version 8). 2020. Available from: http://www.gov.cn/zhengce/zhengceku/2020-08/19/5535757/files/da89edf7cc9244fbb34ecf6c61df40bf.pdf. Accessed April 6, 2022.
   Google Scholar
• Wang Z, Yang L. Chinese herbal medicine: fighting SARS-CoV-2 infection on all fronts. J Ethnopharmacol. 2021;270:113869. doi:10.1016/j.jep.2021.113869
   PubMed Web of Science ®Google Scholar
• Yang L, Wang Z. Natural products, alone or in combination with FDA-approved drugs, to treat COVID-19 and lung cancer. Biomedicines. 2021;9(6):689. doi:10.3390/biomedicines9060689
   PubMed Web of Science ®Google Scholar
• Wang Z, Yang L. Turning the tide: natural products and natural-product-inspired chemicals as potential counters to SARS-CoV-2 infection. Front Pharmacol. 2020;11:1013. doi:10.3389/fphar.2020.01013
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. Curr Protocols Bioinform. 2014;47:8.13.11–24. doi:10.1002/0471250953.bi0813s47
   PubMedGoogle Scholar
• Liao Y, Wang J, Jaehnig EJ, Shi Z, Zhang B. WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 2019;47(W1):W199–w205. doi:10.1093/nar/gkz401
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Shahmoradgoli M, Martínez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612. doi:10.1038/ncomms3612
   PubMed Web of Science ®Google Scholar
• Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–259.
   PubMedGoogle Scholar
• Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213–219. doi:10.1038/nbt.2514
   PubMed Web of Science ®Google Scholar
• Barbie DA, Tamayo P, Boehm JS, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462(7269):108–112. doi:10.1038/nature08460
   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
• Roh W, Chen PL, Reuben A, et al. Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance. Sci Transl Med. 2017;9:379. doi:10.1126/scitranslmed.aah3560
   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
• Fabre J, Giustiniani J, Garbar C, et al. Targeting the tumor microenvironment: the protumor effects of IL-17 related to cancer type. Int J Mol Sci. 2016;17(9). doi:10.3390/ijms17091433
   PubMed Web of Science ®Google Scholar
• Kuen DS, Kim BS, Chung Y. IL-17-producing cells in tumor immunity: friends or foes? Immune Netw. 2020;20(1):e6. doi:10.4110/in.2020.20.e6
   PubMed Web of Science ®Google Scholar
• Huang Q, Han J, Fan J, et al. IL-17 induces EMT via Stat3 in lung adenocarcinoma. Am J Cancer Res. 2016;6(2):440–451.
   PubMed Web of Science ®Google Scholar
• Gu K, Li MM, Shen J, et al. Interleukin-17-induced EMT promotes lung cancer cell migration and invasion via NF-κB/ZEB1 signal pathway. Am J Cancer Res. 2015;5(3):1169–1179.
   PubMed Web of Science ®Google Scholar
• Landvik NE, Hart K, Skaug V, Stangeland LB, Haugen A, Zienolddiny S. A specific interleukin-1B haplotype correlates with high levels of IL1B mRNA in the lung and increased risk of non-small cell lung cancer. Carcinogenesis. 2009;30(7):1186–1192. doi:10.1093/carcin/bgp122
   PubMed Web of Science ®Google Scholar
• Matsubara E, Komohara Y, Shinchi Y, et al. CD163-positive cancer cells are a predictor of a worse clinical course in lung adenocarcinoma. Pathol Int. 2021;71(10):666–673. doi:10.1111/pin.13144
   PubMed Web of Science ®Google Scholar
• Kwiecień I, Polubiec-Kownacka M, Dziedzic D, Wołosz D, Rzepecki P, Domagała-Kulawik J. CD163 and CCR7 as markers for macrophage polarization in lung cancer microenvironment. Cent Eur J Immunol. 2019;44(4):395–402. doi:10.5114/ceji.2019.92795
   PubMed Web of Science ®Google Scholar
• Chung Y, Chang SH, Martinez GJ, et al. Critical regulation of early Th17 cell differentiation by interleukin-1 signaling. Immunity. 2009;30(4):576–587. doi:10.1016/j.immuni.2009.02.007
   PubMed Web of Science ®Google Scholar
• Chen J, Sun W, Zhang H, et al. Macrophages reprogrammed by lung cancer microparticles promote tumor development via release of IL-1β. Cell Mol Immunol. 2020;17(12):1233–1244. doi:10.1038/s41423-019-0313-2
   PubMed Web of Science ®Google Scholar
• Kong H, Wang Y, Zeng X, Wang Z, Wang H, Xie W. Differential expression of inflammasomes in lung cancer cell lines and tissues. Tumour Biol. 2015;36(10):7501–7513. doi:10.1007/s13277-015-3473-4
   PubMedGoogle Scholar
• Van Gorp H, Lamkanfi M. The emerging roles of inflammasome-dependent cytokines in cancer development. EMBO Rep. 2019;20(6). doi:10.15252/embr.201847575
   PubMed Web of Science ®Google Scholar
• Garon EB, Chih-Hsin Yang J, Dubinett SM. The role of interleukin 1β in the pathogenesis of lung cancer. JTO Clin Res Rep. 2020;1(1):100001. doi:10.1016/j.jtocrr.2020.100001
   PubMedGoogle Scholar
• He WT, Wan H, Hu L, et al. Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion. Cell Res. 2015;25(12):1285–1298. doi:10.1038/cr.2015.139
   PubMed Web of Science ®Google Scholar
• Cullen SP, Kearney CJ, Clancy DM, Martin SJ. Diverse activators of the NLRP3 inflammasome promote IL-1β secretion by triggering necrosis. Cell Rep. 2015;11(10):1535–1548. doi:10.1016/j.celrep.2015.05.003
   PubMed Web of Science ®Google Scholar
• Kaplanov I, Carmi Y, Kornetsky R, et al. Blocking IL-1β reverses the immunosuppression in mouse breast cancer and synergizes with anti-PD-1 for tumor abrogation. Proc Natl Acad Sci U S A. 2019;116(4):1361–1369. doi:10.1073/pnas.1812266115
   PubMed Web of Science ®Google Scholar