Prognostic Model and Tumor Immune Microenvironment Analysis of Complement-Related Genes in Gastric Cancer

References

• Dalakas MC, Alexopoulos H, Spaeth PJ. Complement in neurological disorders and emerging complement-targeted therapeutics. Nat Rev Neurol. 2020;16(11):601–617. doi:10.1038/s41582-020-0400-0
   PubMed Web of Science ®Google Scholar
• Mastellos DC, Ricklin D, Lambris JD. Clinical promise of next-generation complement therapeutics. Nat Rev Drug Discov. 2019;18(9):707–729. doi:10.1038/s41573-019-0031-6
   PubMed Web of Science ®Google Scholar
• Peng Q, Li K, Sacks SH, Zhou W. The role of anaphylatoxins C3a and C5a in regulating innate and adaptive immune responses. Inflamm Allergy Drug Targets. 2009;8(3):236–246. doi:10.2174/187152809788681038
   PubMedGoogle Scholar
• Pio R, Ajona D, Lambris JD. Complement inhibition in cancer therapy. Semin Immunol. 2013;25(1):54–64. doi:10.1016/j.smim.2013.04.001
   PubMed Web of Science ®Google Scholar
• Ajona D, Ortiz-Espinosa S, Moreno H, et al. A combined PD-1/C5a blockade synergistically protects against lung cancer growth and metastasis. Cancer Discov. 2017;7(7):694–703. doi:10.1158/2159-8290.CD-16-1184
   PubMed Web of Science ®Google Scholar
• Zha H, Han X, Zhu Y, et al. Blocking C5aR signaling promotes the anti-tumor efficacy of PD-1/PD-L1 blockade. Oncoimmunology. 2017;6(10):e1349587. doi:10.1080/2162402X.2017.1349587
   PubMed Web of Science ®Google Scholar
• Macor P, Capolla S, Tedesco F. Complement as a biological tool to control tumor growth. Front Immunol. 2018;9:2203. doi:10.3389/fimmu.2018.02203
   PubMed Web of Science ®Google Scholar
• Chen J, Sun ZH, Chen LY, et al. C5aR deficiency attenuates the breast cancer development via the p38/p21 axis. Aging. 2020;12(14):14285–14299. doi:10.18632/aging.103468
   PubMedGoogle Scholar
• Piao C, Zhang WM, Li TT, et al. Complement 5a stimulates macrophage polarization and contributes to tumor metastases of colon cancer. Exp Cell Res. 2018;366(2):127–138. doi:10.1016/j.yexcr.2018.03.009
   PubMed Web of Science ®Google Scholar
• Chen J, Wu W, Zhen C, et al. Expression and clinical significance of complement C3, complement C4b1 and apolipoprotein E in pancreatic cancer. Oncol Lett. 2013;6(1):43–48. doi:10.3892/ol.2013.1326
   PubMed Web of Science ®Google Scholar
• Jackson WD, Gulino A, Fossati-Jimack L, et al. C3 drives inflammatory skin carcinogenesis independently of C5. J Invest Dermatol. 2021;141(2):404–414 e406. doi:10.1016/j.jid.2020.06.025
   PubMed Web of Science ®Google Scholar
• Bareke H, Akbuga J. Complement system’s role in cancer and its therapeutic potential in ovarian cancer. Scand J Immunol. 2018;88(1):e12672. doi:10.1111/sji.12672
   PubMed Web of Science ®Google Scholar
• Kleczko EK, Kwak JW, Schenk EL, Nemenoff RA. Targeting the complement pathway as a therapeutic strategy in lung cancer. Front Immunol. 2019;10:954. doi:10.3389/fimmu.2019.00954
   PubMed Web of Science ®Google Scholar
• 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. doi:10.3322/caac.21660
   PubMed Web of Science ®Google Scholar
• Xie J, Fu L, Jin L. Immunotherapy of gastric cancer: past, future perspective and challenges. Pathol Res Pract. 2021;218:153322. doi:10.1016/j.prp.2020.153322
   PubMed Web of Science ®Google Scholar
• Alkasalias T, Moyano-Galceran L, Arsenian-Henriksson M, Lehti K. Fibroblasts in the tumor microenvironment: shield or spear? Int J Mol Sci. 2018;19(5):1532. doi:10.3390/ijms19051532
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013;41(Database issue):D991–995. doi:10.1093/nar/gks1193
   PubMed Web of Science ®Google Scholar
• Blum A, Wang P, Zenklusen JC. SnapShot: TCGA-analyzed tumors. Cell. 2018;173(2):530. doi:10.1016/j.cell.2018.03.059
   PubMed Web of Science ®Google Scholar
• Zhao Y, Li MC, Konate MM, et al. TPM, FPKM, or normalized counts? A comparative study of quantification measures for the analysis of RNA-seq data from the NCI patient-derived models repository. J Transl Med. 2021;19(1):269. doi:10.1186/s12967-021-02936-w
   PubMed Web of Science ®Google Scholar
• Mounir M, Lucchetta M, Silva TC, et al. New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. PLoS Comput Biol. 2019;15(3):e1006701. doi:10.1371/journal.pcbi.1006701
   PubMed Web of Science ®Google Scholar
• Zhang H, Meltzer P, Davis S. RCircos: an R package for Circos 2D track plots. BMC Bioinform. 2013;14:244. doi:10.1186/1471-2105-14-244
   PubMed Web of Science ®Google Scholar
• Angly FE, Fields CJ, Tyson GW. The bio-community Perl toolkit for microbial ecology. Bioinformatics. 2014;30(13):1926–1927. doi:10.1093/bioinformatics/btu130
   PubMed Web of Science ®Google Scholar
• Giorgi FM, Ceraolo C, Mercatelli D. The R Language: an engine for bioinformatics and data science. Life. 2022;12(5):648.
   PubMedGoogle Scholar
• Steenwyk JL, Rokas A. ggpubfigs: colorblind-friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures. Microbiol Resour Announc. 2021;10(44):e0087121. doi:10.1128/MRA.00871-21
   PubMed Web of Science ®Google Scholar
• Yang L, Qu Q, Hao Z, Sha K, Li Z, Li S. Powerful identification of large quantitative trait loci using genome-wide R/glmnet-based regression. J Hered. 2022;113(4):472–478. doi:10.1093/jhered/esac006
   PubMed Web of Science ®Google Scholar
• Liu TT, Li R, Huo C, et al. Identification of CDK2-related immune Forecast model and ceRNA in lung adenocarcinoma, a pan-cancer analysis. Front Cell Dev Biol. 2021;9:682002. doi:10.3389/fcell.2021.682002
   PubMed Web of Science ®Google Scholar
• Canzler S, Hackermuller J. multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. BMC Bioinform. 2020;21(1):561. doi:10.1186/s12859-020-03910-x
   PubMed Web of Science ®Google Scholar
• Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. 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
• 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
• Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 2018;34(13):i555–i564. doi:10.1093/bioinformatics/bty271
   PubMed Web of Science ®Google Scholar
• Suwazono S, Arao H. A newly developed free software tool set for averaging electroencephalogram implemented in the Perl programming language. Heliyon. 2020;6(11):e05580. doi:10.1016/j.heliyon.2020.e05580
   PubMed Web of Science ®Google Scholar
• Pio R, Corrales L, Lambris JD. The role of complement in tumor growth. Adv Exp Med Biol. 2014;772:229–262. doi:10.1007/978-1-4614-5915-6_11
   PubMed Web of Science ®Google Scholar
• Bao D, Zhang C, Li L, et al. Integrative analysis of complement system to prognosis and immune infiltrating in colon cancer and gastric cancer. Front Oncol. 2020;10:553297. doi:10.3389/fonc.2020.553297
   PubMed Web of Science ®Google Scholar
• Riihila P, Nissinen L, Knuutila J, Rahmati Nezhad P, Viiklepp K, Kahari VM. Complement system in cutaneous squamous cell carcinoma. Int J Mol Sci. 2019;20(14):3550. doi:10.3390/ijms20143550
   PubMed Web of Science ®Google Scholar
• Xu B, Wang L, Zhan H, et al. Investigation of the mechanism of complement system in diabetic nephropathy via bioinformatics analysis. J Diabetes Res. 2021;2021:5546199. doi:10.1155/2021/5546199
   PubMed Web of Science ®Google Scholar
• Fu J, Li K, Zhang W, et al. Large-scale public data reuse to model immunotherapy response and resistance. Genome Med. 2020;12(1):21. doi:10.1186/s13073-020-0721-z
   PubMed Web of Science ®Google Scholar
• Kolev M, Markiewski MM. Targeting complement-mediated immunoregulation for cancer immunotherapy. Semin Immunol. 2018;37:85–97. doi:10.1016/j.smim.2018.02.003
   PubMed Web of Science ®Google Scholar
• Reis ES, Mastellos DC, Hajishengallis G, Lambris JD. New insights into the immune functions of complement. Nat Rev Immunol. 2019;19(8):503–516. doi:10.1038/s41577-019-0168-x
   PubMed Web of Science ®Google Scholar
• Zappasodi R, Merghoub T, Wolchok JD. Emerging concepts for immune checkpoint blockade-based combination therapies. Cancer Cell. 2018;33(4):581–598. doi:10.1016/j.ccell.2018.03.005
   PubMed Web of Science ®Google Scholar
• Zhao Q, Cao L, Guan L, et al. Immunotherapy for gastric cancer: dilemmas and prospect. Brief Funct Genomics. 2019;18(2):107–112. doi:10.1093/bfgp/ely019
   PubMed Web of Science ®Google Scholar
• Hu JY, Wang Y, Tong XM, Yang T. When to consider logistic LASSO regression in multivariate analysis? Eur J Surg Oncol. 2021;47(8):2206. doi:10.1016/j.ejso.2021.04.011
   PubMed Web of Science ®Google Scholar
• Guler H, Guler EO. Mixed Lasso estimator for stochastic restricted regression models. J Appl Stat. 2021;48(13–15):2795–2808. doi:10.1080/02664763.2021.1922614
   PubMed Web of Science ®Google Scholar
• Olingy CE, Dinh HQ, Hedrick CC. Monocyte heterogeneity and functions in cancer. J Leukoc Biol. 2019;106(2):309–322. doi:10.1002/JLB.4RI0818-311R
   PubMed Web of Science ®Google Scholar
• Brossart P, Wirths S, Brugger W, Kanz L. Dendritic cells in cancer vaccines. Exp Hematol. 2001;29(11):1247–1255. doi:10.1016/S0301-472X(01)00730-5
   PubMed Web of Science ®Google Scholar
• Wang L, Lu Q, Gao W, Yu S. Recent advancement on development of drug-induced macrophage polarization in control of human diseases. Life Sci. 2021;284:119914. doi:10.1016/j.lfs.2021.119914
   PubMed Web of Science ®Google Scholar
• Yunna C, Mengru H, Lei W, Weidong C. Macrophage M1/M2 polarization. Eur J Pharmacol. 2020;877:173090. doi:10.1016/j.ejphar.2020.173090
   PubMed Web of Science ®Google Scholar
• Najafi M, Hashemi Goradel N, Farhood B, et al. Macrophage polarity in cancer: a review. J Cell Biochem. 2019;120(3):2756–2765. doi:10.1002/jcb.27646
   PubMed Web of Science ®Google Scholar
• Grisaru-Tal S, Itan M, Klion AD, Munitz A. A new Dawn for eosinophils in the tumour microenvironment. Nat Rev Cancer. 2020;20(10):594–607. doi:10.1038/s41568-020-0283-9
   PubMed Web of Science ®Google Scholar
• Borst J, Ahrends T, Babala N, Melief CJM, Kastenmuller W. CD4(+) T cell help in cancer immunology and immunotherapy. Nat Rev Immunol. 2018;18(10):635–647. doi:10.1038/s41577-018-0044-0
   PubMed Web of Science ®Google Scholar
• King C, Tangye SG, Mackay CR. T follicular helper (TFH) cells in normal and dysregulated immune responses. Annu Rev Immunol. 2008;26:741–766. doi:10.1146/annurev.immunol.26.021607.090344
   PubMed Web of Science ®Google Scholar
• Lawal B, Lin LC, Lee JC, et al. Multi-omics data analysis of gene expressions and alterations, cancer-associated fibroblast and immune infiltrations, reveals the onco-immune prognostic relevance of STAT3/CDK2/4/6 in human malignancies. Cancers. 2021;13(5):954. doi:10.3390/cancers13050954
   PubMed Web of Science ®Google Scholar
• Vinay DS, Ryan EP, Pawelec G, et al. Immune evasion in cancer: mechanistic basis and therapeutic strategies. Semin Cancer Biol. 2015;35(Suppl):S185–S198. doi:10.1016/j.semcancer.2015.03.004
   PubMed Web of Science ®Google Scholar
• Jhunjhunwala S, Hammer C, Delamarre L. Antigen presentation in cancer: insights into tumour immunogenicity and immune evasion. Nat Rev Cancer. 2021;21(5):298–312. doi:10.1038/s41568-021-00339-z
   PubMed Web of Science ®Google Scholar
• Kaderbhai C, Tharin Z, Ghiringhelli F. The role of molecular profiling to predict the response to immune checkpoint inhibitors in lung cancer. Cancers. 2019;11(2):201. doi:10.3390/cancers11020201
   PubMed Web of Science ®Google Scholar