Identification of prognostic biomarkers of breast cancer based on the immune-related gene module

References

• Siegel RL, Miller KD, Fuchs HE, et al. Cancer statistics, 2022. CA Cancer J Clin. 2022;72(1):1–12.
   Web of Science ®Google Scholar
• Koren S, Bentires-Alj M. Breast tumor heterogeneity: source of fitness, hurdle for therapy. Mol Cell. 2015;60(4):537–546.
   PubMed Web of Science ®Google Scholar
• Peart O. Metastatic breast cancer. Radiol Technol. 2017;88(5):519M–539M.
   PubMed Web of Science ®Google Scholar
• Liu N, Johnson KJ, Ma CX. Male breast cancer: an updated surveillance, epidemiology, and end results data analysis. Clin Breast Cancer. 2018;18(5):e997–e1002.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang Z. The history and advances in cancer immunotherapy: understanding the characteristics of tumor-infiltrating immune cells and their therapeutic implications. Cell Mol Immunol. 2020;17(8):807–821.
   PubMed Web of Science ®Google Scholar
• Mirgayazova R, Khadiullina R, Mingaleeva R, et al. Novel isatin-based activator of p53 transcriptional functions in tumor cells. Mol Biol Res Commun. 2019;8(3):119–128.
   PubMed Web of Science ®Google Scholar
• Harao M, Forget M-A, Roszik J, et al. 4-1BB-enhanced expansion of CD8+ TIL from triple-negative breast cancer unveils mutation-specific CD8+ T cells. Cancer Immunol Res. 2017;5(6):439–445.
   PubMed Web of Science ®Google Scholar
• Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33(1):1–22.
   PubMed Web of Science ®Google Scholar
• Lê S, Josse J, Husson F. FactoMineR: an R package for multivariate analysis. J Stat Softw. 2008;25(1):1–18.
   Web of Science ®Google Scholar
• Blanche P, Dartigues JF, Jacqmin-Gadda H. Estimating and comparing time-dependent areas under receiver operating characteristic curves for censored event times with competing risks. Stat Med. 2013;32(30):5381–5397.
   PubMed Web of Science ®Google Scholar
• Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 2013;14:7.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457.
   PubMed Web of Science ®Google Scholar
• Skidmore ZL, Wagner AH, Lesurf R, et al. GenVisR: genomic visualizations in R. Bioinformatics. 2016;32(19):3012–3014.
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545–15550.
   PubMed Web of Science ®Google Scholar
• Cerami E, Gao J, Dogrusoz U, et al. The cBio Cancer Genomics Portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401–404.
   PubMed Web of Science ®Google Scholar
• Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269)pl:pl1.
   PubMed Web of Science ®Google Scholar
• Huang C, Liu Z, Xiao L, et al. Clinical significance of serum CA125, CA19-9, CA72-4, and fibrinogen-to-lymphocyte ratio in gastric cancer with peritoneal dissemination. Front Oncol. 2019;9:1159.
   PubMed Web of Science ®Google Scholar
• Disis ML, Stanton SE. Immunotherapy in breast cancer: an introduction. Breast. 2018;37:196–199.
   PubMed Web of Science ®Google Scholar
• Cassetta L, Pollard JW. Repolarizing macrophages improves breast cancer therapy. Cell Res. 2017;27(8):963–964.
   PubMed Web of Science ®Google Scholar
• Su S, Liao J, Liu J, et al. Blocking the recruitment of naive CD4+ T cells reverses immunosuppression in breast cancer. Cell Res. 2017;27(4):461–482.
   PubMed Web of Science ®Google Scholar
• Carreras J, Lopez-Guillermo A, Kikuti YY, et al. High TNFRSF14 and low BTLA are associated with poor prognosis in follicular lymphoma and in diffuse large B-cell lymphoma transformation. J Clin Exp Hematop. 2019;59(1):1–16.
   PubMed Web of Science ®Google Scholar
• Choi E-K, Kim W-K, Sul O-J, et al. TNFRSF14 deficiency protects against ovariectomy-induced adipose tissue inflammation. J Endocrinol. 2014;220(1):25–33.
   PubMed Web of Science ®Google Scholar
• Zhu YD, Lu MY. Increased expression of TNFRSF14 indicates good prognosis and inhibits bladder cancer proliferation by promoting apoptosis. Mol Med Rep. 2018;18(3):3403–3410.
   PubMed Web of Science ®Google Scholar
• Steinberg MW, Cheung TC, Ware CF. The signaling networks of the herpesvirus entry mediator (TNFRSF14) in immune regulation. Immunol Rev. 2011;244(1):169–187.
   PubMedGoogle Scholar
• Fan Z, Yu P, Wang Y, et al. NK-cell activation by LIGHT triggers tumor-specific CD8+ T-cell immunity to reject established tumors. Blood. 2006;107(4):1342–1351.
   PubMed Web of Science ®Google Scholar
• Hayden MS, Ghosh S. Signaling to NF-κB. Genes Dev. 2004;18(18):2195–2224.
   PubMed Web of Science ®Google Scholar
• DiDonato JA, Mercurio F, Karin M. NF-κB and the link between inflammation and cancer. Immunol Rev. 2012;246(1):379–400.
   PubMed Web of Science ®Google Scholar
• Li Y, Zhao X, Liu Q, et al. Bioinformatics reveal macrophages marker genes signature in breast cancer to predict prognosis. Ann Med. 2021;53(1):1019–1031.
   PubMed Web of Science ®Google Scholar
• Liu B, Sun L, Liu Q, et al. A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. Cancer Cell. 2015;27(3):370–381.
   PubMed Web of Science ®Google Scholar
• Zheng CY, Seabold GK, Horak M, et al. MAGUKs, synaptic development, and synaptic plasticity. Neuroscientist. 2011;17(5):493–512.
   PubMed Web of Science ®Google Scholar
• Müller BM, Kistner U, Kindler S, et al. SAP102, a novel postsynaptic protein that interacts with NMDA receptor complexes in vivo. Neuron. 1996;17(2):255–265.
   PubMed Web of Science ®Google Scholar
• Liu J, Li P, Wang R, et al. High expression of DLG3 is associated with decreased survival from breast cancer. Clin Exp Pharmacol Physiol. 2019;46(10):937–943.
   PubMed Web of Science ®Google Scholar
• Liu B, Xu Y, Zhang L, et al. Hypermethylation of DLG3 promoter upregulates RAC1 and activates the PI3K/AKT signaling pathway to promote breast cancer progression. Evid Based Complement Alternat Med. 2021;2021:8428130.
   PubMed Web of Science ®Google Scholar
• Ghislat G, Cheema AS, Baudoin E, et al. NF-κB-dependent IRF1 activation programs cDC1 dendritic cells to drive antitumor immunity. Sci Immunol. 2021;6(61):eabg3570.
   PubMed Web of Science ®Google Scholar
• Kimbung S, Chang C-Y, Bendahl P-O, et al. Impact of 27-hydroxylase (CYP27A1) and 27-hydroxycholesterol in breast cancer. Endocr Relat Cancer. 2017;24(7):339–349.
   PubMed Web of Science ®Google Scholar
• Inasu M, Bendahl P-O, Fernö M, et al. High CYP27A1 expression is a biomarker of favorable prognosis in premenopausal patients with estrogen receptor positive primary breast cancer. NPJ Breast Cancer. 2021;7(1):127.
   PubMed Web of Science ®Google Scholar
• Farhood B, Najafi M, Mortezaee K. CD8+ cytotoxic T lymphocytes in cancer immunotherapy: a review. J Cell Physiol. 2019;234(6):8509–8521.
   PubMed Web of Science ®Google Scholar
• Xie G, Dong H, Liang Y, et al. CAR-NK cells: a promising cellular immunotherapy for cancer. EBioMedicine. 2020;59:102975.
   PubMed Web of Science ®Google Scholar
• André P, Denis C, Soulas C, et al. Anti-NKG2A mAb is a checkpoint inhibitor that promotes anti-tumor immunity by unleashing both T and NK cells. Cell. 2018;175(7):1731–1743.
   PubMed Web of Science ®Google Scholar
• Tan Y, Sun R, Liu L, et al. Tumor suppressor DRD2 facilitates M1 macrophages and restricts NF-κB signaling to trigger pyroptosis in breast cancer. Theranostics. 2021;11(11):5214–5231.
   PubMed Web of Science ®Google Scholar
• Tu D, Dou J, Wang M, et al. M2 macrophages contribute to cell proliferation and migration of breast cancer. Cell Biol Int. 2021;45(4):831–838.
   PubMed Web of Science ®Google Scholar