102
Views
1
CrossRef citations to date
0
Altmetric
Anticancer Original Research Papers

Identification of T cell-related biomarkers for breast cancer based on weighted gene co-expression network analysis

Pages 298-306 | Received 20 Dec 2021, Accepted 29 Jun 2022, Published online: 13 Jul 2022

References

  • 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.
  • Maughan KL, Lutterbie MA, Ham PS. Treatment of breast cancer. Am Fam Physician. 2010;81(11):1339–1346.
  • Gu G, Dustin D, Fuqua SA. Targeted therapy for breast cancer and molecular mechanisms of resistance to treatment. Curr Opin Pharmacol. 2016;31:97–103.
  • Szostakowska M, Trębińska-Stryjewska A, Grzybowska EA, et al. Resistance to endocrine therapy in breast cancer: molecular mechanisms and future goals. Breast Cancer Res Treat. 2019;173(3):489–497.
  • Kunte S, Abraham J, Montero AJ. Novel HER2-targeted therapies for HER2-positive metastatic breast cancer. Cancer. 2020;126(19):4278–4288.
  • Yin L, Duan JJ, Bian XW, et al. Triple-negative breast cancer molecular subtyping and treatment progress. Breast Cancer Res. 2020;22(1):61.
  • 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.
  • Coulie PG, Van den Eynde BJ, van der Bruggen P, et al. Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy. Nat Rev Cancer. 2014;14(2):135–146.
  • Xie Q, Ding J, Chen Y. Role of CD8(+) T lymphocyte cells: interplay with stromal cells in tumor microenvironment. Acta Pharm Sin B. 2021;11(6):1365–1378.
  • Gu Y, Jin Y, Ding J, et al. Low absolute CD4(+) T cell counts in peripheral blood predict poor prognosis in patients with newly diagnosed multiple myeloma. Leuk Lymphoma. 2020;61(8):1869–1876.
  • Oshi M, Asaoka M, Tokumaru Y, et al. CD8 T cell score as a prognostic biomarker for triple negative breast cancer. Int J Mol Sci. 2020;21(18):6968.
  • Vihervuori H, Autere TA, Repo H, et al. Tumor-infiltrating lymphocytes and CD8(+) T cells predict survival of triple-negative breast cancer. J Cancer Res Clin Oncol. 2019;145(12):3105–3114.
  • Pantelidou C, Sonzogni O, De Oliveria Taveira M, et al. PARP inhibitor efficacy depends on CD8(+) T-cell recruitment via intratumoral STING pathway activation in BRCA-deficient models of triple-negative breast cancer. Cancer Discov. 2019;9(6):722–737.
  • Saint-Antoine MM, Singh A. Network inference in systems biology: recent developments, challenges, and applications. Curr Opin Biotechnol. 2020;63:89–98.
  • Oulas A, Minadakis G, Zachariou M, et al. Systems bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. Brief Bioinform. 2019;20(3):806–824.
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559.
  • Tian Z, He W, Tang J, et al. Identification of important modules and biomarkers in breast cancer based on WGCNA. Onco Targets Ther. 2020;13:6805–6817.
  • Wan Q, Tang J, Han Y, et al. Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma. Exp Eye Res. 2018;166:13–20.
  • Chen S, Yang D, Lei C, et al. Identification of crucial genes in abdominal aortic aneurysm by WGCNA. PeerJ. 2019;7:e7873.
  • Wang H, Liu J, Li J, et al. Identification of gene modules and hub genes in Colon adenocarcinoma associated with pathological stage based on WGCNA analysis. Cancer Genet. 2020;242:1–7.
  • Zhai X, Xue Q, Liu Q, et al. Colon cancer recurrenceassociated genes revealed by WGCNA coexpression network analysis. Mol Med Rep. 2017;16(5):6499–6505.
  • Sun S, Guo W, Wang Z, et al. Development and validation of an immune-related prognostic signature in lung adenocarcinoma. Cancer Med. 2020;9(16):5960–5975.
  • Yoshihara K, Shahmoradgoli M, Martinez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
  • Therneau T, Grambsch P. The Cox model. In: Modeling survival data: extending the Cox model. New York (NY): Springer; 2000. p. 39–77.
  • Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
  • Kanevskiy L, Erokhina S, Kobyzeva P, et al. Dimorphism of HLA-E and its disease association. Int J Mol Sci. 2019;20(21):5496.
  • Ravindranath MH, Filippone EJ, Devarajan A, et al. Enhancing natural killer and CD8(+) T cell-mediated anticancer cytotoxicity and proliferation of CD8(+) T cells with HLA-E monospecific monoclonal antibodies. Monoclon Antib Immunodiagn Immunother. 2019;38(2):38–59.
  • Baldwin KM, Ehrenberg PK, Geretz A, et al. HLA class II diversity in HIV-1 uninfected individuals from the placebo arm of the RV144 Thai vaccine efficacy trial. Tissue Antigens. 2015;85(2):117–126.
  • Lin J, Yu M, Xu X, et al. Identification of biomarkers related to CD8(+) T cell infiltration with gene co-expression network in clear cell renal cell carcinoma. Aging. 2020;12(4):3694–3712.
  • Tu J, Kuang Z, Xie X, et al. Prognostic and predictive value of a mRNA signature in peripheral T-cell lymphomas: a mRNA expression analysis. J Cell Mol Med. 2021;25(1):84–95.
  • Kong Y, Feng ZC, Zhang YL, et al. Identification of immune-related genes contributing to the development of glioblastoma using weighted gene co-expression network analysis. Front Immunol. 2020;11:1281.
  • Yoshimura A, Ito M, Chikuma S, et al. Negative regulation of cytokine signaling in immunity. Cold Spring Harb Perspect Biol. 2018;10(7):a028571.
  • Opal SM, DePalo VA. Anti-inflammatory cytokines. Chest. 2000;117(4):1162–1172.
  • Balkwill FR. The chemokine system and cancer. J Pathol. 2012;226(2):148–157.
  • Han Y, Liu D, Li L. PD-1/PD-L1 pathway: current researches in cancer. Am J Cancer Res. 2020;10(3):727–742.
  • Schutz F, Stefanovic S, Mayer L, et al. PD-1/PD-L1 pathway in breast cancer. Oncol Res Treat. 2017;40(5):294–297.
  • Seliger B. Basis of PD1/PD-L1 therapies. J Clin Med. 2019;8(12):2168.
  • Borst L, van der Burg SH, van Hall T. The NKG2A-HLA-E axis as a novel checkpoint in the tumor microenvironment. Clin Cancer Res. 2020;26(21):5549–5556.
  • Gornalusse GG, Hirata RK, Funk SE, et al. HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells. Nat Biotechnol. 2017;35(8):765–772.
  • van Montfoort N, Borst L, Korrer MJ, et al. NKG2A blockade potentiates CD8 T cell immunity induced by cancer vaccines. Cell. 2018;175(7):1744–1755.e15.
  • Ravindranath MH, Terasaki PI, Pham T, et al. The monospecificity of novel anti-HLA-E monoclonal antibodies enables reliable immunodiagnosis, immunomodulation of HLA-E, and upregulation of CD8+ T lymphocytes. Monoclon Antib Immunodiagn Immunother. 2015;34(3):135–153.
  • Mangalam AK, Taneja V, David CS. HLA class II molecules influence susceptibility versus protection in inflammatory diseases by determining the cytokine profile. J Immunol. 2013;190(2):513–518.
  • Lyu L, Yao J, Wang M, et al. Overexpressed pseudogene HLA-DPB2 promotes tumor immune infiltrates by regulating HLA-DPB1 and indicates a better prognosis in breast cancer. Front Oncol. 2020;10:1245.
  • Mahmoodi M, Nahvi H, Mahmoudi M, et al. HLA-DRB1,-DQA1 and -DQB1 allele and haplotype frequencies in female patients with early onset breast cancer. Pathol Oncol Res. 2012;18(1):49–55.
  • Lin ZH, Xin YN, Dong QJ, et al. Association between HLA-DRB1 alleles polymorphism and hepatocellular carcinoma: a meta-analysis. BMC Gastroenterol. 2010;10(1):145.
  • Zhang Y, Zhang Y, Gu W, et al. TH1/TH2 cell differentiation and molecular signals. Adv Exp Med Biol. 2014;841:15–44.
  • Lin W, Zhang HL, Niu ZY, et al. The disease stage-associated imbalance of Th1/Th2 and Th17/treg in uterine cervical cancer patients and their recovery with the reduction of tumor burden. BMC Womens Health. 2020;20(1):126.
  • Knutson KL, Disis ML. Tumor antigen-specific T helper cells in cancer immunity and immunotherapy. Cancer Immunol Immunother. 2005;54(8):721–728.
  • Tosolini M, Kirilovsky A, Mlecnik B, et al. Clinical impact of different classes of infiltrating T cytotoxic and helper cells (Th1, Th2, Treg, Th17) in patients with colorectal cancer. Cancer Res. 2011;71(4):1263–1271.
  • Osawa E, Nakajima A, Fujisawa T, et al. Predominant T helper type 2-inflammatory responses promote murine colon cancers. Int J Cancer. 2006;118(9):2232–2236.
  • Agita A, Alsagaff MT. Inflammation, immunity, and hypertension. Acta Med Indones. 2017;49(2):158–165.
  • Langfelder P, Luo R, Oldham MC, et al. Is my network module preserved and reproducible? PLoS Comput Biol. 2011;7(1):e1001057.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.