Identification of Cuproptosis-Related Subtypes, Establishment of a Prognostic Signature and Characterization of the Tumor Microenvironment in Gastric Cancer

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. doi:10.3322/caac.21660
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–674. doi:10.1016/j.cell.2011.02.013
   PubMed Web of Science ®Google Scholar
• Kerr JF, Wyllie AH, Currie AR. Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer. 1972;26(4):239–257. doi:10.1038/bjc.1972.33
   PubMed Web of Science ®Google Scholar
• Roberts AW, Seymour JF, Brown JR, et al. Substantial susceptibility of chronic lymphocytic leukemia to BCL2 inhibition: results of a Phase I study of navitoclax in patients with relapsed or refractory disease. J Clin Oncol. 2012;30(5):488–496. doi:10.1200/JCO.2011.34.7898
   PubMed Web of Science ®Google Scholar
• Wilson WH, O’Connor OA, Czuczman MS, et al. Navitoclax, a targeted high-affinity inhibitor of BCL-2, in lymphoid malignancies: a Phase 1 dose-escalation study of safety, pharmacokinetics, pharmacodynamics, and antitumour activity. Lancet Oncol. 2010;11(12):1149–1159. doi:10.1016/S1470-2045(10)70261-8
   PubMed Web of Science ®Google Scholar
• Roberts AW, Davids MS, Pagel JM, et al. Targeting BCL2 with Venetoclax in Relapsed Chronic Lymphocytic Leukemia. N Engl J Med. 2016;374(4):311–322. doi:10.1056/NEJMoa1513257
   PubMed Web of Science ®Google Scholar
• Stilgenbauer S, Eichhorst B, Schetelig J, et al. Venetoclax in relapsed or refractory chronic lymphocytic leukaemia with 17p deletion: a multicentre, open-label, Phase 2 study. Lancet Oncol. 2016;17(6):768–778. doi:10.1016/S1470-2045(16)30019-5
   PubMed Web of Science ®Google Scholar
• Strasser A, Vaux DL. Cell death in the origin and treatment of cancer. Mol Cell. 2020;78(6):1045–1054. doi:10.1016/j.molcel.2020.05.014
   PubMed Web of Science ®Google Scholar
• Tsvetkov P, Coy S, Petrova B, et al. Copper induces cell death by targeting lipoylated TCA cycle proteins. Science. 2022;375(6586):1254–1261. doi:10.1126/science.abf0529
   PubMed Web of Science ®Google Scholar
• The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513(7517):202–209. doi:10.1038/nature13480
   PubMed Web of Science ®Google Scholar
• Cristescu R, Lee J, Nebozhyn M, et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes. Nat Med. 2015;21(5):449–456. doi:10.1038/nm.3850
   PubMed Web of Science ®Google Scholar
• Lei Z, Tan IB, Das K, et al. Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil. Gastroenterology. 2013;145(3):554–565. doi:10.1053/j.gastro.2013.05.010
   PubMed Web of Science ®Google Scholar
• Xiang R, Ge Y, Song W, Ren J, Kong C, Fu T. Pyroptosis Patterns Characterized by Distinct Tumor Microenvironment Infiltration Landscapes in Gastric Cancer. Genes. 2021;12:10. doi:10.3390/genes12101535
   Web of Science ®Google Scholar
• Xiang R, Song W, Ren J, Wu J, Fu J, Fu T. Identification of stem cell-related subtypes and risk scoring for gastric cancer based on stem genomic profiling. Stem Cell Res Ther. 2021;12(1):563. doi:10.1186/s13287-021-02633-x
   PubMed Web of Science ®Google Scholar
• Zhang P, Yang M, Zhang Y, et al. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 2019;27(6):1934–1947 e1935. doi:10.1016/j.celrep.2019.04.052
   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 U S A. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Mariathasan S, Turley SJ, Nickles D, et al. TGFbeta attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554(7693):544–548. doi:10.1038/nature25501
   PubMed Web of Science ®Google Scholar
• Charoentong P, Finotello F, Angelova M, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18(1):248–262. doi:10.1016/j.celrep.2016.12.019
   PubMed Web of Science ®Google Scholar
• 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. doi:10.1038/ncomms3612
   PubMed Web of Science ®Google Scholar
• Melendez B, Van Campenhout C, Rorive S, Remmelink M, Salmon I, D’Haene N. Methods of measurement for tumor mutational burden in tumor tissue. Transl Lung Cancer Res. 2018;7(6):661–667. doi:10.21037/tlcr.2018.08.02
   PubMed Web of Science ®Google Scholar
• Valero C, Lee M, Hoen D, et al. The association between tumor mutational burden and prognosis is dependent on treatment context. Nat Genet. 2021;53(1):11–15. doi:10.1038/s41588-020-00752-4
   PubMed Web of Science ®Google Scholar
• Samstein RM, Lee CH, Shoushtari AN, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019;51(2):202–206. doi:10.1038/s41588-018-0312-8
   PubMed Web of Science ®Google Scholar
• Cao D, Xu H, Xu X, Guo T, Ge W. High tumor mutation burden predicts better efficacy of immunotherapy: a pooled analysis of 103078 cancer patients. Oncoimmunology. 2019;8(9):e1629258. doi:10.1080/2162402X.2019.1629258
   PubMed Web of Science ®Google Scholar
• Jiang P, Gu S, Pan D, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018;24(10):1550–1558. doi:10.1038/s41591-018-0136-1
   PubMed Web of Science ®Google Scholar
• Braun DA, Hou Y, Bakouny Z, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med. 2020;26(6):909–918. doi:10.1038/s41591-020-0839-y
   PubMed Web of Science ®Google Scholar
• Vickers AJ, Elkin EB. Decision curve analysis: a novel method for evaluating prediction models. Med Decis Making. 2006;26(6):565–574. doi:10.1177/0272989X06295361
   PubMed Web of Science ®Google Scholar
• Wang J, Qin D, Tao Z, et al. Identification of cuproptosis-related subtypes, construction of a prognosis model, and tumor microenvironment landscape in gastric cancer. Front Immunol. 2022;13:1056932. doi:10.3389/fimmu.2022.1056932
   PubMed Web of Science ®Google Scholar
• Nie H, Wang H, Zhang M, et al. Comprehensive analysis of cuproptosis-related genes in prognosis, tumor microenvironment infiltration, and immunotherapy response in gastric cancer. J Cancer Res Clin Oncol. 2022. doi:10.1007/s00432-022-04474-4
   Web of Science ®Google Scholar
• Wang XX, Deng SZ, Wu LH, et al. Cuproptosis-Mediated Patterns Characterized by Distinct Tumor Microenvironment and Predicted the Immunotherapy Response for Gastric Cancer. ACS Omega. 2023;8(12):10851–10862. doi:10.1021/acsomega.2c07052
   PubMed Web of Science ®Google Scholar
• Wang Z, Cao L, Zhou S, Lyu J, Gao Y, Yang R. Construction and Validation of a Novel Pyroptosis-Related Four-lncRNA Prognostic Signature Related to Gastric Cancer and Immune Infiltration. Front Immunol. 2022;13:854785. doi:10.3389/fimmu.2022.854785
   PubMed Web of Science ®Google Scholar
• Qiu J, Sun M, Wang Y, Chen B. Identification and validation of an individualized autophagy-clinical prognostic index in gastric cancer patients. Cancer Cell Int. 2020;20:178. doi:10.1186/s12935-020-01267-y
   PubMed Web of Science ®Google Scholar
• Pan J, Zhang X, Fang X, Xin Z. Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics. Front Genet. 2021;12:739470. doi:10.3389/fgene.2021.739470
   PubMed Web of Science ®Google Scholar
• Wei J, Zeng Y, Gao X, Liu T. A novel ferroptosis-related lncRNA signature for prognosis prediction in gastric cancer. BMC Cancer. 2021;21(1):1221. doi:10.1186/s12885-021-08975-2
   PubMed Web of Science ®Google Scholar
• Luo L, Li L, Liu L, et al. A Necroptosis-Related lncRNA-Based Signature to Predict Prognosis and Probe Molecular Characteristics of Stomach Adenocarcinoma. Front Genet. 2022;13:833928. doi:10.3389/fgene.2022.833928
   PubMed Web of Science ®Google Scholar
• Huo J, Fan X, Qi B, Sun P. A Five-Gene Signature Associated With DNA Damage Repair Molecular Subtype Predict Overall Survival for Hepatocellular Carcinoma. Front Genet. 2022;13:771819. doi:10.3389/fgene.2022.771819
   PubMedGoogle Scholar
• Xu L, Deng C, Pang B, et al. TIP: a Web Server for Resolving Tumor Immunophenotype Profiling. Cancer Res. 2018;78(23):6575–6580. doi:10.1158/0008-5472.CAN-18-0689
   PubMed Web of Science ®Google Scholar
• Ostroumov D, Fekete-Drimusz N, Saborowski M, Kuhnel F, Woller N. CD4 and CD8 T lymphocyte interplay in controlling tumor growth. Cell Mol Life Sci. 2018;75(4):689–713. doi:10.1007/s00018-017-2686-7
   PubMed Web of Science ®Google Scholar
• Melssen M, Slingluff CL. Vaccines targeting helper T cells for cancer immunotherapy. Curr Opin Immunol. 2017;47:85–92. doi:10.1016/j.coi.2017.07.004
   PubMed Web of Science ®Google Scholar
• Helmink BA, Reddy SM, Gao J, et al. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020;577(7791):549–555. doi:10.1038/s41586-019-1922-8
   PubMed Web of Science ®Google Scholar
• Kim SS, Shen S, Miyauchi S, et al. B Cells Improve Overall Survival in HPV-Associated Squamous Cell Carcinomas and Are Activated by Radiation and PD-1 Blockade. Clin Cancer Res. 2020;26(13):3345–3359. doi:10.1158/1078-0432.CCR-19-3211
   PubMed Web of Science ®Google Scholar
• Pitt JM, Marabelle A, Eggermont A, Soria JC, Kroemer G, Zitvogel L. Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy. Ann Oncol. 2016;27(8):1482–1492. doi:10.1093/annonc/mdw168
   PubMed Web of Science ®Google Scholar
• De Simone M, Arrigoni A, Rossetti G, et al. Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells. Immunity. 2016;45(5):1135–1147. doi:10.1016/j.immuni.2016.10.021
   PubMed Web of Science ®Google Scholar
• Liao W, Overman MJ, Boutin AT, et al. KRAS-IRF2 Axis Drives Immune Suppression and Immune Therapy Resistance in Colorectal Cancer. Cancer Cell. 2019;35(4):559–572 e557. doi:10.1016/j.ccell.2019.02.008
   PubMed Web of Science ®Google Scholar
• Yamauchi Y, Safi S, Blattner C, et al. Circulating and Tumor Myeloid-derived Suppressor Cells in Resectable Non-Small Cell Lung Cancer. Am J Respir Crit Care Med. 2018;198(6):777–787. doi:10.1164/rccm.201708-1707OC
   PubMed Web of Science ®Google Scholar
• Bates GJ, Fox SB, Han C, et al. Quantification of regulatory T cells enables the identification of high-risk breast cancer patients and those at risk of late relapse. J Clin Oncol. 2006;24(34):5373–5380. doi:10.1200/JCO.2006.05.9584
   PubMed Web of Science ®Google Scholar
• Sharma P, Hu-Lieskovan S, Wargo JA, Ribas A. Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy. Cell. 2017;168(4):707–723. doi:10.1016/j.cell.2017.01.017
   PubMed Web of Science ®Google Scholar
• Coutzac C, Pernot S, Chaput N, Zaanan A. Immunotherapy in advanced gastric cancer, is it the future? Crit Rev Oncol Hematol. 2019;133:25–32. doi:10.1016/j.critrevonc.2018.10.007
   PubMed Web of Science ®Google Scholar