Study of Clinical Predictive Value and Immune Characterization of SLFN11 in Clear Cell Renal Cell Carcinoma

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.
   PubMed Web of Science ®Google Scholar
• Qin S, Shi X, Wang C, Jin P, Ma F. Transcription factor and miRNA interplays can manifest the survival of ccRCC patients. Cancers. 2019;11(11):1668. doi:10.3390/cancers11111668
   PubMed Web of Science ®Google Scholar
• Deleuze A, Saout J, Dugay F, et al. Immunotherapy in renal cell carcinoma: the future is now. Int J Mol Sci. 2020;21(7):2532. doi:10.3390/ijms21072532
   PubMed Web of Science ®Google Scholar
• Mavrommatis E, Fish EN, Platanias LC. The schlafen family of proteins and their regulation by interferons. J Interferon Cytokine Res. 2013;33(4):206–210. doi:10.1089/jir.2012.0133
   PubMed Web of Science ®Google Scholar
• Murai J, Thomas A, Miettinen M, Pommier Y. Schlafen 11 (SLFN11), a restriction factor for replicative stress induced by DNA-targeting anti-cancer therapies. Pharmacol Ther. 2019;201:94–102. doi:10.1016/j.pharmthera.2019.05.009
   PubMed Web of Science ®Google Scholar
• Zoppoli G, Regairaz M, Leo E, et al. Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents. Proc Natl Acad Sci U S A. 2012;109(37):15030–15035. doi:10.1073/pnas.1205943109
   PubMed Web of Science ®Google Scholar
• Deng Y, Cai Y, Huang Y, et al. High SLFN11 expression predicts better survival for patients with KRAS exon 2 wild type colorectal cancer after treated with adjuvant oxaliplatin-based treatment. BMC Cancer. 2015;15(1):833. doi:10.1186/s12885-015-1840-6
   PubMed Web of Science ®Google Scholar
• Conteduca V, Ku SY, Puca L, et al. SLFN11 expression in advanced prostate cancer and response to platinum-based chemotherapy. Mol Cancer Ther. 2020;19(5):1157–1164. doi:10.1158/1535-7163.MCT-19-0926
   PubMed Web of Science ®Google Scholar
• Tang SW, Bilke S, Cao L, et al. SLFN11 is a transcriptional target of EWS-FLI1 and a determinant of drug response in Ewing sarcoma. Clin Cancer Res. 2015;21(18):4184–4193. doi:10.1158/1078-0432.CCR-14-2112
   PubMed Web of Science ®Google Scholar
• Zhang B, Ramkumar K, Cardnell RJ, et al. A wake-up call for cancer DNA damage: the role of Schlafen 11 (SLFN11) across multiple cancers. Br J Cancer. 2021:1–8. doi:10.1038/s41416-021-01476-w
   PubMed Web of Science ®Google Scholar
• Tomczak K, Czerwińska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol. 2015;19(1a):A68–A77.
   Google Scholar
• Clough E, Barrett T. The gene expression omnibus database. Methods Mol Biol. 2016;1418:93–110.
   PubMedGoogle Scholar
• Chandrashekar DS, Bashel B, Balasubramanya SAH, et al. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia. 2017;19(8):649–658. doi:10.1016/j.neo.2017.05.002
   PubMed Web of Science ®Google Scholar
• Uhlen M, Zhang C, Lee S, et al. A pathology atlas of the human cancer transcriptome. Science. 2017;357(6352):6352. doi:10.1126/science.aan2507
   Web of Science ®Google Scholar
• Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database):D561–D568. doi:10.1093/nar/gkq973
   PubMed Web of Science ®Google Scholar
• Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. Jvenn: an interactive venn diagram viewer. BMC Bioinform. 2014;15(1):293. doi:10.1186/1471-2105-15-293
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. ClusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   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
• Li T, Fu J, Zeng Z, et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 2020;48(W1):W509–W514. doi:10.1093/nar/gkaa407
   PubMed Web of Science ®Google Scholar
• Ru B, Wong CN, Tong Y, et al. TISIDB: an integrated repository portal for tumor-immune system interactions. Bioinformatics. 2019;35(20):4200–4202. doi:10.1093/bioinformatics/btz210
   PubMed Web of Science ®Google Scholar
• Kruppa J, Jung K. Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. BMC Bioinform. 2017;18(1):232. doi:10.1186/s12859-017-1645-5
   PubMed Web of Science ®Google Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12(1):77. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Tronik-Le Roux D, Sautreuil M, Bentriou M, et al. Comprehensive landscape of immune-checkpoints uncovered in clear cell renal cell carcinoma reveals new and emerging therapeutic targets. Cancer Immunol Immunother. 2020;69(7):1237–1252. doi:10.1007/s00262-020-02530-x
   PubMed Web of Science ®Google Scholar
• Wu Z, Zhang Y, Chen X, et al. Characterization of the prognostic values of the CXCR1-7 in Clear Cell Renal Cell Carcinoma (ccRCC) microenvironment. Front Mol Biosci. 2020;7:601206. doi:10.3389/fmolb.2020.601206
   PubMed Web of Science ®Google Scholar
• Esteban E, Exposito F, Crespo G, et al. Circulating levels of the interferon-γ-regulated chemokines CXCL10/CXCL11, IL-6 and HGF predict outcome in metastatic renal cell carcinoma patients treated with antiangiogenic therapy. Cancers. 2021;13(11):2849. doi:10.3390/cancers13112849
   PubMed Web of Science ®Google Scholar
• Giuliano S, Dufies M, Ndiaye PD, et al. Resistance to lysosomotropic drugs used to treat kidney and breast cancers involves autophagy and inflammation and converges in inducing CXCL5. Theranostics. 2019;9(4):1181–1199. doi:10.7150/thno.29093
   PubMed Web of Science ®Google Scholar
• Dai S, Zeng H, Liu Z, et al. Intratumoral CXCL13 + CD8 + T cell infiltration determines poor clinical outcomes and immunoevasive contexture in patients with clear cell renal cell carcinoma. J Immunother Cancer. 2021;9(2):e001823. doi:10.1136/jitc-2020-001823
   PubMed Web of Science ®Google Scholar
• Luan J, Gao X, Hu F, Zhang Y, Gou X. SLFN11 is a general target for enhancing the sensitivity of cancer to chemotherapy (DNA-damaging agents). J Drug Target. 2020;28(1):33–40. doi:10.1080/1061186X.2019.1616746
   PubMed Web of Science ®Google Scholar
• Lok BH, Gardner EE, Schneeberger VE, et al. PARP inhibitor activity correlates with SLFN11 expression and demonstrates synergy with temozolomide in small cell lung cancer. Clin Cancer Res. 2017;23(2):523–535. doi:10.1158/1078-0432.CCR-16-1040
   PubMed Web of Science ®Google Scholar
• Mao S, Chaerkady R, Yu W, et al. Resistance to pyrrolobenzodiazepine dimers is associated with SLFN11 downregulation and can be reversed through inhibition of ATR. Mol Cancer Ther. 2021;20(3):541–552. doi:10.1158/1535-7163.MCT-20-0351
   PubMed Web of Science ®Google Scholar
• Berns K, Berns A. Awakening of “Schlafen11” to tackle chemotherapy resistance in SCLC. Cancer Cell. 2017;31(2):169–171. doi:10.1016/j.ccell.2017.01.013
   PubMed Web of Science ®Google Scholar
• Zhou C, Liu C, Liu W, et al. SLFN11 inhibits hepatocellular carcinoma tumorigenesis and metastasis by targeting RPS4X via mTOR pathway. Theranostics. 2020;10(10):4627–4643. doi:10.7150/thno.42869
   PubMed Web of Science ®Google Scholar
• Kagami T, Yamade M, Suzuki T, et al. The first evidence for SLFN11 expression as an independent prognostic factor for patients with esophageal cancer after chemoradiotherapy. BMC Cancer. 2020;20(1):1123. doi:10.1186/s12885-020-07574-x
   PubMed Web of Science ®Google Scholar
• He T, Zhang M, Zheng R, et al. Methylation of SLFN11 is a marker of poor prognosis and cisplatin resistance in colorectal cancer. Epigenomics. 2017;9(6):849–862. doi:10.2217/epi-2017-0019
   PubMed Web of Science ®Google Scholar
• Peng Y, Wang L, Wu L, Zhang L, Nie G, Guo M. Methylation of SLFN11 promotes gastric cancer growth and increases gastric cancer cell resistance to cisplatin. J Cancer. 2019;10(24):6124–6134. doi:10.7150/jca.32511
   PubMed Web of Science ®Google Scholar
• Mauney CH, Hollis T. SAMHD1: recurring roles in cell cycle, viral restriction, cancer, and innate immunity. Autoimmunity. 2018;51(3):96–110. doi:10.1080/08916934.2018.1454912
   PubMed Web of Science ®Google Scholar
• Zhang Z, Zheng L, Yu Y, et al. Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review). Int J Oncol. 2020;56(4):879–888.
   PubMed Web of Science ®Google Scholar
• Isnaldi E, Ferraioli D, Ferrando L, et al. Schlafen-11 expression is associated with immune signatures and basal-like phenotype in breast cancer. Breast Cancer Res Treat. 2019;177(2):335–343. doi:10.1007/s10549-019-05313-w
   PubMed Web of Science ®Google Scholar
• Hinshaw DC, Shevde LA. The tumor microenvironment innately modulates cancer progression. Cancer Res. 2019;79(18):4557–4566. doi:10.1158/0008-5472.CAN-18-3962
   PubMed Web of Science ®Google Scholar
• Liao G, Wang P, Wang Y. Identification of the prognosis value and potential mechanism of immune checkpoints in renal clear cell carcinoma microenvironment. Front Oncol. 2021;11:720125. doi:10.3389/fonc.2021.720125
   PubMed Web of Science ®Google Scholar
• Agresta L, Lehn M, Lampe K, et al. CD244 represents a new therapeutic target in head and neck squamous cell carcinoma. J Immunother Cancer. 2020;8(1):e000245. doi:10.1136/jitc-2019-000245
   PubMed Web of Science ®Google Scholar
• Mollica Poeta V, Massara M, Capucetti A, Bonecchi R. Chemokines and chemokine receptors: new targets for cancer immunotherapy. Front Immunol. 2019;10:379. doi:10.3389/fimmu.2019.00379
   PubMed Web of Science ®Google Scholar
• Zheng Z, Cai Y, Chen H, et al. CXCL13/CXCR5 axis predicts poor prognosis and promotes progression through PI3K/AKT/mTOR pathway in clear cell renal cell carcinoma. Front Oncol. 2019;8:682. doi:10.3389/fonc.2018.00682
   PubMed Web of Science ®Google Scholar