Identification of a costimulatory molecule-based signature for predicting prognosis risk and immunotherapy response in patients with lung adenocarcinoma

References

• Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61:69–12.
   PubMed Web of Science ®Google Scholar
• Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424.
   PubMed Web of Science ®Google Scholar
• Chen Z, Fillmore CM, Hammerman PS, Kim CF, Wong -K-K. Non-small-cell lung cancers: a heterogeneous set of diseases. Nat Rev Cancer. 2014;14(8):535–546. doi:10.1038/nrc3775.
   PubMed Web of Science ®Google Scholar
• Herbst RS, Baas P, Kim DW, Felip E, Felip E, Pérez-Gracia JL, Han JY, Molina J, Kim JH, Arvis CD, Ahn MJ. Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial. Lancet (London, England). 2016;387:1540–1550. doi:10.1016/S0140-6736(15)01281-7.
   PubMed Web of Science ®Google Scholar
• Borghaei H, Paz-Ares L, Horn L, Vokes EE, Felip E, Holgado E, Barlesi F, Kohlhaufl M. Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung Cancer. N Engl J Med. 2015;373:1627–1639. doi:10.1056/NEJMoa1507643.
   PubMed Web of Science ®Google Scholar
• Reck M, Rodriguez-Abreu D, Robinson AG, Hui R, Csőszi T, Fülöp A, Gottfried M, Peled N, Tafreshi A, Cuffe S, et al. Pembrolizumab versus chemotherapy for PD-L1–positive non–small-cell lung cancer. N Engl J Med. 2016;375(19):1823–1833. doi:10.1056/NEJMoa1606774.
   PubMed Web of Science ®Google Scholar
• Nurieva R, Thomas S, Nguyen T, Martin-Orozco N, Wang Y, Kaja M-K, Yu X-Z, Dong C. T-cell tolerance or function is determined by combinatorial costimulatory signals. Embo J. 2006;25(11):2623–2633. doi:10.1038/sj.emboj.7601146.
   PubMed Web of Science ®Google Scholar
• Singh S, Hassan D, Aldawsari HM, Molugulu N, Shukla R, Kesharwani P. Immune checkpoint inhibitors: a promising anticancer therapy. Drug Discov Today. 2020;25(1):223–229. doi:10.1016/j.drudis.2019.11.003.
   PubMed Web of Science ®Google Scholar
• Bluestone JA. New perspectives of CD28-B7-mediated T cell costimulation. Immunity. 1995;2:555–559. doi:10.1016/1074-7613(95)90000-4.
   PubMed Web of Science ®Google Scholar
• Goronzy JJ, Weyand CM. T-cell co-stimulatory pathways in autoimmunity. Arthritis Res Ther. 2008;10(Suppl 1):S3. doi:10.1186/ar2414.
   PubMedGoogle Scholar
• Sanmamed MF, Chen L. A paradigm shift in cancer immunotherapy: from enhancement to normalization. Cell. 2019;176:677. doi:10.1016/j.cell.2019.01.008.
   PubMed Web of Science ®Google Scholar
• Fife BT, Bluestone JA. Control of peripheral T-cell tolerance and autoimmunity via the CTLA-4 and PD-1 pathways. Immunol Rev. 2008;224:166–182. doi:10.1111/j.1600-065X.2008.00662.x.
   PubMed Web of Science ®Google Scholar
• Janakiram M, Chinai JM, Zhao A, Sparano JA, Zang X. HHLA2 and TMIGD2: new immunotherapeutic targets of the B7 and CD28 families. Oncoimmunology. 2015;4:e1026534.
   PubMed Web of Science ®Google Scholar
• Zhang C, Zhang Z, Li F, Shen Z, Qiao Y, Li L, Liu S, Song M, Zhao X, Ren F, et al. Large-scale analysis reveals the specific clinical and immune features of B7-H3 in glioma. Oncoimmunology. 2018;7(11):e1461304. doi:10.1080/2162402X.2018.1461304.
   PubMed Web of Science ®Google Scholar
• Ward-Kavanagh LK, Lin WW, Sedy JR, Ware C. The TNF receptor superfamily in co-stimulating and co-inhibitory responses. Immunity. 2016;44(5):1005–1019. doi:10.1016/j.immuni.2016.04.019.
   PubMed Web of Science ®Google Scholar
• Dostert C, Grusdat M, Letellier E, Brenner D. The TNF family of ligands and receptors: communication modules in the immune system and beyond. Physiol Rev. 2019;99(1):115–160. doi:10.1152/physrev.00045.2017.
   PubMed Web of Science ®Google Scholar
• Croft M, Benedict CA, Ware CF. Clinical targeting of the TNF and TNFR superfamilies. Nat Rev Drug Discov. 2013;12(2):147–168. doi:10.1038/nrd3930.
   PubMed Web of Science ®Google Scholar
• Schildberg FA, Klein SR, Freeman GJ, Sharpe A. Coinhibitory pathways in the B7-CD28 ligand-receptor family. Immunity. 2016;44(5):955–972. doi:10.1016/j.immuni.2016.05.002.
   PubMed Web of Science ®Google Scholar
• Liu J, Lichtenberg T, Hoadley KA, et al. An Integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell. 2018;173:400–16.e11.
   PubMed Web of Science ®Google Scholar
• Takeuchi T, Tomida S, Yatabe Y, Kosaka T, Osada H, Yanagisawa K, Mitsudomi T, Takahashi T. Expression profile-defined classification of lung adenocarcinoma shows close relationship with underlying major genetic changes and clinicopathologic behaviors. J clin oncol. 2006;24:1679–1688. doi:10.1200/JCO.2005.03.8224.
   PubMed Web of Science ®Google Scholar
• Tomida S, Takeuchi T, Shimada Y, Arima C, Matsuo K, Mitsudomi T, Yatabe Y, Takahashi T. Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis. J clin oncol. 2009;27(17):2793–2799. doi:10.1200/JCO.2008.19.7053.
   PubMed Web of Science ®Google Scholar
• Hou J, Aerts J, den Hamer B, van IJcken W, den Bakker M, Riegman P, van der Leest C, van der Spek P, Foekens JA, Hoogsteden HC, et al. Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PloS One. 2010;5(4):e10312. doi:10.1371/journal.pone.0010312.
   PubMed Web of Science ®Google Scholar
• Rousseaux S, Debernardi A, Jacquiau B, Vitte A-L, Vesin A, Nagy-Mignotte H, Moro-Sibilot D, Brichon P-Y, Lantuejoul S, Hainaut P, et al. Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers. Sci Transl Med. 2013;5(186):186ra66. doi:10.1126/scitranslmed.3005723.
   PubMed Web of Science ®Google Scholar
• Okayama H, Kohno T, Ishii Y, Shimada Y, Shiraishi K, Iwakawa R, Furuta K, Tsuta K, Shibata T, Yamamoto S, et al. Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res. 2012;72(1):100–111. doi:10.1158/0008-5472.CAN-11-1403.
   PubMed Web of Science ®Google Scholar
• Botling J, Edlund K, Lohr M, Hellwig B, Holmberg L, Lambe M, Berglund A, Ekman S, Bergqvist M, Ponten F, et al. Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clin Cancer Res. 2013;19(1):194–204. doi:10.1158/1078-0432.CCR-12-1139.
   PubMed Web of Science ®Google Scholar
• Sato M, Larsen JE, Lee W, Sun H, Shames DS, Dalvi MP, Ramirez RD, Tang H, DiMaio JM, Gao B, et al. Human lung epithelial cells progressed to malignancy through specific oncogenic manipulations. Mol Cancer Res. 2013;11(6):638–650. doi:10.1158/1541-7786.MCR-12-0634-T.
   PubMed Web of Science ®Google Scholar
• Der SD, Sykes J, Pintilie M, Zhu C-Q, Strumpf D, Liu N, Jurisica I, Shepherd FA, Tsao M-S. Validation of a histology-independent prognostic gene signature for early-stage, non-small-cell lung cancer including stage IA patients. J Thoracic Oncol. 2014;9(1):59–64. doi:10.1097/JTO.0000000000000042.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2012;72:100–111. doi:10.1038/nmeth.3337.
   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;18:248–262.
   PubMed Web of Science ®Google Scholar
• Jiang P, Gu S, Pan D, Fu J, Sahu A, Hu X, Li Z, Traugh N, Bu X, Li B, 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
• Zheng S, Luo X, Dong C, Zheng D, Xie J, Zhuge L, Sun Y, Chen H. A B7-CD28 family based signature demonstrates significantly different prognoses and tumor immune landscapes in lung adenocarcinoma. Int J Cancer. 2018;143(10):2592–2601. doi:10.1002/ijc.31764.
   PubMed Web of Science ®Google Scholar
• Rody A, Holtrich U, Pusztai L, Liedtke C, Gaetje R, Ruckhaeberle E, Solbach C, Hanker L, Ahr A, Metzler D, et al. T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Res. 2009;11(2):R15. doi:10.1186/bcr2234.
   PubMed Web of Science ®Google Scholar
• Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013;14(1):7. doi:10.1186/1471-2105-14-7.
   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
• Turley SJ, Cremasco V, Astarita JL. Immunological hallmarks of stromal cells in the tumour microenvironment. Nat Rev Immunol. 2015;15(11):669–682. doi:10.1038/nri3902.
   PubMed Web of Science ®Google Scholar
• Topalian SL, Taube JM, Pardoll DM. Neoadjuvant checkpoint blockade for cancer immunotherapy. Science (New York, NY). 2020;367(6477):eaax0182.
   Google Scholar
• Tang J, Jiang W, Liu D, Luo J, Wu X, Pan Z, Ding P, Li Y. The comprehensive molecular landscape of the immunologic co-stimulator B7 and TNFR ligand receptor families in colorectal cancer: immunotherapeutic implications with microsatellite instability. Oncoimmunology. 2018;7(10):e1488566. doi:10.1080/2162402X.2018.1488566.
   PubMed Web of Science ®Google Scholar
• Xu W, Li Y, Yuan WW, Yin Y, Song -W-W, Wang Y, Huang -Q-Q, Zhao W-H, Wu J-Q. Membrane-Bound CD40L promotes senescence and initiates senescence-associated secretory phenotype via NF-kappaB activation in lung adenocarcinoma. Cell Physiol Biochem. 2018;48(4):1793–1803. doi:10.1159/000492352.
   PubMedGoogle Scholar
• Mu CY, Qin PX, Qu QX, Chen C, Huang JA. Soluble CD40 in plasma and malignant pleural effusion with non-small cell lung cancer: A potential marker of prognosis. Chronic Dis Transl Med. 2015;1:36–41. doi:10.1016/j.cdtm.2015.02.010.
   PubMedGoogle Scholar
• Lin S, Wu B, Lin Y, Wang M, Zhu Y, Jiang J, Zhang L, Lin J. Expression and clinical significance of decoy receptor 3 in acute-on-chronic liver failure. Biomed Res Int. 2019;2019:9145736. doi:10.1155/2019/9145736.
   PubMed Web of Science ®Google Scholar
• Lin WW, Hsieh SL, Herbst RS, Baas P, Kim D-W, Felip E, Pérez-Gracia JL, Han J-Y, Molina J, Kim J-H. Decoy receptor 3: a pleiotropic immunomodulator and biomarker for inflammatory diseases, autoimmune diseases and cancer. Biochem Pharmacol. 2011;81:838–847. doi:10.1016/j.bcp.2011.01.011.
   PubMed Web of Science ®Google Scholar
• Yu KY, Kwon B, Ni J, Zhai Y, Ebner R, Kwon BS. A newly identified member of tumor necrosis factor receptor superfamily (TR6) suppresses LIGHT-mediated apoptosis. J Biol Chem. 1999;274:13733–13736.
   PubMed Web of Science ®Google Scholar
• Hsieh S-L, Lin -W-W. Decoy receptor 3: an endogenous immunomodulator in cancer growth and inflammatory reactions. J Biomed Sci. 2017;24(1):39. doi:10.1186/s12929-017-0347-7.
   PubMedGoogle Scholar
• Bossen C, Schneider P. BAFF, APRIL and their receptors: structure, function and signaling. Semin Immunol. 2006;18(5):263–275. doi:10.1016/j.smim.2006.04.006.
   PubMed Web of Science ®Google Scholar
• Sun B, Wang H, Wang X, Huang H, Ding W, Jing R, Shi G, Zhu L. A proliferation-inducing ligand: a new biomarker for non-small cell lung cancer. Exp Lung Res. 2009;35(6):486–500. doi:10.1080/01902140902759274.
   PubMed Web of Science ®Google Scholar
• Pelekanou V, Kampa M, Kafousi M, Darivianaki K, Sanidas E, Tsiftsis DD, Stathopoulos EN, Tsapis A, Castanas E. Expression of TNF-superfamily members BAFF and APRIL in breast cancer: immunohistochemical study in 52 invasive ductal breast carcinomas. BMC Cancer. 2008;8(1):76. doi:10.1186/1471-2407-8-76.
   PubMedGoogle Scholar
• Bojarska-Junak A, Hus I, Chocholska S, Wąsik-Szczepanek E, Sieklucka M, Dmoszyńska A, Roliński J. BAFF and APRIL expression in B-cell chronic lymphocytic leukemia: correlation with biological and clinical features. Leuk Res. 2009;33(10):1319–1327. doi:10.1016/j.leukres.2009.03.030.
   PubMed Web of Science ®Google Scholar
• Gross JA, Dillon SR, Mudri S, Johnston J, Littau A, Roque R, Rixon M, Schou O, Foley KP, Haugen H, et al. TACI-Ig neutralizes molecules critical for B cell development and autoimmune disease. Impaired B Cell Maturation in Mice Lacking BLyS Immunity. 2001;15:289–302.
   PubMed Web of Science ®Google Scholar
• Qin H, Wei G, Sakamaki I, Dong Z, Cheng WA, Smith DL, Wen F, Sun H, Kim K, Cha S, et al. Novel BAFF-receptor antibody to natively folded recombinant protein eliminates drug-resistant human B-cell malignancies in vivo. Clin Cancer Res. 2018;24(5):1114–1123. doi:10.1158/1078-0432.CCR-17-1193.
   PubMed Web of Science ®Google Scholar
• Eby MT, Jasmin A, Kumar A, Sharma K, Chaudhary PM. TAJ, a novel member of the tumor necrosis factor receptor family, activates the c-Jun N-terminal kinase pathway and mediates caspase-independent cell death. J Biol Chem. 2000;275(20):15336–15342. doi:10.1074/jbc.275.20.15336.
   PubMed Web of Science ®Google Scholar
• Shao L, Zuo X, Yang Y, Zhang Y, Yang N, Shen B, Wang J, Wang X, Li R, Jin G, et al. The inherited variations of a p53-responsive enhancer in 13q12.12. Confer Lung Cancer Risk by Attenuating TNFRSF19 Expression Genome Biology. 2019;20:103.
   Google Scholar
• Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science (New York, NY). 2015;348(6230):124–128. doi:10.1126/science.aaa1348.
   Google Scholar
• Gong Z, Jia Q, Chen J, Diao X, Gao J, Wang X, Zhu B. Impaired cytolytic activity and loss of clonal neoantigens in elderly patients with lung adenocarcinoma. J Thoracic Oncol. 2019;14(5):857–866. doi:10.1016/j.jtho.2019.01.024.
   PubMed Web of Science ®Google Scholar
• Herbst RS, Soria J-C, Kowanetz M, Fine GD, Hamid O, Gordon MS, Sosman JA, McDermott DF, Powderly JD, Gettinger SN, et al. Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature. 2014;515(7528):563–567. doi:10.1038/nature14011.
   PubMed Web of Science ®Google Scholar