Identification of a costimulatory molecule-based signature to predict prognostic risk of pancreatic adenocarcinoma

References

• Agarwal S, Loder S, Brownley C, Cholok D, Mangiavini L, Li J, et al. 2016. Inhibition of Hif1α prevents both trauma-induced and genetic heterotopic ossification. Proc Natl Acad Sci U S A. 201515397.
   Web of Science ®Google Scholar
• Bin Z, Guangbo Z, Yan G, Huan Z, Desheng L, Xueguang Z. 2014. Overexpression of B7-H3 in CD133 + colorectal cancer cells is associated with cancer progression and survival in human patients. J Surg Res. 188(2):396–403. doi:10.1016/j.jss.2014.01.014.
   PubMed Web of Science ®Google Scholar
• Cameron DG, Moffatt DJ, Mantsch HH, Kauppinen JK. 1981. Fourier self-deconvolution: A method for resolving intrinsically overlapped bands. Appl Spectrosc. 35(3):271–276.
   Web of Science ®Google Scholar
• Catalano V, Turdo A, Di Franco S, Dieli F, Todaro M, Stassi G. 2013. Tumor and its microenvironment: a synergistic interplay. Sem Cancer Biol. 23:522–532. doi:10.1016/j.semcancer.2013.08.007.
   PubMed Web of Science ®Google Scholar
• Cawley GC, Talbot NLC. 2008. Efficient approximate leave-one-out cross-validation for kernel logistic regression. Mach Learn. 71(2-3):243–264.
   Web of Science ®Google Scholar
• Chang JS, Hsu YL, Kuo PL, Chiang LC, Lin C. 2010. Upregulation of Fas/Fas ligand-mediated apoptosis by gossypol in an immortalized human alveolar lung cancer cell line. Clin Exper Pharmacol Physiol. 31(10):716–722.
   Google Scholar
• Chen B, Khodadoust MS, Liu CL, Newman AM, Alizadeh AA. 2018. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 1711:243.
   PubMedGoogle Scholar
• Choi C, Bakir I, Hart A, Graham T. 2017. Clonal evolution of colorectal cancer in IBD. Nat Rev Gastroenterol Hepatol. 14(4):218–229. doi:10.1038/nrgastro.2017.1.
   PubMed Web of Science ®Google Scholar
• Crawford H, Pasca di Magliano M, Banerjee S. 2019. Signaling networks that control cellular plasticity in pancreatic tumorigenesis, progression, and metastasis. Gastroenterology. 156(7):2073–2084. doi:10.1053/j.gastro.2018.12.042.
   PubMed Web of Science ®Google Scholar
• Croft M, Benedict C, Ware C. 2013. Clinical targeting of the TNF and TNFR superfamilies. Nat Rev Drug Discov. 12(2):147–168. doi:10.1038/nrd3930.
   PubMed Web of Science ®Google Scholar
• Dostert C, Grusdat M, Letellier E, Brenner D. 2019. The TNF family of ligands and receptors: communication modules in the immune system and beyond. Physiol Rev. 99(1):115–160. doi:10.1152/physrev.00045.2017.
   PubMed Web of Science ®Google Scholar
• Fernández-Nogueira P, Bragado P, Almendro V, Ametller E, Rios J, Choudhury S, et al. 2016. Differential expression of neurogenes among breast cancer subtypes identifies high risk patients. Oncotarget. 7(5):5313–5326. doi:10.18632/oncotarget.6543.
   PubMedGoogle Scholar
• Ferri M, Saez M, Figueras J, Fort E, Sabat M, López-Ben S, et al. 2016. Improved pancreatic adenocarcinoma diagnosis in jaundiced and non-jaundiced pancreatic adenocarcinoma patients through the combination of routine clinical markers associated to pancreatic adenocarcinoma pathophysiology. PloS One. 11(1):e0147214. doi:10.1371/journal.pone.0147214.
   PubMed Web of Science ®Google Scholar
• Henriksen S, Madsen P, Larsen A, Johansen M, Pedersen I, Krarup H, et al. 2017. Cell-free DNA promoter hypermethylation in plasma as a predictive marker for survival of patients with pancreatic adenocarcinoma. Oncotarget. 8(55):93942–93956. doi:10.18632/oncotarget.21397.
   PubMedGoogle Scholar
• Hua D, Sun J, Mao Y, Chen L, Wu Y, Zhang X. 2012. B7-H1 expression is associated with expansion of regulatory T cells in colorectal carcinoma. World J Gastroenterol. 18(9):971–978. doi:10.3748/wjg.v18.i9.971.
   PubMed Web of Science ®Google Scholar
• Janakiram M, Chinai J, Zhao A, Sparano J, Zang X. 2015. HHLA2 and TMIGD2: new immunotherapeutic targets of the B7 and CD28 families. Oncoimmunology. 4(8):e1026534. doi:10.1080/2162402x.2015.1026534.
   PubMed Web of Science ®Google Scholar
• Janakiram N, Mohammed A, Bryant T, Ritchie R, Stratton N, Jackson L, et al. 2017. Loss of natural killer T cells promotes pancreatic cancer in LSL-Kras mice. Immunology. 152(1):36–51. doi:10.1111/imm.12746.
   PubMed Web of Science ®Google Scholar
• Jin G, Ruan Q, Shangguan F, Lan L. 2021. RUNX2 and LAMC2: promising pancreatic cancer biomarkers identified by an integrative data mining of pancreatic adenocarcinoma tissues. Aging. 13. doi:10.18632/aging.203589.
   Google Scholar
• Jr F. 2015. rms: Regression Modeling Strategies.
   Google Scholar
• Kere J, Srivastava AK, Montonen O, Zonana J, Thomas N, Ferguson B, Munoz F, Morgan D, Clarke A, Baybayan P, et al. 1996. X–linked anhidrotic (hypohidrotic) ectodermal dysplasia is caused by mutation in a novel transmembrane protein. Nat Genet. 13(4):409–416.
   PubMed Web of Science ®Google Scholar
• Kowalczyk-Quintas C, Willen L, Dang A, Sarrasin H, Tardivel A, Hermes K, et al. 2014. Generation and characterization of function-blocking anti-ectodysplasin A (EDA) monoclonal antibodies that induce ectodermal dysplasia. J Biol Chem. 289(7):4273–4285. doi:10.1074/jbc.M113.535740.
   PubMed Web of Science ®Google Scholar
• Lee B, Lipton L, Cohen J, Tie J, Javed A, Li L, et al. 2019. Circulating tumor DNA as a potential marker of adjuvant chemotherapy benefit following surgery for localized pancreatic cancer. Ann Oncol Off J Eur Soc Med Oncol. 30(9):1472–1478. doi:10.1093/annonc/mdz200.
   PubMed Web of Science ®Google Scholar
• Li T, Fan J, Wang B, Traugh N, Chen Q, Liu J, et al. 2017. TIMER: A web server for comprehensive analysis of tumor-infiltrating immune cells. Cancer Res. 77(21):e108–e110. doi:10.1158/0008-5472.can-17-0307.
   PubMed Web of Science ®Google Scholar
• Loosen S, Tacke F, Püthe N, Binneboesel M, Wiltberger G, Alizai P, et al. 2019. High baseline soluble urokinase plasminogen activator receptor (suPAR) serum levels indicate adverse outcome after resection of pancreatic adenocarcinoma. Carcinogenesis. 40(8):947–955. doi:10.1093/carcin/bgz033.
   PubMed Web of Science ®Google Scholar
• Mayakonda A, Lin D, Assenov Y, Plass C, Koeffler H. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 28(11):1747–1756. doi:10.1101/gr.239244.118.
   PubMed Web of Science ®Google Scholar
• Murray P, Wynn T. 2011. Protective and pathogenic functions of macrophage subsets. Nat Rev Immunol. 11(11):723–737. doi:10.1038/nri3073.
   PubMed Web of Science ®Google Scholar
• Neoptolemos J, Kleeff J, Michl P, Costello E, Greenhalf W, Palmer D. 2018. Therapeutic developments in pancreatic cancer: current and future perspectives. Nat Rev Gastroenterol Hepatol. 15(6):333–348. doi:10.1038/s41575-018-0005-x.
   PubMed Web of Science ®Google Scholar
• Nie J, Yang X. 2017. Modulation of synaptic plasticity by exercise training as a basis for ischemic stroke rehabilitation. Cell Mol Neurobiol. 37(1):5–16. doi:10.1007/s10571-016-0348-1.
   PubMed Web of Science ®Google Scholar
• Niki A Ottenhof ANAM, Morsink FHM, Drillenburg P, W ten Kate FJ, Maitra A, Johan Offerhaus G. 2009. Pancreatic intraepithelial neoplasia and pancreatic tumorigenesis: of mice and men. Arch Pathol Lab Med. 133(3):375.
   PubMed Web of Science ®Google Scholar
• Philipp S, Sosna J, Adam D. 2016. Cancer and necroptosis: friend or foe? Cell Mol Sci CMLS. 73:2183–2193. doi:10.1007/s00018-016-2193-2.
   PubMed Web of Science ®Google Scholar
• Pohar M, Stare J. 2006. Relative survival analysis in R. Comput Meth Progr Biomed. 81(3):272–278.
   PubMed Web of Science ®Google Scholar
• Rahib L, Smith B, Aizenberg R, Rosenzweig A, Fleshman J, Matrisian L. 2014. Projecting cancer incidence and deaths to 2030: the unexpected burden of thyroid, liver, and pancreas cancers in the United States. Cancer Res. 74(11):2913–2921. doi:10.1158/0008-5472.can-14-0155.
   PubMed Web of Science ®Google Scholar
• Reis-Filho J, Steele D, Di Palma S, Jones R, Savage K, James M, et al. 2006. Distribution and significance of nerve growth factor receptor (NGFR/p75NTR) in normal, benign and malignant breast tissue. Mod Pathol Off J US Canad Acad Pathol. 19(2):307–319. doi:10.1038/modpathol.3800542.
   PubMed Web of Science ®Google Scholar
• Ritchie M, Phipson B, Wu D, Hu Y, Law C, Shi W, et al. 2015a. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl Acids Res. 43(7):e47. doi:10.1093/nar/gkv007.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Belinda P, Wu D, Hu Y, Law CW, Wei S, et al. 2015b. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl Acids Res. 43(7):e47.
   PubMed Web of Science ®Google Scholar
• Schildberg F, Klein S, Freeman G, Sharpe A. 2016. Coinhibitory pathways in the B7-CD28 ligand-receptor family. Immunity. 44(5):955–972. doi:10.1016/j.immuni.2016.05.002.
   PubMed Web of Science ®Google Scholar
• Shi B, Ding J, Qi J, Gu Z. 2021. Characteristics and prognostic value of potential dependency genes in clear cell renal cell carcinoma based on a large-scale CRISPR-Cas9 and RNAi screening database DepMap. Intern J Med Sci. 18(9):2063–2075. doi:10.7150/ijms.51703.
   PubMed Web of Science ®Google Scholar
• Siegel R, Miller K, Jemal A. 2019. Cancer statistics, 2019. CA Cancer J Clinic. 69(1):7–34. doi:10.3322/caac.21551.
   PubMed Web of Science ®Google Scholar
• Siegel R, Miller K, Jemal A. 2020. Cancer statistics, 2020. CA Cancer J Clinic. 70(1):7–30. doi:10.3322/caac.21590.
   PubMed Web of Science ®Google Scholar
• Sing T, Sander O, Berrenwinkel N, Lengauer T. 2005. ROCR: visualizing classifier performance in R. BIOINFORMATICS -OXFORD-.
   Google Scholar
• Song Q, Shang J, Yang Z, Zhang L, Zhang C, Chen J, et al. 2019. Identification of an immune signature predicting prognosis risk of patients in lung adenocarcinoma. J Translat Med. 17(1):70. doi:10.1186/s12967-019-1824-4.
   PubMed Web of Science ®Google Scholar
• Sun J, Chen L, Zhang G, Jiang J, Zhu M, Tan Y, et al. 2010. Clinical significance and regulation of the costimulatory molecule B7-H3 in human colorectal carcinoma. Cancer Immunol Immunother: CII. 59(8):1163–1171. doi:10.1007/s00262-010-0841-1.
   PubMed Web of Science ®Google Scholar
• Tang J, Jiang W, Liu D, Luo J, Wu X, Pan Z, et al. 2018. The comprehensive molecular landscape of the immunologic co-stimulator B7 and TNFR ligand receptor families in colorectal cancer: immunotherapeutic implications with microsatellite instability. Oncoimmunology. 7(10):e1488566. doi:10.1080/2162402x.2018.1488566.
   PubMed Web of Science ®Google Scholar
• Wang W, Zhao H, Zhang S, Kang E, Chen Y, Ni C, et al. 2009. Patterns of expression and function of the p75(NGFR) protein in pancreatic cancer cells and tumours. J European Soc Surg Oncol Brit Assoc Surg Oncol. 35(8):826–832. doi:10.1016/j.ejso.2008.10.013.
   PubMed Web of Science ®Google Scholar
• Wu J, Wang Y, Jiang Z. 2020. Fusobacterium nucleatumImmune induction identified by TMT proteomics analysis in autoinducer-2 treated macrophages. Expert Rev Proteom. 17(2):175–185. doi:10.1080/14789450.2020.1738223.
   PubMed Web of Science ®Google Scholar
• Wu J, Wang Y, Jiang Z. 2021. TNFSF9 is a prognostic biomarker and correlated with immune infiltrates in pancreatic cancer. J Gastrointest Cancer. 52(1):150–159. doi:10.1007/s12029-020-00371-6.
   PubMed Web of Science ®Google Scholar
• Yan Y, Gao R, Trinh T, Grant M. 2017. Immunodeficiency in pancreatic adenocarcinoma with diabetes revealed by comparative genomics. Clin Cancer Res Off J Amer Assoc Cancer Res. 23(20):6363–6373. doi:10.1158/1078-0432.ccr-17-0250.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. 2012. Clusterprofiler: an R package for comparing biological themes among gene clusters. Omics-a J Integr Biol. 16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Zhang C, Zhang Z, Sun N, Zhang G, Wang F, Luo Y, et al. 2020. Identification of a costimulatory molecule-based signature for predicting prognosis risk and immunotherapy response in patients with lung adenocarcinoma. Oncoimmunology. 9(1):1824641. doi:10.1080/2162402x.2020.1824641.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Yang J, Wang X, Li X. 2021. GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. Scient Rep. 11(1):20441. doi:10.1038/s41598-021-99544-x.
   PubMed Web of Science ®Google Scholar
• Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. 2008. UCSC genome browser tutorial. Genomics. 92(2):75–84.
   PubMed Web of Science ®Google Scholar