Identification of a Four-Gene Signature for Determining the Prognosis of Papillary Thyroid Carcinoma by Integrated Bioinformatics Analysis

References

• Siegel RL, Miller KD, Fuchs HE, et al. Cancer statistics, 2021. CA Cancer J Clin. 2021;71(1):7–33. doi:10.3322/caac.21654
   PubMed Web of Science ®Google Scholar
• Zou M, Baitei EY, Alzahrani AS, et al. Concomitant RAS, RET/ PTC, or BRAF mutations in advanced stage of papillary thyroid carcinoma. Thyroid. 2014;24(8):1256–1266. doi:10.1089/thy.2013.0610
   PubMed Web of Science ®Google Scholar
• Lundgren CI, Hall P, Dickman PW, et al. Clinically significant prognostic factors for differentiated thyroid carcinoma: a population-based, nested case-control study. Cancer-Am Cancer Soc. 2006;106(3):524–531. doi:10.1002/cncr.21653
   PubMed Web of Science ®Google Scholar
• Grant CS. Papillary thyroid cancer: strategies for optimal individualized surgical management. Clin Ther. 2014;36(7):1117–1126. doi:10.1016/j.clinthera.2014.03.016
   PubMed Web of Science ®Google Scholar
• Nath MC, Erickson LA. Aggressive variants of papillary thyroid carcinoma: hobnail, tall cell, columnar, and solid. Adv Anat Pathol. 2018;25(3):172–179. doi:10.1097/PAP.0000000000000184
   PubMed Web of Science ®Google Scholar
• Sywak M, Pasieka JL, Ogilvie T. A review of thyroid cancer with intermediate differentiation. J Surg Oncol. 2004;86(1):44–54. doi:10.1002/jso.20044
   PubMed Web of Science ®Google Scholar
• Regalbuto C, Malandrino P, Tumminia A, et al. A diffuse sclerosing variant of papillary thyroid carcinoma: clinical and pathologic features and outcomes of 34 consecutive cases. Thyroid. 2011;21(4):383–389. doi:10.1089/thy.2010.0331
   PubMed Web of Science ®Google Scholar
• Lam AK, Lo CY. Diffuse sclerosing variant of papillary carcinoma of the thyroid: a 35-year comparative study at a single institution. Ann Surg Oncol. 2006;13(2):176–181. doi:10.1245/ASO.2006.03.062
   PubMed Web of Science ®Google Scholar
• Vuong HG, Kondo T, Pham TQ, et al. Prognostic significance of diffuse sclerosing variant papillary thyroid carcinoma: a systematic review and meta-analysis. Eur J Endocrinol. 2017;176(4):433–441. doi:10.1530/EJE-16-0863
   PubMed Web of Science ®Google Scholar
• Malandrino P, Russo M, Regalbuto C, et al. Outcome of the diffuse sclerosing variant of papillary thyroid cancer: a meta-analysis. Thyroid. 2016;26(9):1285–1292. doi:10.1089/thy.2016.0168
   PubMed Web of Science ®Google Scholar
• Axelsson TA, Hrafnkelsson J, Olafsdottir EJ, et al. Tall cell variant of papillary thyroid carcinoma: a population-based study in Iceland. Thyroid. 2015;25(2):216–220. doi:10.1089/thy.2014.0075
   PubMed Web of Science ®Google Scholar
• Liu Z, Zeng W, Chen T, et al. A comparison of the clinicopathological features and prognoses of the classical and the tall cell variant of papillary thyroid cancer: a meta-analysis. Oncotarget. 2017;8(4):6222–6232. doi:10.18632/oncotarget.14055
   PubMedGoogle Scholar
• Longheu A, Canu GL, Cappellacci F, et al. Tall cell variant versus conventional papillary thyroid carcinoma: a retrospective analysis in 351 consecutive patients. J Clin Med. 2020;10(1). doi:10.3390/jcm10010070
   PubMed Web of Science ®Google Scholar
• Munari E, Mariotti FR, Quatrini L, et al. PD-1/PD-L1 in cancer: pathophysiological, diagnostic and therapeutic aspects. Int J Mol Sci. 2021;22(10). doi:10.3390/ijms22105123
   Web of Science ®Google Scholar
• Girolami I, Pantanowitz L, Mete O, et al. Programmed Death-Ligand 1 (PD-L1) is a potential biomarker of disease-free survival in papillary thyroid carcinoma: a systematic review and meta-analysis of PD-L1 immunoexpression in follicular epithelial derived thyroid carcinoma. Endocr Pathol. 2020;31(3):291–300. doi:10.1007/s12022-020-09630-5
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Tibshirani R. The lasso method for variable selection in the Cox model. Stat Med. 1997;16(4):385–395. doi:10.1002/(sici)1097-0258(19970228)16:4<385:aid-sim380>3.0.co;2-3
   PubMed Web of Science ®Google Scholar
• Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33(1):1–22.
   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. 2011:1277. doi:10.1186/1471-2105-12-77
   Web of Science ®Google Scholar
• Kopetz S, Tabernero J, Rosenberg R, et al. Genomic classifier coloprint predicts recurrence in stage II colorectal cancer patients more accurately than clinical factors. Oncologist. 2015;20(2):127–133. doi:10.1634/theoncologist.2014-0325
   PubMed Web of Science ®Google Scholar
• Li X, Xie M, Yin S, et al. Identification and validation of a six immune-related genes signature for predicting prognosis in patients with stage II colorectal cancer. Front Genet. 2021:12666003. doi:10.3389/fgene.2021.666003
   Web of Science ®Google Scholar
• Shen Y, Dong S, Liu J, et al. Identification of potential biomarkers for thyroid cancer using bioinformatics strategy: a study based on GEO datasets. Biomed Res Int. 2020:20209710421. doi:10.1155/2020/9710421
   Web of Science ®Google Scholar
• Liu L, He C, Zhou Q, et al. Identification of key genes and pathways of thyroid cancer by integrated bioinformatics analysis. J Cell Physiol. 2019;234(12):23647–23657. doi:10.1002/jcp.28932
   PubMed Web of Science ®Google Scholar
• Zhang B, Chen Z, Wang Y, et al. Integrated bioinformatics analysis for the identification of key genes and signaling pathways in thyroid carcinoma. Exp Ther Med. 2021;21(4):298. doi:10.3892/etm.2021.9729
   PubMed Web of Science ®Google Scholar
• Pan Y, Wu L, He S, et al. Identification of hub genes in thyroid carcinoma to predict prognosis by integrated bioinformatics analysis. Bioengineered. 2021;12(1):2928–2940. doi:10.1080/21655979.2021.1940615
   PubMed Web of Science ®Google Scholar
• Ren H, Liu X, Li F, et al. Identification of a six gene prognosis signature for papillary thyroid cancer using multi-omics methods and bioinformatics analysis. Front Oncol. 2021;11:624421. doi:10.3389/fonc.2021.624421
   PubMed Web of Science ®Google Scholar
• Wan Y, Zhang X, Leng H, et al. Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis. Peerj. 2020;8:e9120. doi:10.7717/peerj.9120
   PubMed Web of Science ®Google Scholar
• Zhang S, Wang Q, Han Q, et al. Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods. Biosci Rep. 2019;39(4). doi:10.1042/BSR20190083
   Web of Science ®Google Scholar
• Liu Y, Gao S, Jin Y, et al. Bioinformatics analysis to screen key genes in papillary thyroid carcinoma. Oncol Lett. 2020;19(1):195–204. doi:10.3892/ol.2019.11100
   PubMed Web of Science ®Google Scholar
• Faiyaz UHM, King LM, Krakow D, et al. Mutations in orthologous genes in human spondyloepimetaphyseal dysplasia and the brachymorphic mouse. Nat Genet. 1998;20(2):157–162. doi:10.1038/2458
   PubMed Web of Science ®Google Scholar
• Xu ZH, Freimuth RR, Eckloff B, et al. Human 3’-phosphoadenosine 5’-phosphosulfate synthetase 2 (PAPSS2) pharmacogenetics: gene resequencing, genetic polymorphisms and functional characterization of variant allozymes. Pharmacogenetics. 2002;12(1):11–21. doi:10.1097/00008571-200201000-00003
   PubMedGoogle Scholar
• Ibeawuchi C, Schmidt H, Voss R, et al. Exploring prostate cancer genome reveals simultaneous losses of PTEN, FAS and PAPSS2 in patients with PSA recurrence after radical prostatectomy. Int J Mol Sci. 2015;16(2):3856–3869. doi:10.3390/ijms16023856
   PubMed Web of Science ®Google Scholar
• Xu P, Xi Y, Zhu J, et al. Intestinal sulfation is essential to protect against colitis and colonic carcinogenesis. Gastroenterology. 2021;161(1):271–286. doi:10.1053/j.gastro.2021.03.048
   PubMed Web of Science ®Google Scholar
• Steiglitz BM, Keene DR, Greenspan DS. PCOLCE2 encodes a functional procollagen C-proteinase enhancer (PCPE2) that is a collagen-binding protein differing in distribution of expression and post-translational modification from the previously described PCPE1. J Biol Chem. 2002;277(51):49820–49830. doi:10.1074/jbc.M209891200
   PubMed Web of Science ®Google Scholar
• Wu ZH, Zhou T, Sun HY. DNA methylation-based diagnostic and prognostic biomarkers of nasopharyngeal carcinoma patients. Medicine. 2020;99(24):e20682. doi:10.1097/MD.0000000000020682
   PubMed Web of Science ®Google Scholar
• Garlanda C, Bottazzi B, Magrini E, et al. PTX3, a humoral pattern recognition molecule, in innate immunity, tissue repair, and cancer. Physiol Rev. 2018;98(2):623–639. doi:10.1152/physrev.00016.2017
   PubMed Web of Science ®Google Scholar
• Rubino M, Kunderfranco P, Basso G, et al. Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer. Oncoimmunology. 2017;6(7):e1333215. doi:10.1080/2162402X.2017.1333215
   PubMed Web of Science ®Google Scholar
• Gordon KJ, Dong M, Chislock EM, et al. Loss of type III transforming growth factor beta receptor expression increases motility and invasiveness associated with epithelial to mesenchymal transition during pancreatic cancer progression. Carcinogenesis. 2008;29(2):252–262. doi:10.1093/carcin/bgm249
   PubMed Web of Science ®Google Scholar
• Zhang S, Sun WY, Wu JJ, et al. Decreased expression of the type III TGF-beta receptor enhances metastasis and invasion in hepatocellullar carcinoma progression. Oncol Rep. 2016;35(4):2373–2381. doi:10.3892/or.2016.4615
   PubMed Web of Science ®Google Scholar
• Hempel N, How T, Dong M, et al. Loss of betaglycan expression in ovarian cancer: role in motility and invasion. Cancer Res. 2007;67(11):5231–5238. doi:10.1158/0008-5472.CAN-07-0035
   PubMed Web of Science ®Google Scholar
• Mammadova-Bach E, Gil-Pulido J, Sarukhanyan E, et al. Platelet glycoprotein VI promotes metastasis through interaction with cancer cell-derived galectin-3. Blood. 2020;135(14):1146–1160. doi:10.1182/blood.2019002649
   PubMed Web of Science ®Google Scholar
• Miguchi M, Hinoi T, Shimomura M, et al. Gasdermin c is upregulated by inactivation of transforming growth factor beta receptor type II in the presence of mutated apc, promoting colorectal cancer proliferation. PLoS One. 2016;11(11):e166422. doi:10.1371/journal.pone.0166422
   PubMed Web of Science ®Google Scholar
• Tu CF, Wu MY, Lin YC, et al. FUT8 promotes breast cancer cell invasiveness by remodeling TGF-beta receptor core fucosylation. Breast Cancer Res. 2017;19(1):111. doi:10.1186/s13058-017-0904-8
   PubMed Web of Science ®Google Scholar
• Ward NP, DeNicola GM. Sulfur metabolism and its contribution to malignancy. Int Rev Cell Mol Biol. 2019;347:39–103. doi:10.1016/bs.ircmb.2019.05.001
   PubMed Web of Science ®Google Scholar