116
Views
0
CrossRef citations to date
0
Altmetric
Original Research

Comprehensive Analysis of the PROSER2-AS1-Related ceRNA Network and Immune Cell Infiltration in Papillary Thyroid Carcinoma

, , &
Pages 1647-1663 | Published online: 16 Feb 2022

References

  • La Vecchia C, Negri E. Thyroid cancer: the thyroid cancer epidemic - overdiagnosis or a real increase? Nat Rev Endocrinol. 2017;13(6):318–319. doi:10.1038/nrendo.2017.53
  • Morris LGT, Tuttle RM, Davies L. Changing trends in the incidence of thyroid cancer in the United States. JAMA Otolaryngol Head Neck Surg. 2016;142(7):709–711. doi:10.1001/jamaoto.2016.0230
  • Katoh H, Yamashita K, Enomoto T, Watanabe M. Classification and general considerations of thyroid cancer. Ann Clin Pathol. 2015;3(1):1045.
  • Xing M. Molecular pathogenesis and mechanisms of thyroid cancer. Nat Rev Cancer. 2013;13(3):184–199. doi:10.1038/nrc3431
  • Tian W, Xi H. Analysis of the survival status of patients with thyroid carcinoma. Chin J Pract Surg. 2016;36(5):489–493.
  • Cheetham S, Gruhl F, Mattick J, Dinger M. Long noncoding RNAs and the genetics of cancer. Br J Cancer. 2013;108(12):2419–2425. doi:10.1038/bjc.2013.233
  • Murugan AK, Munirajan AK, Alzahrani AS. Long noncoding RNAs: emerging players in thyroid cancer pathogenesis. Endocr Relat Cancer. 2018;25(2):R59–R82. doi:10.1530/ERC-17-0188
  • Qi P, Du X. The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine. Mod Pathol. 2013;26(2):155–165. doi:10.1038/modpathol.2012.160
  • Zhang J, Du Y, Zhang X, Li M, Li X. Downregulation of BANCR promotes aggressiveness in papillary thyroid cancer via the MAPK and PI3K pathways. J Cancer. 2018;9(7):1318. doi:10.7150/jca.20150
  • Zhu H, Lv Z, An C, et al. Onco-lncRNA HOTAIR and its functional genetic variants in papillary thyroid carcinoma. Sci Rep. 2016;6(1):1–7. doi:10.1038/s41598-016-0001-8
  • Liu L, Yang J, Zhu X, Li D, Lv Z, Zhang X. Long noncoding RNA H19 competitively binds miR‐17‐5p to regulate YES 1 expression in thyroid cancer. FEBS J. 2016;283(12):2326–2339. doi:10.1111/febs.13741
  • Liu J, Dong H, Yang Y, et al. Upregulation of long noncoding RNA MALAT1 in papillary thyroid cancer and its diagnostic value. Future Oncol. 2018;14(29):3015–3022. doi:10.2217/fon-2018-0416
  • Jendrzejewski J, Thomas A, Liyanarachchi S, et al. PTCSC3 is involved in papillary thyroid carcinoma development by modulating S100A4 gene expression. J Clin Endocrinol Metab. 2015;100(10):E1370–E1377. doi:10.1210/jc.2015-2247
  • He H, Li W, Liyanarachchi S, et al. Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2. J Clin Endocrinol Metab. 2015;100(1):E164–E172. doi:10.1210/jc.2014-2147
  • Wang Y, He H, Li W, et al. MYH9 binds to lncRNA gene PTCSC2 and regulates FOXE1 in the 9q22 thyroid cancer risk locus. Proc Natl Acad Sci. 2017;114(3):474–479. doi:10.1073/pnas.1619917114
  • Wang C, Yan G, Zhang Y, Jia X, Bu P. Long non-coding RNA MEG3 suppresses migration and invasion of thyroid carcinoma by targeting of Rac1. Neoplasma. 2015;62(4):541–549. doi:10.4149/neo_2015_065
  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–358. doi:10.1016/j.cell.2011.07.014
  • Spill F, Reynolds DS, Kamm RD, Zaman MH. Impact of the physical microenvironment on tumor progression and metastasis. Curr Opin Biotechnol. 2016;40:41–48. doi:10.1016/j.copbio.2016.02.007
  • Del Prete A, Schioppa T, Tiberio L, Stabile H, Sozzani S. Leukocyte trafficking in tumor microenvironment. Curr Opin Pharmacol. 2017;35:40–47. doi:10.1016/j.coph.2017.05.004
  • Arneth B. Tumor microenvironment. Medicina. 2020;56(1):15. doi:10.3390/medicina56010015
  • Hirsch FR, Scagliotti GV, Mulshine JL, et al. Lung cancer: current therapies and new targeted treatments. Lancet. 2017;389(10066):299–311. doi:10.1016/S0140-6736(16)30958-8
  • Mould RC, van Vloten JP, AuYeung AW, Karimi K, Bridle BW. Immune responses in the thyroid cancer microenvironment: making immunotherapy a possible mission. Endocr Relat Cancer. 2017;24(12):T311–T329. doi:10.1530/ERC-17-0316
  • Selamat SA, Chung BS, Girard L, et al. Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res. 2012;22(7):1197–1211. doi:10.1101/gr.132662.111
  • Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and bioConductor. Bioinformatics. 2007;23(14):1846–1847. doi:10.1093/bioinformatics/btm254
  • Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • 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. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102
  • Bindea G, Mlecnik B, Tosolini M, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39(4):782–795. doi:10.1016/j.immuni.2013.10.003
  • Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013;14(1):1–15. doi:10.1186/1471-2105-14-7
  • Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–W102. doi:10.1093/nar/gkx247
  • 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
  • Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Pulido TH, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA. 2017;23(7):1080–1087. doi:10.1261/rna.060814.117
  • Wen X, Gao L, Guo X, et al. lncSLdb: a resource for long non-coding RNA subcellular localization. Database. 2018;2018. doi:10.1093/database/bay085
  • Miao Y-R, Liu W, Zhang Q, Guo A-Y. lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs. Nucleic Acids Res. 2018;46(D1):D276–D280. doi:10.1093/nar/gkx1004
  • Sticht C, De La Torre C, Parveen A, Gretz N. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 2018;13(10):e0206239. doi:10.1371/journal.pone.0206239
  • Dykes IM, Emanueli C. Transcriptional and post-transcriptional gene regulation by long non-coding RNA. Genom Proteom Bioinform. 2017;15(3):177–186. doi:10.1016/j.gpb.2016.12.005
  • Chen F, Yin S, Zhu J, et al. lncRNA DGCR5 acts as a tumor suppressor in papillary thyroid carcinoma via sequestering miR‑2861. Exp Ther Med. 2019;17(1):895–900. doi:10.3892/etm.2018.7012
  • Li X, Zhong W, Xu Y, Yu B, Liu H. Silencing of lncRNA LINC00514 inhibits the malignant behaviors of papillary thyroid cancer through miR-204–3p/CDC23 axis. Biochem Biophys Res Commun. 2019;508(4):1145–1148. doi:10.1016/j.bbrc.2018.12.051
  • Feng L, Yang B, Tang XD. Long noncoding RNA LINC00460 promotes carcinogenesis via sponging miR‐613 in papillary thyroid carcinoma. J Cell Physiol. 2019;234(7):11431–11439. doi:10.1002/jcp.27799
  • Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15(1):7–21. doi:10.1038/nrg3606
  • Hudson WH, Prokhnevska N, Gensheimer J, et al. Expression of novel long noncoding RNAs defines virus-specific effector and memory CD8+ T cells. Nat Commun. 2019;10(1):1–11. doi:10.1038/s41467-018-07956-7
  • Liu SJ, Horlbeck MA, Cho SW, et al. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science. 2017;355:6320. doi:10.1126/science.aah7111
  • Heward JA, Lindsay MA. Long non-coding RNAs in the regulation of the immune response. Trends Immunol. 2014;35(9):408–419. doi:10.1016/j.it.2014.07.005
  • Chen YG, Satpathy AT, Chang HY. Gene regulation in the immune system by long noncoding RNAs. Nat Immunol. 2017;18(9):962–972. doi:10.1038/ni.3771
  • Lapeyre-Prost A, Terme M, Pernot S, et al. Immunomodulatory activity of VEGF in cancer. Int Rev Cell Mol Biol. 2017;330:295–342. doi:10.1016/bs.ircmb.2016.09.007
  • Terme M, Pernot S, Marcheteau E, et al. VEGFA-VEGFR pathway blockade inhibits tumor-induced regulatory T-cell proliferation in colorectal cancer. Cancer Res. 2013;73(2):539–549. doi:10.1158/0008-5472.CAN-12-2325
  • Nishida J, Miyazono K, Ehata S. Decreased TGFBR3/betaglycan expression enhances the metastatic abilities of renal cell carcinoma cells through TGF-β-dependent and-independent mechanisms. Oncogene. 2018;37(16):2197–2212. doi:10.1038/s41388-017-0084-0
  • Fang W-Y, Kuo Y-Z, Chang J-Y, et al. The tumor suppressor TGFBR3 blocks lymph node metastasis in head and neck cancer. Cancers. 2020;12(6):1375. doi:10.3390/cancers12061375
  • Hanks BA, Holtzhausen A, Evans KS, et al. Type III TGF-β receptor downregulation generates an immunotolerant tumor microenvironment. J Clin Invest. 2013;123(9):3925–3940. doi:10.1172/JCI65745