Prognostic Score Model Based on Ten Differentially Methylated Genes for Predicting Clinical Outcomes in Patients with Adenocarcinoma of the Colon

References

• Dekker E, Tanis PJ, Vleugels JLA, Kasi PM, Wallace MB. Colorectal cancer. Lancet. 2019;394(10207):1467–1480. doi:10.1016/S0140-6736(19)32319-031631858
   PubMed Web of Science ®Google Scholar
• Paschke S, Jafarov S, Staib L. Are colon and rectal cancer two different tumor entities? A proposal to abandon the term colorectal cancer. Int J Mol Sci. 2018;19(9):2577–2590. doi:10.3390/ijms19092577
   PubMed Web of Science ®Google Scholar
• Buchwald P, Hall C, Davidson C, et al. Improved survival for rectal cancer compared to colon cancer: the four cohort study. ANZ J Surg. 2018;88(3):E114–e117. doi:10.1111/ans.1373027618786
   PubMed Web of Science ®Google Scholar
• Arnold M, Sierra MS, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global patterns and trends in colorectal cancer incidence and mortality. Gut. 2017;66(4):683–691. doi:10.1136/gutjnl-2015-31091226818619
   PubMed Web of Science ®Google Scholar
• Dienstmann R, Salazar R, Tabernero J. Personalizing colon cancer adjuvant therapy: selecting optimal treatments for individual patients. J Clin Oncol. 2015;33(16):1787–1796. doi:10.1200/JCO.2014.60.021325918287
   PubMed Web of Science ®Google Scholar
• Zhou R, Zhang J, Zeng D, et al. Immune cell infiltration as a biomarker for the diagnosis and prognosis of stage I–III colon cancer. Cancer Immunol Immunother. 2019;68(3):433–442.30564892
   PubMed Web of Science ®Google Scholar
• Xu G, Zhang M, Zhu H, Xu J. A 15-gene signature for prediction of colon cancer recurrence and prognosis based on SVM. Gene. 2017;604:33–40. doi:10.1016/j.gene.2016.12.01627998790
   PubMed Web of Science ®Google Scholar
• Yang H, Liu H, Lin HC, et al. Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients. Aging. 2019;11(19):8710–8727. doi:10.18632/aging.10236531612869
   PubMedGoogle Scholar
• Galamb O, Kalmár A, Péterfia B, et al. Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. Epigenetics. 2016;11(8):588–602. doi:10.1080/15592294.2016.119089427245242
   PubMed Web of Science ®Google Scholar
• Molnár B, Galamb O, Péterfia B, et al. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer. 2018;18(1):695. doi:10.1186/s12885-018-4609-x29945573
   PubMed Web of Science ®Google Scholar
• Yang C, Zhang Y, Xu X, Li W. Molecular subtypes based on DNA methylation predict prognosis in colon adenocarcinoma patients. Aging. 2019;11(24):11880–11892. doi:10.18632/aging.10249231852837
   PubMedGoogle Scholar
• Liu T, Li C, Jin L, Li C, Wang L. The prognostic value of m6A RNA methylation regulators in colon adenocarcinoma. Med Sci Monit. 2019;25:9435–9445.31823961
   PubMed Web of Science ®Google Scholar
• Zhao QQ, Jiang C, Gao Q, et al. Gene expression and methylation profiles identified CXCL3 and CXCL8 as key genes for diagnosis and prognosis of colon adenocarcinoma. J Cell Physiol. 2020;235(5):4902–4912. doi:10.1002/jcp.2936831709538
   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/gkv00725605792
   PubMed Web of Science ®Google Scholar
• Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. P Natl Acad Sci USA. 1998;95(25):14863–14868. doi:10.1073/pnas.95.25.14863
   PubMed Web of Science ®Google Scholar
• Wang L, Cao C, Ma Q, et al. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol. 2014;14:169. doi:10.1186/1471-2229-14-16924939556
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559. doi:10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar
• Cao J, Zhang SA. Bayesian extension of the hypergeometric test for functional enrichment analysis. Biometrics. 2014;70(1):84–94. doi:10.1111/biom.1212224320951
   PubMed Web of Science ®Google Scholar
• Zou KH, Tuncali K, Silverman SG. Correlation and simple linear regression. Radiology. 2003;227(3):617–622. doi:10.1148/radiol.227301149912773666
   PubMed Web of Science ®Google Scholar
• Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. doi:10.1038/nprot.2008.21119131956
   PubMed Web of Science ®Google Scholar
• Wang P, Wang Y, Hang B, Zou X, Mao JH. A novel gene expression-based prognostic scoring system to predict survival in gastric cancer. Oncotarget. 2016;7(34):55343–55351. doi:10.18632/oncotarget.1053327419373
   PubMedGoogle Scholar
• Wang D, Wu TT, Zhao Y. Penalized empirical likelihood for the sparse cox regression model. J Stat Plan Infer. 2019;201:71–85. doi:10.1016/j.jspi.2018.12.001
   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;2-39044528
   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;12:77. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Shan S, Chen W, Jia JD. Transcriptome analysis revealed a highly connected gene module associated with cirrhosis to hepatocellular carcinoma development. Front Genet. 2019;10:305. doi:10.1007/s00262-018-2289-731001331
   PubMed Web of Science ®Google Scholar
• Costa-Pinheiro P, Montezuma D, Henrique R, Jerónimo C. Diagnostic and prognostic epigenetic biomarkers in cancer. Epigenomics. 2015;7(6):1003–1015. doi:10.2217/epi.15.5626479312
   PubMed Web of Science ®Google Scholar
• Sauerbrei W, Taube SE, McShane LM, Cavenagh MM, Altman DG. Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): an abridged explanation and elaboration. J Natl Cancer Inst. 2018;110(8):803–811. doi:10.1093/jnci/djy08829873743
   PubMedGoogle Scholar
• Das V, Kalita J, Pal M. Predictive and prognostic biomarkers in colorectal cancer: a systematic review of recent advances and challenges. Biomed Pharmacother. 2017;87:8–19. doi:10.1016/j.biopha.2016.12.06428040600
   PubMed Web of Science ®Google Scholar
• Hong SN. Genetic and epigenetic alterations of colorectal cancer. Intest Res. 2018;16(3):327–337. doi:10.5217/ir.2018.16.3.32730090031
   PubMed Web of Science ®Google Scholar
• Ewing I, Hurley JJ, Josephides E, Millar A. The molecular genetics of colorectal cancer. Frontline Gastroenterol. 2014;5(1):26–30. doi:10.1136/flgastro-2013-10032924416503
   PubMedGoogle Scholar
• Wang Y, Zhang M, Hu X, Qin W, Wu H, Wei M. Colon cancer-specific diagnostic and prognostic biomarkers based on genome-wide abnormal DNA methylation. Aging. 2020;12(22):22626–22655. doi:10.18632/aging.10387433202377
   PubMedGoogle Scholar
• de Sousa EMF, Colak S, Buikhuisen J, et al. Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients. Cell Stem Cell. 2011;9(5):476–485. doi:10.1016/j.stem.2011.10.00822056143
   PubMed Web of Science ®Google Scholar
• Moh MC, Shen S. The roles of cell adhesion molecules in tumor suppression and cell migration: a new paradox. Cell Adh Migr. 2009;3(4):334–336. doi:10.4161/cam.3.4.924619949308
   PubMed Web of Science ®Google Scholar
• Wang W, Yu S, Huang S, et al. A complex role for calcium signaling in colorectal cancer development and progression. Mol Cancer Res. 2019;17(11):2145–2153. doi:10.1158/1541-7786.MCR-19-042931366605
   PubMed Web of Science ®Google Scholar
• Raynal NJ, Lee JT, Wang Y, et al. Targeting calcium signaling induces epigenetic reactivation of tumor suppressor genes in cancer. Cancer Res. 2016;76(6):1494–1505. doi:10.1158/0008-5472.CAN-14-239126719529
   PubMed Web of Science ®Google Scholar
• Centuori SM, Gomes CJ, Trujillo J, et al. Deoxycholic acid mediates non-canonical EGFR-MAPK activation through the induction of calcium signaling in colon cancer cells. BBA-Biomembranes. 2016;1861(7):663–670. doi:10.1016/j.bbalip.2016.04.00627086143
   PubMed Web of Science ®Google Scholar
• Li Q, Ye L, Zhang X, et al. FZD8, a target of p53, promotes bone metastasis in prostate cancer by activating canonical Wnt/β-catenin signaling. Cancer Lett. 2017;402:166–176. doi:10.1016/j.canlet.2017.05.02928602974
   PubMed Web of Science ®Google Scholar
• Chen W, Liu Z, Mai W, Xiao Y, You X, Qin L. FZD8 indicates a poor prognosis and promotes gastric cancer invasion and metastasis via B-catenin signaling pathway. Ann Clin Lab Sci. 2020;50(1):13–23.32161008
   PubMed Web of Science ®Google Scholar
• Ide T, Chu K, Aaronson SA, Lee SW. GAMT joins the p53 network: branching into metabolism. Cell Cycle. 2010;9(9):1706–1710. doi:10.4161/cc.9.9.1147320404548
   PubMed Web of Science ®Google Scholar
• Ide T, Brown-Endres L, Chu K, et al. GAMT, a p53-inducible modulator of apoptosis, is critical for the adaptive response to nutrient stress. Mol Cell. 2009;36(3):379–392. doi:10.1016/j.molcel.2009.09.03119917247
   PubMed Web of Science ®Google Scholar
• Lian S, Meng L, Xing X, Yang Y, Qu L, Shou C. PRL-3 promotes cell adhesion by interacting with JAM2 in colon cancer. Oncol Lett. 2016;12(3):1661–1666. doi:10.3892/ol.2016.483627588115
   PubMed Web of Science ®Google Scholar
• Lin X, Chen W, Wei F, Zhou BP, Hung MC, Xie X. POMC maintains tumor-initiating properties of tumor tissue-derived long-term-cultured breast cancer stem cells. Int J Cancer. 2017;140(11):2517–2525. doi:10.1002/ijc.3065828214331
   PubMed Web of Science ®Google Scholar
• Davis CA, Haberland M, Arnold MA, et al. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Mol Cell Biol. 2006;26(7):2626–2636. doi:10.1128/MCB.26.7.2626-2636.200616537907
   PubMed Web of Science ®Google Scholar
• Qiao L, Zheng J, Jin X, et al. Ginkgolic acid inhibits the invasiveness of colon cancer cells through AMPK activation. Oncol Lett. 2017;14(5):5831–5838. doi:10.3892/ol.2017.696729113214
   PubMed Web of Science ®Google Scholar
• Tong W, Wang Q, Sun D, Suo J. Curcumin suppresses colon cancer cell invasion via AMPK-induced inhibition of NF-κB, uPA activator and MMP9. Oncol Lett. 2016;12(5):4139–4146. doi:10.3892/ol.2016.514827895783
   PubMed Web of Science ®Google Scholar
• Liu J, Long S, Wang H, et al. Blocking AMPK/ULK1-dependent autophagy promoted apoptosis and suppressed colon cancer growth. Cancer Cell Int. 2019;19:336. doi:10.1186/s12935-019-1054-031871431
   PubMed Web of Science ®Google Scholar
• Yagi T, Kubota E, Koyama H, et al. Glucagon promotes colon cancer cell growth via regulating AMPK and MAPK pathways. Oncotarget. 2018;9(12):10650–10664. doi:10.18632/oncotarget.2436729535833
   PubMedGoogle Scholar
• Galon J, Pagès F, Marincola FM, et al. Cancer classification using the immunoscore: a worldwide task force. J Transl Med. 2012;10:205. doi:10.1186/1479-5876-10-20523034130
   PubMed Web of Science ®Google Scholar
• Mlecnik B, Bindea G, Pagès F, Galon J. Tumor immunosurveillance in human cancers. Cancer Metastasis Rev. 2011;30(1):5–12. doi:10.1007/s10555-011-9270-721249426
   PubMed Web of Science ®Google Scholar
• Yin Z, Yan X, Wang Q, et al. Detecting prognosis risk biomarkers for colon cancer through multi-omics-based prognostic analysis and target regulation simulation modeling. Front Genet. 2020;11:524. doi:10.3389/fgene.2020.0052432528533
   PubMed Web of Science ®Google Scholar