Identification of methylation-driven genes related to the prognosis of papillary renal cell carcinoma: a study based on The Cancer Genome Atlas

Cancer Cell International
Zeyu LiuJingnan Xu

Abstract

Aberrant DNA methylation patterns are involved in the pathogenesis of papillary renal cell carcinoma (pRCC). This study aimed to investigate the potential of methylation-driven genes as biomarkers in determining the prognosis of pRCC by bioinformatics analysis. DNA methylation and transcriptome profiling data were downloaded from The Cancer Genome Atlas database. Methylation-driven genes (MDGs) were obtained using MethylMix R package. A Cox regression model was used to screen for pRCC prognosis-related MDGs, and a linear risk model based on MDG methylation profiles was constructed. A combined methylation and gene expression survival analysis was performed to further explore the prognostic value of MDGs independently. A total of 31 MDGs were obtained. Univariate and multivariate Cox regression analysis identified eight genes (CASP1, CD68, HOXD3, HHLA2, HOXD9, HOXA10-AS, TMEM71, and PLA2G16), which were used to construct a predictive model associated with overall survival in pRCC patients. Combined DNA methylation and gene expression survival analysis revealed that C19orf33, GGT6, GIPC2, HHLA2, HOXD3, HSD17B14, PLA2G16, and TMEM71 were significantly associated with patients' survival. Through the analysis of MDGs in pRCC, this st...Continue Reading

References

Mar 18, 2005·Annual Review of Immunology·Rebecca J GreenwaldArlene H Sharpe
Dec 31, 2005·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Mar 22, 2007·Journal of Cell Science·Irina NazarenkoChristine Sers
May 27, 2008·Nature Reviews. Immunology·Weiping Zou, Lieping Chen
Mar 28, 2009·Cellular and Molecular Life Sciences : CMLS·Igor P Pogribny, Frederick A Beland
Jun 10, 2009·Current Genomics·B SadikovicM Zielenska
Apr 2, 2010·Nature Reviews. Cancer·Nilay Shah, Saraswati Sukumar
Dec 27, 2011·Expert Opinion on Pharmacotherapy·Eduard VrdoljakLaszlo Torday
Jan 20, 2012·Nature·Till StrowigRichard Flavell
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Jun 16, 2012·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Sandra SteffensAndres J Schrader
Sep 1, 2012·Clinical & Experimental Metastasis·Cheng ShaoqiangZhang Qingyuan
Nov 22, 2013·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Deneen M WellikMarian A Ros
Dec 12, 2013·Virchows Archiv : an International Journal of Pathology·Carl Ludwig BehnesHeinz-Joachim Radzun
Aug 26, 2014·Methods in Molecular Biology·Ferdinand MarlétazPeter W H Holland
Nov 12, 2014·BMJ : British Medical Journal·Eric JonaschW Kimryn Rathmell
Dec 19, 2014·Annals of Surgical Oncology·Joshua T ByersYuwen Zhu
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 13, 2015·Bioinformatics·Wencke WalterMercedes Ricote
Mar 10, 2016·Journal of Clinical Pathology·Jacques RaphaelS Verma
Jun 4, 2016·Cancer Research·Michael KlutsteinHoward Cedar
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Dec 10, 2016·Trends in Biochemical Sciences·Jianjin ShiFeng Shao
Feb 12, 2017·Pharmacology & Therapeutics·Subhankar Biswas, C Mallikarjuna Rao
Sep 29, 2017·Frontiers in Immunology·Melvin Kantono, Beichu Guo
Apr 19, 2018·Bioinformatics·Pierre-Louis CedozOlivier Gevaert
Jun 11, 2019·CNS Neuroscience & Therapeutics·Kuan-Yu WangTao Jiang
Aug 14, 2019·Journal of Cellular Biochemistry·Yi Duan, Dong Zhang
Sep 14, 2019·Cancer Cell International·Liwei WangZhiwen Chen

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Software Mentioned

MethylMix package
cBioPortal
Goplot
clusterprofiler
R
limma
MethylMix

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