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Research Paper

Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis

ORCID Icon, ORCID Icon, , , , , , , & show all
Pages 1289-1301 | Received 16 Mar 2020, Accepted 01 May 2020, Published online: 04 Jun 2020

References

  • Rouprêt M, Babjuk M, Compérat E, et al. European association of urology guidelines on upper urinary tract urothelial carcinoma: 2017 update. Eur Urol. 2018;73:111–122.
  • Akita H, Kikuchi E, Hayakawa N, et al. Performance of diffusion-weighted MRI post-CT urography for the diagnosis of upper tract urothelial carcinoma: comparison with selective urine cytology sampling. Clin Imaging. 2018;52:208–215.
  • Messer J, Shariat SF, Brien JC, et al. Urinary cytology has a poor performance for predicting invasive or high-grade upper-tract urothelial carcinoma. BJU Int. 2011;108:701–705.
  • Baylin SB, Jones PA. Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol. 2016;8:a019505.
  • Jones PA, Issa JPJ, Baylin S. Targeting the cancer epigenome for therapy. Nat Rev Genet. 2016;15:630–641.
  • Makabe T, Arai E, Hirano T, et al. Genome-wide DNA methylation profile of early-onset endometrial cancer: its correlation with genetic aberrations and comparison with late-onset endometrial cancer. Carcinogenesis. 2019;40:611–623.
  • Kuramoto J, Arai E, Tian Y, et al. Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis. Carcinogenesis. 2017;38:261–270.
  • Arai E, Gotoh M, Tian Y, et al. Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Int J Cancer. 2015;137:2589–2606.
  • Nishiyama N, Arai E, Nagashio R, et al. Copy number alterations in urothelial carcinomas: their clinicopathological significance and correlation with DNA methylation alterations. Carcinogenesis. 2011;32:462–469.
  • Nishiyama N, Arai E, Chihara Y, et al. Genome-wide DNA methylation profiles in urothelial carcinomas and urothelia at the precancerous stage. Cancer Sci. 2010;101:231–240.
  • Nakagawa T, Kanai Y, Ushijima S, et al. DNA hypomethylation on pericentromeric satellite regions significantly correlates with loss of heterozygosity on chromosome 9 in urothelial carcinomas. J Urol. 2005;173:243–246.
  • Porten SP. Epigenetic Alterations in Bladder Cancer. Curr Urol Rep. 2018;19:102.
  • Schulz WA, Goering W. DNA methylation in urothelial carcinoma. Epigenomics. 2016;8:1415–1428.
  • The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507:315–322.
  • Tsumura K, Arai E, Tian Y, et al. Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. Carcinogenesis. 2019;40:1308–1319.
  • Jones PA, Liang G. Rethinking how DNA methylation patterns are maintained. Nat Rev Genet. 2009;10:805–811.
  • Nakagawa T, Kanai Y, Ushijima S, et al. DNA hypermethylation on multiple CpG islands associated with increased DNA methyltransferase DNMT1 protein expression during multistage urothelial carcinogenesis. J Urol. 2005;173:1767–1771.
  • Ohara K, Arai E, Takahashi Y, et al. Genes involved in development and differentiation are commonly methylated in cancers derived from multiple organs: a single-institutional methylome analysis using 1007 tissue specimens. Carcinogenesis. 2017;38:241–251.
  • Larsen LK, Lind GE, Guldberg P, et al. DNA-methylation-based detection of urological cancer in urine: overview of biomarkers and considerations on biomarker design, source of DNA, and detection technologies. Int J Mol Sci. 2019;20:E2657.
  • Moss TJ, Qi Y, Xi L, et al. Comprehensive genomic characterization of upper tract urothelial carcinoma. Eur Urol. 2017;72:641–649.
  • Arai E, Miura F, Totoki Y, et al. Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation. Epigenomics. 2018;10:955–979.
  • Bibikova M, Le J, Barnes B, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics. 2009;1:177–200.
  • Komaki S, Shiwa Y, Furukawa R, et al. iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation. Hum Genome Var. 2018;5:18008.
  • Hachiya T, Furukawa R, Shiwa Y, et al. Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. NPJ Genom Med. 2017;2:11.
  • Habuchi T, Takahashi R, Yamada H, et al. Metachronous multifocal development of urothelial cancers by intraluminal seeding. Lancet. 1993;342:1087–1088.
  • Sidransky D, Frost P, Von Eschenbach A, et al. Clonal origin of bladder cancer. N Engl J Med. 1992;326:737–740.
  • Kakizoe T. Development and progression of urothelial carcinoma. Cancer Sci. 2006;97:821–828.
  • Jones TD, Wang M, Eble JN, et al. Molecular evidence supporting field effect in urothelial carcinogenesis. Clin Cancer Res. 2005;11:6512–6519.
  • Yamanoi K, Arai E, Tian Y, et al. Epigenetic clustering of gastric carcinomas based on DNA methylation profiles at the precancerous stage: its correlation with tumor aggressiveness and patient outcome. Carcinogenesis. 2015;36:509–520.
  • Arai E, Kanai Y, Ushijima S, et al. Regional DNA hypermethylation and DNA methyltransferase (DNMT) 1 protein overexpression in both renal tumors and corresponding nontumorous renal tissues. Int J Cancer. 2006;119:288–296.
  • Yokoyama T, Miura F, Araki H, et al. Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape. BMC Genomics. 2015;16:594.
  • Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465–476.
  • Yamamoto H, Watanabe Y, Oikawa R, et al. BARHL2 methylation using gastric wash DNA or gastric juice exosomal DNA is a useful marker for early detection of gastric cancer in an H. pylori-independent manner. Clin Transl Gastroenterol. 2016;7:e184.
  • Rauch TA, Wang Z, Wu X, et al. DNA methylation biomarkers for lung cancer. Tumour Biol. 2012;33:287–296.
  • Wu X, Rauch TA, Zhong X, et al. CpG island hypermethylation in human astrocytomas. Cancer Res. 2010;70:2718–2727.
  • Ding Q, Chen H, Xie X, et al. BARHL2 differentially regulates the development of retinal amacrine and ganglion neurons. J Neurosci. 2009;29:3992–4003.
  • Nagashio R, Arai E, Ojima H, et al. Carcinogenetic risk estimation based on quantification of DNA methylation levels in liver tissue at the precancerous stage. Int J Cancer. 2011;129:1170–1179.
  • Yamada K, Ono M, Perkins ND, et al. Identification and functional characterization of FMN2, a regulator of the cyclin-dependent kinase inhibitor p21. Mol Cell. 2013;49:922–933.
  • Li DJ, Feng ZC, Li XR, et al. Involvement of methylation-associated silencing of formin 2 in colorectal carcinogenesis. World J Gastroenterol. 2018;24:5013–5024.
  • Ahmed SM, Thériault BL, Uppalapati M, et al. KIF14 negatively regulates Rap1a-Radil signaling during breast cancer progression. J Cell Biol. 2012;199:951–967.
  • Yotani T, Yamada Y, Arai E, et al. Novel method for DNA methylation analysis using high-performance liquid chromatography and its clinical application. Cancer Sci. 2018;109:1690–1700.
  • World Health Organization Classification of Tumours. Pathology and genetics of tumours of the urinary system and male genital organs. JN E, Sauter G, JI E, et al., editors. Lyon: IARC Press; 2004.
  • Brierley JD, Gospodarowicz MK, Wittekind C, editors. TNM classification of malignant tumours, eighth edition. Oxford (UK): John Wiley & Sons, Inc.; 2017.
  • Kanai Y, Nishihara H, Miyagi Y, et al. The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: standard operating procedures based on empirical analyses. Pathol Int. 2018;68:63–90.
  • Shen L, Guo Y, Chen X, et al. Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques. 2007;42:48–58.