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

Fujimoto, M. Stanley; Arai, Eri; Tsumura, Koji; Yotani, Takuya; Yamada, Yuri; Takahashi, Yoshinori; Maeshima, Akiko Miyagi; Fujimoto, Hiroyuki; Yoshida, Teruhiko; Kanai, Yae

doi:10.1080/15592294.2020.1767374

Cited by 12 publications

(17 citation statements)

References 43 publications

(55 reference statements)

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“…Moreover, among the genes included in Table 2 , only three showed a significant correlation between the levels of DNA methylation and expression ( P < 0.05 and r < −0.2 or r > 0.2) (Additional file 1 : Table S5). These findings are consistent with our previous studies, which revealed that even DNA methylation alterations at CpG sites not involved in regulating the expression of functionally important genes can become excellent surrogate markers for DNA methylation diagnostics [ 41 , 42 ]. Particularly at the carcinogenic risk stage, but not in established cancers, it is feasible that DNA methylation alterations would not yet have expanded immediately to involve important tumor-related genes [ 19 – 22 ].…”

Section: Discussionsupporting

confidence: 93%

Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis

et al. 2022

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Background In recent years, non-alcoholic steatohepatitis (NASH) has become the main cause of hepatocellular carcinoma (HCC). As a means of improving the treatment of NASH-related HCCs based on early detection, this study investigated the feasibility of carcinogenic risk estimation in patients with NASH. Results Normal liver tissue (NLT), non-cancerous liver tissue showing histological findings compatible with non-alcoholic fatty liver from patients without HCC (NAFL-O), non-cancerous liver tissue showing NASH from patients without HCC (NASH-O), non-cancerous liver tissue showing non-alcoholic fatty liver from patients with HCC (NAFL-W), non-cancerous liver tissue showing NASH from patients with HCC (NASH-W) and NASH-related HCC were analyzed. An initial cohort of 171 tissue samples and a validation cohort of 55 tissue samples were used. Genome-wide DNA methylation screening using the Infinium HumanMethylation450 BeadChip and DNA methylation quantification using high-performance liquid chromatography (HPLC) with a newly developed anion-exchange column were performed. Based on the Infinium assay, 4050 CpG sites showed alterations of DNA methylation in NASH-W samples relative to NLT samples. Such alterations at the precancerous NASH stage were inherited by or strengthened in HCC samples. Receiver operating characteristic curve analysis identified 415 CpG sites discriminating NASH-W from NLT samples with area under the curve values of more than 0.95. Among them, we focused on 21 CpG sites showing more than 85% specificity, even for discrimination of NASH-W from NASH-O samples. The DNA methylation status of these 21 CpG sites was able to predict the coincidence of HCC independently from histopathological findings such as ballooning and fibrosis stage. The methylation status of 5 candidate marker CpG sites was assessed using a HPLC-based system, and for 3 of them sufficient sensitivity and specificity were successfully validated in the validation cohort. By combining these 3 CpG sites including the ZC3H3 gene, NAFL-W and NASH-W samples from which HCCs had already arisen were confirmed to show carcinogenic risk with 95% sensitivity in the validation cohort. Conclusions After a further prospective validation study using a larger cohort, carcinogenic risk estimation in liver biopsy specimens of patients with NASH may become clinically applicable using this HPLC-based system for quantification of DNA methylation.

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Section: Discussionsupporting

confidence: 93%

Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis

et al. 2022

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“…On the other hand, other marker CpG sites, position 1 of cg02046247 and position 2 of cg19918599, included in Table 3 are located outside CpG islands (open sea regions) in intergenic regions and would not participate in regulating the expression of specific genes. This is consistent with the results of our previous studies, indicating that even DNA methylation alterations at CpG sites not involved in the expression of functionally important genes would be potentially excellent surrogate markers for cancer diagnostics (Fujimoto et al 2020 ; Nagashio et al 2011 ). In general, most 5-methylcytosine residues seem to be controlled in a coordinated manner with their neighbors, rather than being independent, resulting in a domain wherein all CpG sites show largely similar methylation levels (Yokoyama et al 2015 ).…”

Section: Discussionsupporting

confidence: 92%

“…The PCR and sequencing primers were designed using PSQ Assay Design Software Version 1.0.6 (Biotage, Uppsala, Sweden). To overcome any PCR bias, we optimized the PCR conditions: 0%, 50%, and 100% of the fully methylated control DNA (Epitect methylated human control DNA, QIAGEN) were used as a template to test the linearity of the protocol, as described previously (Fujimoto et al 2020 ; Nagashio et al 2011 ). The optimized PCR conditions, i.e., PCR cycle and DNA polymerase, for each primer set are summarized in Table S2.…”

Section: Methodsmentioning

confidence: 99%

Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling

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Fujimoto

Ito

et al. 2021

J Cancer Res Clin Oncol

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Purpose The present study was conducted to clarify the clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma (PDAC). Methods Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analyzed fresh-frozen tissues from an initial cohort (17 samples of normal control pancreatic tissue [C] from 17 patients without PDAC, and 34 samples of non-cancerous pancreatic tissue [N] and 82 samples of cancerous tissue [T] both obtained from 82 PDAC patients) and formalin-fixed paraffin-embedded T samples from 34 patients in a validation cohort. Results The DNA methylation profiles of N samples tended to differ from those of C samples, and 91,907 probes showed significant differences in DNA methylation levels between C and T samples. Epigenetic clustering of T samples was significantly correlated with a larger tumor diameter and early recurrence (ER), defined as relapse within 6 months after surgery. Three marker CpG sites, applicable to formalin-fixed paraffin-embedded surgically resected materials regardless of their tumor cell content, were identified for prediction of ER. The sensitivity and specificity for detection of patients belonging to the ER group using a panel combining these three marker CpG sites, including a CpG site in the CDK14 gene, were 81.8% and 71.7% and 88.9% and 70.4% in the initial and validation cohorts, respectively. Conclusion These findings indicate that DNA methylation alterations may have a clinicopathological impact on PDAC. Application of our criteria will ultimately allow prediction of ER after surgery to improve the outcome of PDAC patients.

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“…The PCR and sequencing primers for the promoter regions of the TRIM58 and ZNF132 genes were designed using PSQ Assay Design Software Version 1.0.6 (Biotage, Uppsala, Sweden). To overcome any PCR bias, we optimized the PCR conditions: 0, 50 and 100% of the fully methylated control DNA (Epitect methylated human control DNA, QIAGEN) was used as a template, as described previously ( 24 ), and the linearity of the measured values and their consistency with the theoretical values were confirmed. As a result of this optimization experiment, both PCR reactions were performed using HotStarTaq DNA polymerase (QIAGEN).…”

Section: Methodsmentioning

confidence: 99%

DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’-type lung adenocarcinomas

et al. 2020

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Although some previous studies have examined epigenomic alterations in lung adenocarcinomas, correlations between epigenomic events and genomic driver mutations have not been fully elucidated. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of adjacent normal lung tissue (N) and the corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF, and HER2 and fusions involving ALK, RET, and ROS1, were examined. DNA methylation levels in 12,629 probes from N samples were significantly correlated with recurrence-free survival. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver aberrations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups. After siRNA knockdown of ZNF132, which showed DNA hypermethylation only in the pan-negative group and was correlated with vascular invasion, the proliferation, apoptosis and migration of cancer cell lines were examined. ZNF132 knockdown led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of “pan-negative” lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression.

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

Cited by 12 publications

References 43 publications

Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis

Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis

Clinicopathological impacts of DNA methylation alterations on pancreatic ductal adenocarcinoma: prediction of early recurrence based on genome-wide DNA methylation profiling

DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’-type lung adenocarcinomas

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