Quantification of CpG methylation at the 5′‐region of XIST by pyrosequencing from human serum

Song, Min-Ae; Park, Jung Hoon; Jeong, Kyoung-Sin; Park, Dong Soo; Kang, Minhee; Lee, Suman

doi:10.1002/elps.200600852

Cited by 23 publications

(10 citation statements)

References 24 publications

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“…To quantify the methylation levels of XIST promoter we analyzed a region previously described as methylated on Xi chromosome [40], using Pyrosequencing technology.…”

Section: Methodsmentioning

confidence: 99%

Misbehaviour of XIST RNA in Breast Cancer Cells

et al. 2009

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A role of X chromosome inactivation process in the development of breast cancer have been suggested. In particular, the relationship between the breast cancer predisposing gene BRCA1 and XIST, the main mediator of X chromosome inactivation, has been intensely investigated, but still remains controversial. We investigated this topic by assessing XIST behaviour in different groups of breast carcinomas and in a panel of breast cancer cell lines both BRCA1 mutant and wild type. In addition, we evaluated the occurrence of broader defects of heterochromatin in relation to BRCA1 status in breast cancer cells. We provide evidence that in breast cancer cells BRCA1 is involved in XIST regulation on the active X chromosome, but not in its localization as previously suggested, and that XIST can be unusually expressed by an active X and can decorate it. This indicates that the detection of XIST cloud in cancer cell is not synonymous of the presence of an inactive X chromosome. Moreover, we show that global heterochromatin defects observed in breast tumor cells are independent of BRCA1 status. Our observations sheds light on a possible previously uncharacterized mechanism of breast carcinogenesis mediated by XIST misbehaviour, particularly in BRCA1-related cancers. Moreover, the significant higher levels of XIST-RNA detected in BRCA1-associated respect to sporadic basal-like cancers, opens the possibility to use XIST expression as a marker to discriminate between the two groups of tumors.

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“…To quantify the methylation levels of XIST promoter we analyzed a region previously described as methylated on Xi chromosome [40], using Pyrosequencing technology.…”

Section: Methodsmentioning

confidence: 99%

Misbehaviour of XIST RNA in Breast Cancer Cells

et al. 2009

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“…Like the level of XIST expression (as described above), the methylation status of the XIST gene appears to differ between seminomatous and nonseminomatous TGCTs as well [30]. Similarly, the 5′ region of XIST has been found to be relatively more unmethylated in the serum of patients with prostate cancer than in normal male serum [31]. …”

Section: Xist and Male Cancermentioning

confidence: 99%

Expression and Function of a Large Non‐coding RNA Gene XIST in Human Cancer

et al. 2011

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Background X inactive-specific transcript (XIST) RNA is involved in X chromosome silencing in female cells and allows X chromosome equilibration with males. X inactive-specific transcript expression has been found to be dysregulated in a variety of human cancers when compared to normal cells; meanwhile, the inactivated X chromosome has been noted to be conspicuously absent in human cancer specimens, whereas X chromosome duplications are widely noted. The specific pathways whereby changes in X chromosome status and XIST expression occur in cancer remain incompletely described. Nevertheless, a role for XIST in BRCA1-mediated epigenetic activity has been proposed. Methods Here we review the data regarding XIST expression and X chromosome status in a variety of female, male, and non–sex-related human cancers. Conclusions It is not yet known whether X chromosome duplication, XIST dysregulation, and over-expression of X-linked genes represent important factors in tumorgenesis or are simply a consequence of overall epigenetic instability in these cancers.

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“…Target pyrosequencing of DMPs combines a simple reaction protocol with reproducible and accurate measures of degree of methylation [25, 26]. The PCR reactions designed for CXXC4 failed, so the CpG site for MSI2 was available for pyrosequencing.…”

Section: Resultsmentioning

confidence: 99%

Differential DNA methylation of MSI2 and its correlation with diabetic traits

et al. 2017

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Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach. Among them, three CpG sites were overlapped; they were mapped to the MSI2 and CXXC4 genes. In a DNA methylation replication study done by pyrosequencing (n = 440), the CpG site of MSI2 were shown to have strong associations with the T2D group (p value = 2.20E-16). The differential methylation of MSI2 at chr17:55484635 was associated with diabetes-related traits, in particular with insulin sensitivity (QUICKI, p value = 2.20E-16) and resistance (HOMA-IR, p value = 1.177E-07). In human pancreatic islets, at the single-base resolution (using whole-genome bisulfite sequencing), the 292 CpG sites in the ±5kb at chr17:55484635 were found to be significantly hypo-methylated in donors with T2D (average decrease = 13.91%, 95% confidence interval (CI) = 4.18~ 17.06) as compared to controls, and methylation patterns differed by sex (-9.57%, CI = -16.76~ -6.89) and age (0.12%, CI = -11.17~ 3.77). Differential methylation of the MSI2 gene (chr17:55484635) in blood and islet cells is strongly related to hyperglycemia. Our findings suggest that epigenetic perturbation on the target site of MSI2 gene in circulating blood and pancreatic islets should represent or affect hyperglycemia.

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Quantification of CpG methylation at the 5′‐region of XIST by pyrosequencing from human serum

Cited by 23 publications

References 24 publications

Misbehaviour of XIST RNA in Breast Cancer Cells

Misbehaviour of XIST RNA in Breast Cancer Cells

Expression and Function of a Large Non‐coding RNA Gene XIST in Human Cancer

Differential DNA methylation of MSI2 and its correlation with diabetic traits

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