Impact of ZBTB7A hypomethylation and expression patterns on treatment response to hydroxyurea
Vasiliki ChondrouEleana F. StavrouΓεώργιος ΜαρκόπουλοςAlexandra Kouraklis‐SymeonidisV. FotopoulosArgiris SymeonidisEfthymia VlachakiPanagiota ChalkiaGeorge P. PatrinosAdamantia PapachatzopoulouArgyro Sgourou
14
Citation
50
Reference
10
Related Paper
Citation Trend
Abstract:
We aimed to clarify the emerging epigenetic landscape in a group of genes classified as "modifier genes" of the β-type globin genes (HBB cluster), known to operate in trans to accomplish the two natural developmental switches in globin expression, from embryonic to fetal during the first trimester of conception and from fetal to adult around the time of birth. The epigenetic alterations were determined in adult sickle cell anemia (SCA) homozygotes and SCA/β-thalassemia compound heterozygotes of Greek origin, who are under hydroxyurea (HU) treatment. Patients were distinguished in HU responders and HU non-responders (those not benefited from the HU) and both, and in vivo and in vitro approaches were implemented. We examined the CpG islands' DNA methylation profile of BCL11A, KLF1, MYB, MAP3K5, SIN3A, ZBTB7A, and GATA2, along with γ-globin and LRF/ZBTB7A expression levels. In vitro treatment of hematopoietic stem cells (HSCs) with HU induced a significant DNA hypomethylation pattern in ZBTB7A (p*, 0.04) and GATA2 (p*, 0.03) CpGs exclusively in the HU non-responders. Also, this group of patients exhibited significantly elevated baseline methylation patterns in ZBTB7A, before the HU treatment, compared to HU responders (p*, 0.019) and to control group of healthy individuals (p*, 0.021), which resembles a potential epigenetic barrier for the γ-globin expression. γ-Globin expression in vitro matched with detected HbF levels during patients' monitoring tests (in vivo) under HU treatment, implying a good reproducibility of the in vitro HU epigenetic effect. LRF/ZBTB7A expression was elevated only in the HU non-responders under the influence of HU. This is one of the very first pharmacoepigenomic studies indicating that the hypomethylation of ZBTB7A during HU treatment enhances the LRF expression, which by its turn suppresses the HbF resumption in the HU non-responders. Its role as an epigenetic regulator of hemoglobin switching is also supported by the wide distribution of ZBTB7A-binding sites within the 5′ CpG sequences of all studied human HBB cluster "modifier genes." Also, the baseline methylation level of selective CpGs in ZBTB7A and GATA2 could be an indicator of the negative HU response among the β-type hemoglobinopathy patients.Keywords:
GATA2
CpG site
The aetiology of OSCC remains unclear, however, aberrant methylation of CpG island promoters of tumor suppressor genes have been identified as contributory developmental pathways in several cancers. The aim of this study was to determine the presence of RUNX3 gene methylation and how its association with patients? demographic variables such as gender, age, histologic class and tumor location could be of diagnostic value for OSCC. Sixty-seven formalin-fixed paraffin-embedded (FFPE) solid tissue blocks of OSCC, and nine blocks of benign oral lesions of epithelial origin retrieved from the archives of the Department of Oral Pathology, University College Hospital, Ibadan, South-West Nigeria were used for the analyses. Frequency of CpG island methylation in the promoter region of RUNX3 was determined by methylation-specific polymerase chain reaction (MSP). Association between gender, age, tumor location, histologic class and promoter methylation in RUNX3 was assessed with Pearson?s ?2 test. Overall, 45% (30/67) of OSCC demonstrated methylation in the RUNX3 promoter indicating a high frequency of methylation of the CpG island promoter region of RUNX3. There was no association between gender, age, histologic class and promoter methylation in RUNX3 (P > 0.05), however a significant association was observed between tumor location and promoter methylation of RUNX3 (P < 0.05). Aberrant methylation of the CpG island promoter region of RUNX3 together with tumor location could therefore be critical in the development and diagnosis of OSCC.
CpG site
Cite
Citations (0)
CpG site
Differentially methylated regions
Illumina Methylation Assay
Cite
Citations (75)
Objective To investigate the methylation status of 5'CpG island of the promoter region of HOXA10 gene,and to explore the pathogenic role of the methylation status on endometriosis.Methods Thirty patients with endometriosis,who were admitted to Zhujiang Hospital of Southern Medical University from Sep.2007 to May 2008,and 25 healthy women were involved in present study.Of the 30 patients with endometriosis,10 were in stages Ⅰ-Ⅱ,and 20 in stages Ⅲ-Ⅳ.The specimens of endometrial tissue were collected from 30 patients with endometriosis and 25 healthy women,and the methylation status in 5'CpG island of HOXA10 gene promoter region was detected by using methylation-specific PCR technique(MSP).Results Different methylation levels in 5'CpG island in promoter region of HOXA10 gene were detected from the patients in different clinical stage of endometriosis.Methylation in 5'CpG island of the promoter region of HOXA10 gene was observed in 11 of 20(55%) patients in endometriosis stages Ⅲ-Ⅳ,and 1 of 10(10%) patients in endometriosis stages Ⅰ-Ⅱ.The methylation level in 5'CpG island of the promoter region of HOXA10 gene of the patients in endometriosis stages Ⅲ-Ⅳ was higher than that of the patients in endometriosis stages Ⅰ-Ⅱ(P0.05).However,no methylation was found in the endometrial tissue of 25 healthy women.Conclusion The methylation in 5'CpG island of the promoter region of HOXA10 gene may play an important role in the pathogenesis and development of endometriosis.
CpG site
Pathogenesis
Cite
Citations (0)
CpG site
Breakpoint
Cite
Citations (0)
The 5′ region for the endothelin receptor B (EDNRB) gene is a complex CpG island giving rise to four individual transcripts initiating within the island. Here, for the first time, we analyze the relationship between methylation and gene expression in a CpG island located in the 5′ region of a gene with multiple transcription start sites. The CpG island was unmethylated in normal prostate and bladder tissue, whereas it became methylated in apparently normal colonic epithelium. Tumors derived from these tissues were frequently hypermethylated relative to the respective normal tissues. Analysis of 11 individual CpG sites located throughout the CpG island showed that specific sites with high methylation levels in several tumors were also methylated in normal tissues, suggesting that they might serve as foci for further de novo methylation. This region also had high levels of methylation in several cancer cell lines, and we found that a low methylation level in a small region within the 5′ region correlated with expression of the 5′-most transcript. Interestingly, almost complete methylation 200–1000 bp downstream of the transcriptional start site did not block expression of this transcript. Finally, we show that treatment with 5-aza-2′-deoxycytidine can induce transcriptional activation of the four EDNRB transcripts. Our results show the existence of differential, tissue-dependent methylation at the EDNRB 5′ region, suggest the existence of a spreading mechanism for de novo methylation, starting from methylation hotspots, and show that hypermethylation immediately 3′ to a transcriptional start site does not prevent initiation.
CpG site
Transcription
Cite
Citations (93)
To examine methylation of the peroxisome proliferator-activated receptor γ (PPARγ) gene and its relationship with child weight status, at birth and 9 years.We measured PPARγ methylation across 23 CpG sites using the Infinium Illumina 450 k array for children from the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort at birth (N = 373) and 9 years (N = 245).Methylation level correlation patterns across the 23 PPARγ CpG sites were conserved between birth and 9-year ages. We found high inter-CpG correlations between sites 1-3 (methylation block 1) and also between sites 18-23 (methylation block 2) for both time points, although these patterns were less pronounced at 9 years. Additionally, sites 1-3 (north shore) had the highest intra-CpG correlations over time (r = 0.24, 0.42, and 0.3; P = 0.002, P < 0.001, P < 0.001, respectively). PPARγ methylation levels tended to increase with age, and the largest differences were observed for north shore sites (7.4%). Adjusting for sex, both site 1 and site 20 (gene body) methylation at birth was significantly and inversely associated with birth weight (β = -0.13, P = 0.033; β = -0.09, P = 0.025, respectively). Similarly, we found that site 1 and site 20 methylation at 9 years was significantly and inversely associated with 9-year BMI z-score (β = -0.41, P = 0.015; β = -0.23, P = 0.045, respectively).Our results indicate that PPARγ methylation is highly organized and conserved over time, and highlight the potential functional importance of north shore sites, adding to a better understanding of regional human methylome patterns. Overall, our results suggest that PPARγ methylation may be associated with child body size.
CpG site
Cite
Citations (16)
Abstract Background The ESR 1 gene suffers methylation changes in many types of cancers, including breast cancer (BC), the most frequently diagnosed cancer in women that is also present in men. Methylation at promoter A of ESR 1 is the worse prognosis in terms of overall survival; thus, the early detection, prognostic, and prediction of therapy involve some methylation biomarkers. Methods Therefore, our study aimed to examine the methylation levels at the ESR 1 gene in samples from Mexican BC patients and its possible association with menopausal status. Results We identified a novel 151-bp CpG island in the promoter A of the ESR 1 gene. Interestingly, methylation levels at this CpG island in positive ERα tumors were approximately 50% less than negative ERα or control samples. Furthermore, methylation levels at ESR 1 were associated with menopausal status. In postmenopausal patients, the methylation levels were 1.5-fold higher than in premenopausal patients. Finally, according to tumor malignancy, triple-negative cancer subtypes had higher ESR 1 methylation levels than luminal/HER2+ or luminal A subtypes. Conclusions Our findings suggest that methylation at this novel CpG island might be a promising prognosis marker
CpG site
Cite
Citations (5)
Objective The aim of this study is to investigate the CpG island methylation status of TIMP- 3 in HCC cell lines, to treate the HCC cells that exhibit positive methylation with DNA methyltransferase in- hibitor(5-Aza-CdR), and to observe the influence of 5-Aza-CdR on the expression of TIMP-3 mRNA and its CpG island methylation degree. Methods TIMP-3 CpG methylation status of HCC cells were examined using MSP assay. Methylation-positive HCC cells were treated with DNA methyltransferase inhibitor(5-Aza- CdR)(intervention group), and the difference of TIMP-3 mRNA expression was observed between interven- tion group and control group. Pyrosequencing method was applied to quantitatively examine the CpG island methylation percentage. Results The methylation of TIMP-3 CpG islands in C3A, HepG-2, and Hep-3B was positive. The results showed that TIMP-3 mRNA expression was increased(P 0.05) and the methylation level was decreased(P 0.05) in the intervention group compared to control group. Conclusion 5-Aza-CdR could remarkably reduce the level of the CpG island methylation and increase the expression of TIMP-3 mR- NA in HCC cells.
CpG site
DNMT1
DNA methyltransferase
Pyrosequencing
Bisulfite sequencing
Cite
Citations (0)
Objective To investigate the change of methylation levels of the long interspersed nucleotide acids element-1(LINE-1) promotor by using bisulfite sequencing PCR(BSP) in peripheral plasma of hepatocellular carcinoma(HCC).Methods BSP method was used to detect the methylation levels of the LINE-1 promotor in 67 plasma samples from 33 cases of HCC(HCC group),18 cases of cirrhosis(cirrhosis group) and 16 healthy volunteers(normal group).Results The results of BSP showed that methylation levels of the LINE-1 promotor in patients with HCC were significantly lower than those in cirrhosis group and normal group(P 0.05).The receiver-operating characteristic curve analysis of methylation of some CpG sites(site 1,site 7,site 8) in the LINE1 promotor revealed an important diagnostic efficacy for HCC,and the sensitivity and specificity of the site 1,site 7,site 8 were 80.0% and 78.8%,81.8% and 71.4%,82.9% and 75.8%,respectively.Conclusion The promotor of LINE-1 has hypomethylation in HCC,and methylation of some CpG sites(site 1,site 7,site 8) in peripheral plasma may be important diagnostic efficacy for HCC.
CpG site
Bisulfite sequencing
Cite
Citations (0)
Objective To investigate the role of CpG island methylation of INSL3 gene in cryp-torchid mice induced by DEHP. Methods CpG islands in INSL3 gene were predicted with MethPrim-er software. The status of methylation of CpG islands in INSL3 gene was analyzed using methylation-specific PCR(MS-PCR). The levels of INSL3 mRNA in rats of the experimental and control group were detected and compared by RT-PCR methods. Results The methylated CpG islands in the first exon of INSL3 were merely noted in cryptorchid mice, while not in normal mice. The levels of INSL3 mRNA reduced significantly in cryptorchid mice. Conclusions The hypermethylation of CpO islands in the first exon of INSL3 may probably cause low INSL3 expression in cryptorchid mice, which can be closely related with the pathogenesis of cryptorchid.
Key words:
Insulin-like factor 3; Cryptorchidsm; DNA methylation
CpG site
Pathogenesis
Cite
Citations (0)