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Harada S, Taketomi Y, Aiba T, Kawaguchi M, Hirabayashi T, Uranbileg B, Kurano M, Yatomi Y, Murakami M. The Lysophospholipase PNPLA7 Controls Hepatic Choline and Methionine Metabolism. Biomolecules 2023; 13:biom13030471. [PMID: 36979406 PMCID: PMC10046082 DOI: 10.3390/biom13030471] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
The in vivo roles of lysophospholipase, which cleaves a fatty acyl ester of lysophospholipid, remained unclear. Recently, we have unraveled a previously unrecognized physiological role of the lysophospholipase PNPLA7, a member of the Ca2+-independent phospholipase A2 (iPLA2) family, as a key regulator of the production of glycerophosphocholine (GPC), a precursor of endogenous choline, whose methyl groups are preferentially fluxed into the methionine cycle in the liver. PNPLA7 deficiency in mice markedly decreases hepatic GPC, choline, and several metabolites related to choline/methionine metabolism, leading to various symptoms reminiscent of methionine shortage. Overall metabolic alterations in the liver of Pnpla7-null mice in vivo largely recapitulate those in methionine-deprived hepatocytes in vitro. Reduction of the methyl donor S-adenosylmethionine (SAM) after methionine deprivation decreases the methylation of the PNPLA7 gene promoter, relieves PNPLA7 expression, and thereby increases GPC and choline levels, likely as a compensatory adaptation. In line with the view that SAM prevents the development of liver cancer, the expression of PNPLA7, as well as several enzymes in the choline/methionine metabolism, is reduced in human hepatocellular carcinoma. These findings uncover an unexplored role of a lysophospholipase in hepatic phospholipid catabolism coupled with choline/methionine metabolism.
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Affiliation(s)
- Sayaka Harada
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoshitaka Taketomi
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Toshiki Aiba
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Mai Kawaguchi
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Tetsuya Hirabayashi
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Baasanjav Uranbileg
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Makoto Kurano
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
- Correspondence: ; Tel.: +81-3-5841-1431
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2
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Chen D, Wang M, Guo Y, Wu W, Ji X, Dou X, Tang H, Zong Z, Zhang X, Xiong D. An aberrant DNA methylation signature for predicting the prognosis of head and neck squamous cell carcinoma. Cancer Med 2021; 10:5936-5947. [PMID: 34313009 PMCID: PMC8419750 DOI: 10.1002/cam4.4142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignancy worldwide with a poor prognosis. DNA methylation is an epigenetic modification that plays a critical role in the etiology and pathogenesis of HNSCC. The current study aimed to develop a predictive methylation signature based on bioinformatics analysis to improve the prognosis and optimize therapeutic outcome in HNSCC. Clinical information and methylation sequencing data of patients with HNSCC were downloaded from The Cancer Genome Atlas database. The R package was used to identify differentially methylated genes (DMGs) between HNSCC and adjacent normal tissues. We identified 22 DMGs associated with 246 differentially methylated sites. Patients with HNSCC were classified into training and test groups. Cox regression analysis was used to build a risk score formula based on the five methylation sites (cg26428455, cg13754259, cg17421709, cg19229344, and cg11668749) in the training group. The Kaplan–Meier survival curves showed that the overall survival (OS) rates were significantly different between the high‐ and low‐risk groups sorted by the signature in the training group (median: 1.38 vs. 1.57 years, log‐rank test, p < 0.001). The predictive power was then validated in the test group (median: 1.34 vs. 1.75 years, log‐rank test, p < 0.001). The area under the receiver operating characteristic curve (area under the curve) based on the signature for predicting the 5‐year survival rates, was 0.7 in the training and 0.73 in test groups, respectively. The results of multivariate Cox regression analysis showed that the riskscore (RS) signature based on the five methylation sites was an independent prognostic tool for OS prediction in patients. In addition, a predictive nomogram model that incorporated the RS signature and patient clinical information was developed. The innovative methylation signature‐based model developed in our study represents a robust prognostic tool for guiding clinical therapy and predicting the OS in patients with HNSCC.
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Affiliation(s)
- Dayang Chen
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Mengmeng Wang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Ying Guo
- Department of Clinical Laboratory, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wei Wu
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiang Ji
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xiaowen Dou
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Huamei Tang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Zengyan Zong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Dan Xiong
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, China.,School of Medicine, Anhui University of Science and Technology, Huainan, China
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Application of 5-Methylcytosine DNA Glycosylase to the Quantitative Analysis of DNA Methylation. Int J Mol Sci 2021; 22:ijms22031072. [PMID: 33499041 PMCID: PMC7865733 DOI: 10.3390/ijms22031072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 02/03/2023] Open
Abstract
In higher eukaryotes DNA methylation is a prominent epigenetic mark important for chromatin structure and gene expression. Thus, profiling DNA methylation is important for predicting gene expressions associated with specific traits or diseases. DNA methylation is achieved by DNA methyltransferases and can be actively removed by specific enzymes in a replication-independent manner. DEMETER (DME) is a bifunctional 5-methylcytosine (5mC) DNA glycosylase responsible for active DNA demethylation that excises 5mC from DNA and cleaves a sugar-phosphate bond generating a single strand break (SSB). In this study, DME was used to analyze DNA methylation levels at specific epialleles accompanied with gain or loss of DNA methylation. DME treatment on genomic DNA generates SSBs in a nonsequence-specific fashion proportional to 5mC density, and thus DNA methylation levels can be easily measured when combined with the quantitative PCR (qPCR) method. The DME-qPCR analysis was applied to measure DNA methylation levels at the FWA gene in late-flowering Arabidopsis mutants and the CNR gene during fruit ripening in tomato. Differentially methylated epialleles were successfully distinguished corresponding to their expression levels and phenotypes. DME-qPCR is proven a simple yet effective method for quantitative DNA methylation analysis, providing advantages over current techniques based on methylation-sensitive restriction digestion.
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Aiba T, Saito T, Hayashi A, Sato S, Yunokawa H, Fukami M, Hayashi Y, Mizuno K, Sato Y, Kojima Y, Ohsako S. Exploring disease-specific methylated CpGs in human male genital abnormalities by using methylated-site display-amplified fragment length polymorphism (MSD-AFLP). J Reprod Dev 2019; 65:491-497. [PMID: 31462596 PMCID: PMC6923155 DOI: 10.1262/jrd.2019-069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The incidence of male reproductive system disorders, especially hypospadias, has been increasing in developed countries since the latter half of the 20th century. Endocrine-disrupting chemicals from the environment are considered to be involved in hypospadias onset through epigenetic alterations. This pilot study aimed to explore disease-specific methylated CpGs in human patient samples using the methylated-site display-amplified fragment length polymorphism (MSD-AFLP) technique developed by our research group [1]. We compared clinical samples from hypospadias and phimosis patients. Foreskin and blood samples were collected from one- to two-year-old patients with hypospadias (N = 3) and phimosis (N = 3) during surgical treatment. MSD-AFLP analysis showed significantly decreased CpG-methylation levels of genes such as MYH11 and increased CpG-methylation levels of genes such as PLA2G15 in hypospadias patients. Hierarchical clustering analysis showed that genes with significantly altered CpG levels were more markedly altered in DNA from blood than from foreskin. Because of the small number of samples, further investigation is necessary to elucidate the association between variations in CpG levels in foreskin and blood DNA and male genital abnormalities. However, our MSD-AFLP method appears to be a useful tool for exploring disease-specific methylated-CpGs in human epidemiological studies.
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Affiliation(s)
- Toshiki Aiba
- Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.,Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Toshiyuki Saito
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Akiko Hayashi
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | | | | | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Yutaro Hayashi
- Department of Pediatric Urology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Kentaro Mizuno
- Department of Pediatric Urology, Nagoya City University, Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Yuichi Sato
- Department of Urology, Fukushima Medical University, School of Medicine, Fukushima 960-1295, Japan
| | - Yoshiyuki Kojima
- Department of Urology, Fukushima Medical University, School of Medicine, Fukushima 960-1295, Japan
| | - Seiichiroh Ohsako
- Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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Aiba T, Saito T, Hayashi A, Sato S, Yunokawa H, Maruyama T, Fujibuchi W, Ohsako S. Does the prenatal bisphenol A exposure alter DNA methylation levels in the mouse hippocampus?: An analysis using a high-sensitivity methylome technique. Genes Environ 2018; 40:12. [PMID: 29881475 PMCID: PMC5985587 DOI: 10.1186/s41021-018-0099-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Background There is still considerable debate about the effects of exposure to bisphenol A (BPA) an endocrine disrupter at low doses. Recently, many studies using animal models have shown that prenatal BPA exposure induces behavioral and neuronal disorders due to epigenetic changes in the brain. However, striking evidence of epigenomic changes has to be shown. Methods To investigate whether low-dose BPA exposure in the fetal stage can alter CpG methylation levels in the central nervous system, the hippocampus of the inbred C57BL/6 J mouse as the target tissue was collected to detect alterations in CpG methylation levels using a highly sensitive method of genome-wide DNA methylation analysis, methylated site display-amplified fragment length polymorphism (MSD-AFLP). Results BPA showed the sex-hormone like effects on male reproductive organs. Although we examined the methylation levels of 43,840 CpG sites in the control and BPA (200 μg/kg/day)-treated group (6 mice per group), we found no statistically significant changes in methylation levels in any CpG sites. Conclusions At least under the experimental condition in this study, it is considered that the effect of low-dose BPA exposure during the fetal stage on hippocampal DNA methylation levels is extremely small.
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Affiliation(s)
- Toshiki Aiba
- 1Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654 Japan.,2Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555 Japan
| | - Toshiyuki Saito
- 2Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555 Japan
| | - Akiko Hayashi
- 2Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555 Japan
| | - Shinji Sato
- Maze, Inc, 1-2-17 Sennincho, Hachioji-shi, Tokyo, 193-0835 Japan
| | | | - Toru Maruyama
- 4Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Wataru Fujibuchi
- 4Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Seiichiroh Ohsako
- 1Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654 Japan
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Kuluev BR, Baymiev AK, Gerashchenkov GA, Chemeris DA, Zubov VV, Kuluev AR, Baymiev AK, Chemeris AV. Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541805006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Latchney SE, Fields AM, Susiarjo M. Linking inter-individual variability to endocrine disruptors: insights for epigenetic inheritance. Mamm Genome 2018; 29:141-152. [PMID: 29218402 PMCID: PMC5849504 DOI: 10.1007/s00335-017-9729-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/02/2017] [Indexed: 01/11/2023]
Abstract
Endocrine disrupting chemicals (EDCs) can induce a myriad of adverse health effects. An area of active investigation is the multi- and transgenerational inheritance of EDC-induced adverse health effects referring to the transmission of phenotypes across multiple generations via the germline. The inheritance of EDC-induced adverse health effects across multiple generations can occur independent of genetics, spurring much research into the transmission of underlying epigenetic mechanisms. Epigenetic mechanisms play important roles in the development of an organism and are responsive to environmental exposures. To date, rodent studies have demonstrated that acquired epigenetic marks, particularly DNA methylation, that are inherited following parental EDC exposure can escape embryonic epigenome reprogramming. The acquired epimutations can lead to subsequent adult-onset diseases. Increasing studies have reported inter-individual variations that occur with epigenetic inheritance. Factors that underlie differences among individuals could reveal previously unidentified mechanisms of epigenetic transmission. In this review, we give an overview of DNA methylation and posttranslational histone modification as the potential mechanisms for disease transmission, and define the requirements for multi- and transgenerational epigenetic inheritance. We subsequently evaluate rodent studies investigating how acquired changes in epigenetic marks especially DNA methylation across multiple generations can vary among individuals following parental EDC exposure. We also discuss potential sources of inter-individual variations and the challenges in identifying these variations. We conclude our review discussing the challenges in applying rodent generational studies to humans.
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Affiliation(s)
- Sarah E Latchney
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ashley M Fields
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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Kurita H, Aiba T, Saito T, Ohsako S. Detection of dioxin-induced demethylation of mouse Cyp1a1 gene promoter by a new labeling method for short DNA fragments possessing 5'-methylcytosine at the end. Genes Environ 2018; 40:1. [PMID: 29339976 PMCID: PMC5761092 DOI: 10.1186/s41021-017-0089-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
Abstract
Environmental factors stimulate alteration of DNA methylation level. Investigation of the genome-wide DNA methylation status is important for environmental health studies. We here designed a genomic DNA amplification and labeling protocol using a methylation-sensitive restriction enzyme HinP1 I. This method can specifically amplify genomic DNA fragments possessing methyl-CpG at the end. The fragments are a relatively short size and dominantly located on CpG-islands. By using the samples prepared by this method, a dioxin-induced change in the methylation level of the mouse Cyp1a1 promoter was successfully evaluated using oligonucleotide probes covalently bound onto a glass plate. The method developed in this paper would be useful for other genome-wide analysis platforms for the large scale epigenome-wide association studies (EWAS) including human epidemiological samples.
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Affiliation(s)
- Hisaka Kurita
- Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan.,Laboratory of Medical Therapeutics and Molecular Therapeutics, Gifu Pharmaceutical University, Daigaku-Nishi, Gifu, 501-1196 Japan
| | - Toshiki Aiba
- Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan.,Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555 Japan
| | - Toshiyuki Saito
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555 Japan
| | - Seiichiroh Ohsako
- Laboratory of Environmental Health Science, Center for Disease Biology and Integrative Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan.,Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
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