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Gallimore F, Fandy TE. Therapeutic Applications of Azanucleoside Analogs as DNA Demethylating Agents. EPIGENOMES 2023; 7:12. [PMID: 37489400 PMCID: PMC10366911 DOI: 10.3390/epigenomes7030012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/26/2023] Open
Abstract
Azanucleosides, such as 5-azacytidine and decitabine, are DNA demethylating agents used in the treatment of acute myeloid leukemia and myelodysplastic syndromes. Researchers continue to explore their utility in the treatment of other hematologic and solid tumors. Based on the capacity of the compounds to inhibit DNA methyltransferase enzymes and the important role of DNA methylation in health and disease, it is essential to understand the molecular changes that azanucleosides induce and how these changes may improve treatment outcomes in subsets of patients. This review summarizes the molecular and therapeutic actions of azanucleosides and discusses recent clinical trials of these compounds as single agents or in combination therapy for the treatment of cancer and related conditions.
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Affiliation(s)
- Fallon Gallimore
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV 25304, USA
| | - Tamer E Fandy
- Department of Pharmaceutical & Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV 25304, USA
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Merchant JP, Zhu K, Henrion MYR, Zaidi SSA, Lau B, Moein S, Alamprese ML, Pearse RV, Bennett DA, Ertekin-Taner N, Young-Pearse TL, Chang R. Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer's disease. Commun Biol 2023; 6:503. [PMID: 37188718 PMCID: PMC10185548 DOI: 10.1038/s42003-023-04791-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Despite decades of genetic studies on late-onset Alzheimer's disease, the underlying molecular mechanisms remain unclear. To better comprehend its complex etiology, we use an integrative approach to build robust predictive (causal) network models using two large human multi-omics datasets. We delineate bulk-tissue gene expression into single cell-type gene expression and integrate clinical and pathologic traits, single nucleotide variation, and deconvoluted gene expression for the construction of cell type-specific predictive network models. Here, we focus on neuron-specific network models and prioritize 19 predicted key drivers modulating Alzheimer's pathology, which we then validate by knockdown in human induced pluripotent stem cell-derived neurons. We find that neuronal knockdown of 10 of the 19 targets significantly modulates levels of amyloid-beta and/or phosphorylated tau peptides, most notably JMJD6. We also confirm our network structure by RNA sequencing in the neurons following knockdown of each of the 10 targets, which additionally predicts that they are upstream regulators of REST and VGF. Our work thus identifies robust neuronal key drivers of the Alzheimer's-associated network state which may represent therapeutic targets with relevance to both amyloid and tau pathology in Alzheimer's disease.
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Affiliation(s)
- Julie P Merchant
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kuixi Zhu
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Marc Y R Henrion
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, Pembroke Place, L3 5QA, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi
| | - Syed S A Zaidi
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Branden Lau
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
- Arizona Research Labs, Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Sara Moein
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Melissa L Alamprese
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA.
| | - Rui Chang
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Neurology, University of Arizona, Tucson, AZ, USA.
- INTelico Therapeutics LLC, Tucson, AZ, USA.
- PATH Biotech LLC, Tucson, AZ, USA.
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LncRNA XR_351665 Contributes to Chronic Pain-Induced Depression by Upregulating DNMT1 via Sponging miR-152-3p. THE JOURNAL OF PAIN 2023; 24:449-462. [PMID: 36257574 DOI: 10.1016/j.jpain.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Chronic pain is frequently comorbid with depression. However, the mechanisms underlying chronic pain-induced depression remain unclear. Here, we found that DNA methyltransferase 1 (DNMT1) was upregulated in the central amygdala (CeA) of spared nerve injury (SNI)-induced chronic pain-depression rats, and knockdown of DNMT1 could improve the depression-like behaviors in SNI rats. Additionally, a panel of differentially expressed lncRNAs, including 38 upregulated and 12 downregulated lncRNAs, were identified by microarray analysis. Bioinformatics analysis suggested that the upregulated lncRNA XR_351665 was the upstream molecule to regulate DNMT1 expression. The knockdown of XR_351665 significantly alleviated the depression-like behaviors in SNI rats, whereas overexpression of XR_351665 induced the depression-like behaviors in naïve rats. Further mechanism-related researches uncovered that XR_351665 functioned as a competing endogenous RNA (ceRNA) to upregulate DNMT1 by competitively sponging miR-152-3p, and subsequently promoted the development of chronic pain-induced depression. Our findings suggest that lncRNA XR_351665 is involved in the development of chronic pain-induced depression by upregulating DNMT1 via sponging miR-152-3p. These data provide novel insight into understanding the pathogenesis of chronic pain-induced depression and identify a potential therapeutic target. PERSPECTIVE: LncRNA XR_351665 in CeA functions as a ceRNA to block the inhibitory effect of miR-152-3p on DNMT1 and contributes to the development of chronic pain-induced depression. These data suggest that manipulation of XR_351665/miR-152-3p/DNMT1 axis may be a potential method to attenuate chronic pain-induced depression.
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Dietary Restriction and Rapamycin Affect Brain Aging in Mice by Attenuating Age-Related DNA Methylation Changes. Genes (Basel) 2022; 13:genes13040699. [PMID: 35456505 PMCID: PMC9030181 DOI: 10.3390/genes13040699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 02/07/2023] Open
Abstract
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging rate at the molecular level. To understand the mechanism behind the impacts of dietary restriction and rapamycin on aging, DNA methylation and gene expression changes were measured in the hippocampi of different-aged mice. Examining the single-base resolution of DNA methylation, we discovered that both dietary restriction and rapamycin treatment can maintain DNA methylation in a younger state compared to normal-aged mice. Through functional enrichment analysis of genes in which DNA methylation or gene expression can be affected by DR/RALL, we found that DR/RALL may retard aging through a relationship in which DNA methylation and gene expression work together not only in the same gene but also in the same biological process. This study is instructive for understanding the maintenance of DNA methylation by DR/RALL in the aging process, as well as the role of DR and RALL in the amelioration of aging.
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Iqbal MA, Li M, Lin J, Zhang G, Chen M, Moazzam NF, Qian W. Preliminary Study on the Sequencing of Whole Genomic Methylation and Transcriptome-Related Genes in Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14051163. [PMID: 35267472 PMCID: PMC8909391 DOI: 10.3390/cancers14051163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Epigenetic alterations are critical for tumor onset and development. DNA methylation is one of the most studied pathways concerning various types of cancer. A promising and exciting avenue of research is the discovery of biomarkers of early-stage malignancies for disease prevention and prognostic indicators following cancer treatment by examining the DNA methylation modification of relevant genes implicated in cancer development. We have made significant advances in the study of DNA methylation and thyroid cancer. This study is novel in that it distinguished methylation changes that occurred primarily in the gene body region of the aforementioned hypermethylated or hypomethylated thyroid cancer genes. Our findings imply that exposing whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer provides new insight into the carcinogenesis of thyroid cancer, demonstrating that gene expression mediated by DNA methylation modifications may play a significant role in tumor growth. Abstract Thyroid carcinoma is the most prevalent endocrine cancer globally and the primary cause of cancer-related mortality. Epigenetic modifications are progressively being linked to metastasis. This study aimed to examine whole-genome DNA methylation patterns and the gene expression profiles in thyroid cancer tissue samples using a MethylationEPIC BeadChip (850K), RNA sequencing, and a targeted bisulfite sequencing assay. The results of the Illumina Infinium human methylation kit (850K) analyses identified differentially methylated CpG locations (DMPs) and differentially methylated CpG regions (DMRs) encompassing nearly the entire genome with high resolution and depth. Gene ontology and KEGG pathway analyses revealed that the genes associated with DMRs belonged to various domain-specific ontologies, including cell adhesion, molecule binding, and proliferation. The RNA-Seq study found 1627 differentially expressed genes, 1174 of which that were up-regulated and 453 of which that were down-regulated. The targeted bisulfite sequencing assay revealed that CHST2, DPP4, DUSP6, ITGA2, SLC1A5, TIAM1, TNIK, and ABTB2 methylation levels were dramatically lowered in thyroid cancer patients when compared to the controls, but GALNTL6, HTR7, SPOCD1, and GRM5 methylation levels were significantly raised. Our study revealed that the whole-genome DNA methylation patterns and gene expression profiles in thyroid cancer shed new light on the tumorigenesis of thyroid cancer.
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Affiliation(s)
- Muhammad Asad Iqbal
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
| | - Mingyang Li
- Department of Basic Medical Sciences, Affiliated to School of Medicine, Jiangsu University, Zhenjiang 212002, China;
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Guoliang Zhang
- Department of General Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | - Miao Chen
- Department of Pathology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212132, China;
| | | | - Wei Qian
- Department of Otolaryngology-Head & Neck Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang 212002, China;
- Correspondence: ; Tel.: +86-0511-88917833 or +86-1535-8586188
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Hong L, Chen W, He L, Tan H, Peng D, Zhao G, Shi X, Wang L, Liu M, Jiang H. Effect of Naoluoxintong on the NogoA/RhoA/ROCK pathway by down-regulating DNA methylation in MCAO rats. JOURNAL OF ETHNOPHARMACOLOGY 2021; 281:114559. [PMID: 34461189 DOI: 10.1016/j.jep.2021.114559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Naoluoxintong (NLXT) is a traditional Chinese Medicine (TCM) prescription that is clinically used in the treatment of ischemic stroke (IS). However, its therapeutic mechanism remains unclear. AIM OF THE STUDY To obtain the mechanism of NLXT by observing the protective effects of NLXT on the NogoA/RhoA/Rock pathway in a rat model of IS by regulating DNA methylation. MATERIALS AND METHODS Rats were divided into five groups using a random number table: normal group, model group, NLXT group, blocker group I (NLXT + SGI-1027) and blocker group II (NLXT + Y27632). The right middle cerebral artery occlusion-reperfusion (MCAO/R) rat model was made, and the regional cerebral blood flow (rCBF) of each group was detected using laser Doppler. The methylation levels of CpG sites of neurite outgrowth inhibitor protein-A (Nogo-A), Nogo receptor (NgR), ras homolog gene family member A (RhoA) and rho-associated coiled-coil protein kinase 2 (ROCK2) genes in rat brain tissue were detected using the bisulfite method. Reverse transcription-polymerase chain reaction (RT-PCR) was used to detect NogoA, RhoA, NgR1, NgR2 and ROCK2 mRNA expression in rat brain tissue. NogoA, RhoA, NgR1, NgR2 and ROCK2 proteins were detected using immunoblotting in rat brain tissue. RESULTS After the modeling of middle cerebral artery occlusion (MCAO), neurological deficit test was made to ensure the success of the modeling. At each time point after surgery, the rCBF of the other groups decreased compared with the normal group (P < 0.01 or P < 0.05). Meanwhile, the rCBF increased in blocker group I as well as blocker group II after 3 days (P < 0.05). There were differences in the DNA methylation sites of NogoA, RhoA, NgR and ROCK2 genes between the model group and the NLXT group (P < 0.05). Compared with the normal group, NogoA, NgR1, NgR2, RhoA and ROCK2 gene expression in the model group increased observably (P < 0.01). In comparison with the model group, NogoA and NgR1 gene expression in the blocker group II was prominently observed on the 1st day. NogoA, NgR1, NgR2, RhoA and ROCK2 gene expression remarkably reduced (P < 0.01) on the 3rd and 7th days. Compared with the normal group, NogoA, RhoA, NgR1, NgR2 and ROCK2 protein expression in the model group increased observably (P < 0.01). In comparison with the model group, NogoA, RhoA, NgR1, NgR2 and ROCK2 protein expression in the other groups declined prominently (P < 0.01). CONCLUSION NLXT can reduce the DNA methylation level of NogoA pathway after IS, thus inhibit the expression of NogoA/RhoA/ROCK pathway from producing anti-cerebral ischemia pharmacological effect.
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Affiliation(s)
- Lu Hong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Weidong Chen
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, Anhui, 230012, China
| | - Ling He
- Key Laboratory of Xin'an Medicine Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China; School of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China.
| | - Hui Tan
- Key Laboratory of Xin'an Medicine Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China; School of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Daiyin Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, Anhui, 230012, China
| | - Guodong Zhao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Xiaoqian Shi
- Department of Pharmacy, Huaibei People's Hospital, Huaibei, Anhui, 235000, China
| | - Lei Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, Anhui, 230012, China
| | - Mingming Liu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Huihui Jiang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
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Chao CC, Shen PW, Tzeng TY, Kung HJ, Tsai TF, Wong YH. Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging. Biomedicines 2021; 9:1635. [PMID: 34829864 PMCID: PMC8615703 DOI: 10.3390/biomedicines9111635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.
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Affiliation(s)
- Chuan-Chuan Chao
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Department of Neurology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Wen Shen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan;
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tsai-Yu Tzeng
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA 95817, USA
| | - Ting-Fen Tsai
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Hui Wong
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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Wang Y, Tang L, Yang L, Lv P, Mai S, Xu L, Wang Z. DNA Methylation-Mediated Low Expression of CFTR Stimulates the Progression of Lung Adenocarcinoma. Biochem Genet 2021; 60:807-821. [PMID: 34498165 DOI: 10.1007/s10528-021-10128-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
In recent years, the mortality rate of lung adenocarcinoma (LUAD) is persistently increasing, which has already caused a huge impact on human living standards. Hence, there is an urgent need to probe the molecular mechanism of LUAD progression, so as to disclose prognostic and diagnostic markers for patients with LUAD. Methylation 450 K data and mRNA expression data of LUAD were obtained via bioinformatics analysis to screen methylation-driven genes. The expression of the target gene was detected through qRT-PCR, while the methylation level was evaluated via methylation-specific PCR (MSP). The impact of the gene on cell proliferation, migration, invasion, apoptosis and cell cycle was measured through CCK-8, wound healing, Transwell invasion assay, and flow cytometry. CFTR was defined by bioinformatics analysis as the target gene for this study. qRT-PCR revealed that CFTR was lowly expressed in LUAD cells. MSP displayed that the CFTR promoter region in LUAD cells was hypermethylated, and demethylation could pronouncedly increase the level of CFTR mRNA in LUAD cells. Cell biological functional experiments exhibited that CFTR hindered cell proliferation, migration, and invasion, fostered cell apoptosis of LUAD, and blocked the cell cycle in G2-M phase. CFTR was hypermethylated in LUAD, which mediated the low expression of CFTR in LUAD to stimulate the progression of LUAD.
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Affiliation(s)
- Yue Wang
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Lu Tang
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Liangliang Yang
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Peiyun Lv
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Shixiong Mai
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Li Xu
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China
| | - Zhenxing Wang
- Department of Thoracic Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Street, Erdao District, Changchun, 130033, China.
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Chen Q, Li D, Jin W, Shi Y, Li Z, Ma P, Sun J, Chen S, Li P, Lin P. Research Progress on the Correlation Between Epigenetics and Schizophrenia. Front Neurosci 2021; 15:688727. [PMID: 34366776 PMCID: PMC8334178 DOI: 10.3389/fnins.2021.688727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose of the Review Nowadays, the incidence of schizophrenia is noticeably increased. If left undiagnosed and untreated, it will lead to impaired social functions, repeated hospital admissions, decline in quality of life and life expectancy. However, the diagnosis of schizophrenia is complicated and challenging. Both genetic and environmental factors are considered as important contributors to the development and progression of this disorder. The environmental factors have been linked to changes in gene expression through epigenetic modulations, which have raised more and more research interests in recent years. This review article is to summarize the current findings and understanding of epigenetic modulation associated with pathogenesis of schizophrenia, aiming to provide useful information for further research in developing biomarkers for schizophrenia. Recent Findings Three major types of epigenetic modulations have been described in this article. Firstly, both DNA hypermethylation and hypomethylated have been associated with schizophrenia via analyzing post-mortem brain tissues and peripheral blood of patients. Specific changes of non-coding RNAs, particularly microRNAs and long-chain non-coding RNAs, have been observed in central and peripheral samples of schizophrenia patients, indicating their significant diagnostic value for the disease, and may also potentially predict treatment response. The correlation between histone modification and schizophrenia, however, is largely unclear. Summary Epigenetic modulations, including DNA methylation, ncRNA transcriptional regulation and histone modification, play an important role in the pathogenesis of schizophrenia. Therefore, tests of these epigenetic alterations may be utilized to assist in the diagnosis and determination of strategies of individualized treatment in clinical practice.
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Affiliation(s)
- Qing Chen
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weifeng Jin
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Shi
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenhua Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peijun Ma
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaqi Sun
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuzi Chen
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Lin
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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12
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Streck EL, Bussular FP, Wessler LB, Duarte MB, Rezende VL, Rodrigues MS, Torres CA, Lemos IS, Candiotto G, Gava FF, de Oliveira J, Valvassori SS. Administration of branched-chain amino acids alters epigenetic regulatory enzymes in an animal model of Maple Syrup Urine Disease. Metab Brain Dis 2021; 36:247-254. [PMID: 33098071 DOI: 10.1007/s11011-020-00631-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/11/2020] [Indexed: 12/13/2022]
Abstract
Maple Syrup Urine Disease (MSUD) is an autosomal recessive inherited disorder that affects the activity of the branched-chainα-keto acid dehydrogenase complex (BCDK). This deficiency on BCDK complex results in the accumulation of branched-chain amino acids (BCAA) leucine, isoleucine, valine, and their corresponding α-keto acids. Epigenetic changes can negatively affect the metabolism of BCAA. These changes are catalyzed by the epigenetic regulatory enzymes, e.g., DNA methyltransferase (DNMT), histone deacetylases (HDAC), and histone acetyltransferases (HAT). However, the impacts of BCAA administration on the activity of epigenetic regulatory enzymes in the brain of MSUD patients are still unknown. In this study, we aimed to demonstrate the impact of BCAA administration on the activity of DNMT, HDAC, and HAT in the brain structures of infant rats, an animal model of MSUD. For that, we administered a BCAA pool to infant rats for 21 days. We demonstrated that BCAA administration significantly increased the DNMT and HDAC activities in the hippocampus and striatum, but not in the cerebral cortex of MSUD infant rats. A positive correlation was observed between HDAC and DNMT activities in the hippocampus and striatum of animals exposed to BCAA injections. Our results showed that the BCAA administration could modulate epigenetic regulatory enzymes, mainly DNMT and HDAC, in the brains of infant rats. Therefore, we suggest that the increase in the activity of DNMT and HDAC in the hippocampus and striatum could partially explain the neurological impairments presented in animal models of MSUD.
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Affiliation(s)
- Emilio L Streck
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil.
| | - Felipe P Bussular
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Leticia B Wessler
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Mariane B Duarte
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Victoria L Rezende
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Matheus S Rodrigues
- Laboratório de Psiquiatria Translacional, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, SC, 88806-000, Brazil
| | - Carolina A Torres
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Isabela S Lemos
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Gabriela Candiotto
- Laboratório de Doenças Neurometabólicas, Laboratório de Neurologia Experimental, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, SC, Criciúma, 88806-000, Brazil
| | - Fernanda F Gava
- Laboratório de Psiquiatria Translacional, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, SC, 88806-000, Brazil
| | - Jade de Oliveira
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, Porto Alegre, 90035-000, Brazil
| | - Samira S Valvassori
- Laboratório de Psiquiatria Translacional, Programa de Pós-graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, SC, 88806-000, Brazil
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Wang YL, Zhang YY. cg04448376, cg24387542, cg08548498, and cg14621323 as a Novel Signature to Predict Prognosis in Kidney Renal Papillary Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4854390. [PMID: 33381555 PMCID: PMC7759405 DOI: 10.1155/2020/4854390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/19/2020] [Accepted: 11/28/2020] [Indexed: 10/26/2022]
Abstract
INTRODUCTION DNA methylation plays a vital role in prognosis prediction of cancers. In this study, we aimed to identify novel DNA methylation site biomarkers and create an efficient methylated site model for predicting survival in kidney renal papillary cell carcinoma (KIRP). METHODS DNA methylation and gene expression profile data were downloaded from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Differential methylated genes (DMGs) and differential expression genes (DEGs) were identified and then searched for the hub genes. Cox proportional hazards regression was applied to identify DNA methylated site biomarkers from the hub genes. Kaplan-Meier survival and ROC analyses were used to validate the effective prognostic ability of the methylation gene site biomarker. The biomarker sites were validated in the GEO cohorts. The GO and KEGG annotation was done to explore the biological function of DNA methylated site signature. RESULTS Nine DMGs with opposite expression patterns containing 47 methylated sites were identified. Finally, four methylated sites were identified using the hazard regression model (cg04448376, cg24387542, cg08548498, and cg14621323) located in UTY, LGALS9B, SLPI, and PFN3, respectively. These sites classified patients into high- and low-risk groups in the training cohort. The 5-year survival rates for patients with low-risk and high-risk scores were 97.5% and 75.9% (P < 0.001). The prognostic accuracy and signature methylation sites were validated in the test (TCGA, n = 87) and GEO cohorts (n = 14). Multivariate regression analysis showed that the signature was an independent prediction prognostic factor for KIRP. Based on this analysis, we developed methylated site signature nomogram that predicts an individual's risk of survival. Functional analysis suggested that these signature genes are involved in the biological processes of protein binding. CONCLUSIONS Our study demonstrated that the methylated gene site signature might be a powerful prognostic tool for evaluating survival rate and guiding tailored therapy for KIRP patients.
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Affiliation(s)
- Ying-Lei Wang
- Department of Urinary Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, China
| | - Ying-Ying Zhang
- Out-patient Department, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, China
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14
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Zhang R, Li Y, Yu H, Liu L, Zhu C, Zuo S, Chen Z. An aberrant DNA methylation signature for predicting hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1667. [PMID: 33490179 PMCID: PMC7812168 DOI: 10.21037/atm-20-7804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background By the time they are clinically diagnosed, patients with hepatocellular carcinoma (HCC) are often at the advanced stage. DNA methylation has become a useful predictor of prognosis for cancer patients. Research on DNA methylation as a biomarker for assessing the risk of occurrence in HCC patients is limited. The purpose of this study was to develop an efficient methylation site model for predicting survival in patients with HCC. Methods DNA methylation and gene expression profile data were extracted from The Cancer Genome Atlas (TCGA) database. Markers of DNA-methylated site in two subsets (the training subset and the test subset) were identified using a random survival forest algorithm and Cox proportional hazards regression. Then, Gene Ontology annotations were applied to investigate the functions of DNA methylation signatures. Results A total of 37 hub genes containing 713 methylated sites were identified among the differentially methylated genes (DMGs) and differentially expressed genes (DEGs). Finally, seven methylation sites (cg12824782, cg24871714, cg18683774, cg22796509, cg19450025, cg10474350, and cg06511917) were identified. In the training group and the test group, the area under the curve predicting the survival of patients with HCC was 0.750 and 0.742, respectively. The seven methylation sites signature could be used to divide the patients in the training group into high- and low-risk subgroups [overall survival (OS): 2.81 vs. 2.11 years; log-rank test, P<0.05]. Then, the prediction ability of the model was validated in the test dataset through risk stratification (OS: 2.04 vs. 2.88 years; log-rank test, P<0.05). Functional analysis demonstrated that these signature genes were related to the activity of DNA-binding transcription activator, RNA polymerase II distal enhancer sequence-specific DNA binding, and enhancer sequence-specific DNA binding. Conclusions The results of this study showed that the signature is useful for predicting the survival of HCC patients and thus, can facilitate treatment-related decision-making.
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Affiliation(s)
- Renhua Zhang
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Yafei Li
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Hao Yu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Lin Liu
- Information Communication Division, Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Changhao Zhu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi Zuo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zili Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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15
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Dong M, Yang Z, Li X, Zhang Z, Yin A. Screening of Methylation Gene Sites as Prognostic Signature in Lung Adenocarcinoma. Yonsei Med J 2020; 61:1013-1023. [PMID: 33251775 PMCID: PMC7700873 DOI: 10.3349/ymj.2020.61.12.1013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/05/2020] [Accepted: 10/18/2020] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Most lung adenocarcinoma (LUAD) patients are diagnosed at the advanced stage and have poor prognosis. DNA methylation plays an important role in the prognosis prediction of cancers. The objective of this study was to identify new DNA methylation sites as biomarkers for LUAD prognosis. MATERIALS AND METHODS We downloaded DNA methylation data from The Cancer Genome Atlas data portal. Cox proportional hazard regression model and random survival forest algorithm were applied to identify the DNA-methylation sites. Methylation of sites were validated in the Gene Expression Omnibus cohorts. Function annotation were done to explore the biological function of DNA methylated sites signature. RESULTS Six DNA methylation sites were identified as prognosis signature. The signature yielded acceptable discrimination between the high-risk group and low-risk group. The discrimination effect of this DNA methylation signature for the OS was obvious, with a median OS of 21.89 months vs. 17.74 months for high-risk vs. low-risk groups. This prognostic prediction model was validated by the test group and GEO dataset. The predictive survival value was higher for the prognostic prediction model than that for the tumor node metastasis stage. Adjuvant hemotherapy could not affect the prediction of the signature. Functional analysis indicated that these signature genes were involved in protein binding and cytoplasm. CONCLUSION We identified the prognostic signature for LUAD by combining six DNA methylation sites. This could service as potential robust and specificity signature in the prognosis prediction of LUAD.
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Affiliation(s)
- Min Dong
- Pulmonology Respiratory and Critical Care Unit, Gansu Province Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Zengli Yang
- Infectious Diseases Unit, First People's Hospital of Guannan County, Guannan, China
| | - Xingfang Li
- Pulmonology Respiratory and Critical Care Unit, Gansu Province Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Zhenxiang Zhang
- Orthopedics, Lanzhou Traditional Chinese Medicine Hospital, Lanzhou, China
| | - Ankang Yin
- Department of General Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, China.
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16
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Mustafin RN, Kazantseva AV, Malykh SB, Khusnutdinova EK. Genetic Mechanisms of Cognitive Development. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542007011x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Ozaki Y, Yoshino Y, Yamazaki K, Ochi S, Iga J, Nagai M, Nomoto M, Ueno S. DRD2 methylation to differentiate dementia with Lewy bodies from Parkinson's disease. Acta Neurol Scand 2020; 141:177-182. [PMID: 31659741 DOI: 10.1111/ane.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/20/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The aim was to clarify whether DRD2 methylation changes in leukocytes of dementia with Lewy bodies (DLB) or Parkinson's disease (PD) patients are seen and can be used to discriminate between them. METHODS Methylation rates were examined in 23 DLB subjects and 23 age- and sex-matched healthy controls and 37 PD patients and 37 age- and sex-matched healthy controls. RESULTS Significant DRD2 DNA methylation changes were found in leukocytes of DLB and PD patients compared with healthy subjects. Discriminant analysis between DLB and PD using seven CpG sites demonstrated sensitivity and specificity of 83.8% and 90.9%, respectively. None of the CpG sites were associated with sex, age, age of onset, disease duration, and any of the neuropsychological tests in DLB and PD patients. CONCLUSION This is the first report showing that DRD2 DNA methylation rates in leukocytes were increased in DLB patients and decreased in PD patients. These results may be an important step in understanding epigenetic mechanisms underlying DLB and PD pathogenesis and providing a novel biomarker for discriminating between them.
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Affiliation(s)
- Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
| | - Jun‐ichi Iga
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
| | - Masahiro Nagai
- Department of Neurology and Clinical Pharmacology Ehime University Graduate School of Medicine Toon Japan
| | - Masahiro Nomoto
- Department of Neurology and Clinical Pharmacology Ehime University Graduate School of Medicine Toon Japan
| | - Shu‐ichi Ueno
- Department of Neuropsychiatry, Molecules and Function Ehime University Graduate School of Medicine Toon Japan
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18
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Li Y, Lv Z, Zhang J, Ma Q, Li Q, Song L, Gong L, Zhu Y, Li X, Hao Y, Yang Y. Profiling of differentially expressed circular RNAs in peripheral blood mononuclear cells from Alzheimer's disease patients. Metab Brain Dis 2020; 35:201-213. [PMID: 31834549 DOI: 10.1007/s11011-019-00497-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/12/2019] [Indexed: 02/08/2023]
Abstract
Expression of circular RNA (circRNA), a class of noncoding RNAs that regulates gene expression, is altered in Alzheimer's disease. This study profiled differentially expressed circRNAs in peripheral blood mononuclear cells (PBMCs) from five patients with Alzheimer's disease compared to healthy controls using circRNA microarrays. We identified a total of 4060 differentially expressed circRNAs (1990 upregulated and 2070 downregulated) in Alzheimer's disease patients. Among these circRNAs, 10 randomly selected circRNAs were verified using qRT-PCR. The top 10 upregulated and downregulated circRNAs were used to predict their target miRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these differentially expressed circRNAs were strongly associated with inflammation, metabolism, and immune responses, which are all risk factors for Alzheimer's disease. The circRNA-miRNA-mRNA network was most involved in the MAPK, mTOR, AMPK, and WNT signaling pathways in Alzheimer's disease. In conclusion, the current study demonstrated the importance of circRNAs in Alzheimer's disease development. Future studies will evaluate some of these circRNAs as biomarkers for early disease detection and to develop therapeutic strategies to clinically control Alzheimer's disease progression.
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Affiliation(s)
- Yanxin Li
- Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Zhanyun Lv
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Jing Zhang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Qianqian Ma
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Qiuhua Li
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Li Song
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Li Gong
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Yunliang Zhu
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Xiangyuan Li
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China
- Jining Medical University, Jining, 272067, China
| | - Yanlei Hao
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China.
- Jining Medical University, Jining, 272067, China.
| | - Yan Yang
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, 272000, China.
- Jining Medical University, Jining, 272067, China.
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Burdeos GC, Blank R, Wolffram S. Influence of quercetin on the global DNA methylation pattern in pigs. Food Funct 2020; 11:7421-7426. [DOI: 10.1039/d0fo00896f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The plant flavonol quercetin causes multiple health-promoting effects in human and animals.
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Affiliation(s)
- Gregor C. Burdeos
- Institute of Animal Nutrition and Physiology
- Christian-Albrechts-University Kiel
- Kiel
- Germany
| | - Ralf Blank
- Institute of Animal Nutrition and Physiology
- Christian-Albrechts-University Kiel
- Kiel
- Germany
| | - Siegfried Wolffram
- Institute of Animal Nutrition and Physiology
- Christian-Albrechts-University Kiel
- Kiel
- Germany
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20
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Pierre WC, Legault L, Londono I, McGraw S, Lodygensky GA. Alteration of the brain methylation landscape following postnatal inflammatory injury in rat pups. FASEB J 2020; 34:432-445. [PMID: 31914673 PMCID: PMC6972494 DOI: 10.1096/fj.201901461r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/26/2019] [Accepted: 10/08/2019] [Indexed: 12/18/2022]
Abstract
Preterm infants are vulnerable to inflammation-induced white matter injury (WMI), which is associated with neurocognitive impairment and increased risk of neuropsychiatric diseases in adulthood. Epigenetic mechanisms, particularly DNA methylation, play a role in normal development and modulate the response to pathological challenges. Our aims were to determine how WMI triggered DNA methylation alterations in brains of neonatal rats and if such changes persisted over time. We used a robust model of WMI by injecting lipopolysaccharide (LPS) or sterile saline in the corpus callosum of 3-day-old (P3) rat pups. Brains were collected 24 hours (P4) and 21 days post-injection (P24). We extracted genomic DNA from the brain to establish genome-wide quantitative DNA methylation profiles using reduced representation bisulfite sequencing. Neonatal LPS exposure induced a persistent increased methylation of genes related to nervous system development and a reduced methylation of genes associated with inflammatory pathways. These findings suggest that early-life neuroinflammatory exposure impacts the cerebral methylation landscape with determining widespread epigenetic modifications especially in genes related to neurodevelopment.
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Affiliation(s)
- Wyston C. Pierre
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Lisa‐Marie Legault
- Department of Biochemistry and Molecular MedicineUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Irene Londono
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Serge McGraw
- Department of Biochemistry and Molecular MedicineUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
- Department of Obstetrics & GynecologyUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
| | - Gregory A. Lodygensky
- Department of PediatricsUniversité de MontréalResearch Center of the CHU Sainte‐JustineMontréalQCCanada
- Department of Pharmacology and PhysiologyUniversité de MontréalMontréalQCCanada
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Beydoun MA, Shaked D, Tajuddin SM, Weiss J, Evans MK, Zonderman AB. Accelerated epigenetic age and cognitive decline among urban-dwelling adults. Neurology 2019; 94:e613-e625. [PMID: 31879275 DOI: 10.1212/wnl.0000000000008756] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Epigenetic modifications are closely linked with aging, but their relationship with cognition remains equivocal. Given known sex differences in epigenetic aging, we explored sex-specific associations of 3 DNA methylation (DNAm)-based measures of epigenetic age acceleration (EAA) with baseline and longitudinal change in cognitive performance among middle-aged urban adults. METHODS We used exploratory data from a subgroup of participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span study with complete DNA samples and whose baseline ages were >50.0 years (2004-2009) to estimate 3 DNAm EAA measures: (1) universal EAA (AgeAccel); (2) intrinsic EAA (IEAA); and (3) extrinsic EAA (EEAA). Cognitive performance was measured at baseline visit (2004-2009) and first follow-up (2009-2013) with 11 test scores covering global mental status and specific domains such as learning/memory, attention, visuospatial, psychomotor speed, language/verbal, and executive function. A series of mixed-effects regression models were conducted adjusting for covariates and multiple testing (n = 147-156, ∼51% men, k = 1.7-1.9 observations/participant, mean follow-up time ∼4.7 years). RESULTS EEAA, a measure of both biological age and immunosenescence, was consistently associated with greater cognitive decline among men on tests of visual memory/visuoconstructive ability (Benton Visual Retention Test: γ11 = 0.0512 ± 0.0176, p = 0.004) and attention/processing speed (Trail-Making Test, part A: γ11 = 0.219 ± 0.080, p = 0.007). AgeAccel and IEAA were not associated with cognitive change in this sample. CONCLUSIONS EEAA capturing immune system cell aging was associated with faster decline among men in domains of attention and visual memory. Larger longitudinal studies are needed to replicate our findings.
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Affiliation(s)
- May A Beydoun
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD.
| | - Danielle Shaked
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD
| | - Salman M Tajuddin
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD
| | - Jordan Weiss
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD
| | - Michele K Evans
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD
| | - Alan B Zonderman
- From the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD
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22
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Griñán-Ferré C, Corpas R, Puigoriol-Illamola D, Palomera-Ávalos V, Sanfeliu C, Pallàs M. Understanding Epigenetics in the Neurodegeneration of Alzheimer's Disease: SAMP8 Mouse Model. J Alzheimers Dis 2019; 62:943-963. [PMID: 29562529 PMCID: PMC5870033 DOI: 10.3233/jad-170664] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is emerging as the missing link among genetic inheritance, environmental influences, and body and brain health status. In the brain, specific changes in nucleic acids or their associated proteins in neurons and glial cells might imprint differential patterns of gene activation that will favor either cognitive enhancement or cognitive loss for more than one generation. Furthermore, derangement of age-related epigenetic signaling is appearing as a significant risk factor for illnesses of aging, including neurodegeneration and Alzheimer’s disease (AD). In addition, better knowledge of epigenetic mechanisms might provide hints and clues in the triggering and progression of AD. Intense research in experimental models suggests that molecular interventions for modulating epigenetic mechanisms might have therapeutic applications to promote cognitive maintenance through an advanced age. The SAMP8 mouse is a senescence model with AD traits in which the study of epigenetic alterations may unveil epigenetic therapies against the AD.
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Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology, Toxicology and Therapeutic Chemistry (Pharmacology Section) and Institute of Neuroscience, University of Barcelona and CIBERNED, Barcelona, Spain
| | - Rubén Corpas
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Dolors Puigoriol-Illamola
- Department of Pharmacology, Toxicology and Therapeutic Chemistry (Pharmacology Section) and Institute of Neuroscience, University of Barcelona and CIBERNED, Barcelona, Spain
| | - Verónica Palomera-Ávalos
- Department of Pharmacology, Toxicology and Therapeutic Chemistry (Pharmacology Section) and Institute of Neuroscience, University of Barcelona and CIBERNED, Barcelona, Spain
| | - Coral Sanfeliu
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Mercè Pallàs
- Department of Pharmacology, Toxicology and Therapeutic Chemistry (Pharmacology Section) and Institute of Neuroscience, University of Barcelona and CIBERNED, Barcelona, Spain
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23
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Harman MF, Martín MG. Epigenetic mechanisms related to cognitive decline during aging. J Neurosci Res 2019; 98:234-246. [PMID: 31045277 DOI: 10.1002/jnr.24436] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 04/04/2019] [Accepted: 04/12/2019] [Indexed: 12/12/2022]
Abstract
Cognitive decline is a hallmark of the aging nervous system, characterized by increasing memory loss and a deterioration of mental capacity, which in turn creates a favorable context for the development of neurodegenerative diseases. One of the most detrimental alterations that occur at the molecular level in the brain during aging is the modification of the epigenetic mechanisms that control gene expression. As a result of these epigenetic-driven changes in the transcriptome most of the functions of the brain including synaptic plasticity, learning, and memory decline with aging. The epigenetic mechanisms altered during aging include DNA methylation, histone modifications, nucleosome remodeling, and microRNA-mediated gene regulation. In this review, we examine the current evidence concerning the changes of epigenetic modifications together with the molecular mechanisms underlying impaired neuronal gene transcription during aging. Herein, we discuss the alterations of DNA methylation pattern that occur in old neurons. We will also describe the most prominent age-related histone posttranslational modifications in the brain since changes in acetylation and methylation of specific lysine residues on H3 and H4 are associated to functional decline in the old. In addition, we discuss the role that changes in the levels of certain miRNAs would play in cognitive decline with aging. Finally, we provide an overview about the mechanisms either extrinsic or intrinsic that would trigger epigenetic changes in the aging brain, and the consequences of these changes, i.e., altered transcriptional profile and reactivation of transposable elements in old brain.
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Affiliation(s)
- María F Harman
- Instituto Ferreyra, INIMEC-CONICET-UNC, Córdoba, Argentina.,Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mauricio G Martín
- Instituto Ferreyra, INIMEC-CONICET-UNC, Córdoba, Argentina.,Facultad de Ciencias Exactas Físicas y Naturales, Cátedra de Química Orgánica, Universidad Nacional de Córdoba, Córdoba, Argentina
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24
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Cosín-Tomás M, Álvarez-López MJ, Companys-Alemany J, Kaliman P, González-Castillo C, Ortuño-Sahagún D, Pallàs M, Griñán-Ferré C. Temporal Integrative Analysis of mRNA and microRNAs Expression Profiles and Epigenetic Alterations in Female SAMP8, a Model of Age-Related Cognitive Decline. Front Genet 2018; 9:596. [PMID: 30619445 PMCID: PMC6297390 DOI: 10.3389/fgene.2018.00596] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/15/2018] [Indexed: 01/05/2023] Open
Abstract
A growing body of research shows that epigenetic mechanisms are critically involved in normal and pathological aging. The Senescence-Accelerated Mouse Prone 8 (SAMP8) can be considered a useful tool to better understand the dynamics of the global epigenetic landscape during the aging process since its phenotype is not fully explained by genetic factors. Here we investigated dysfunctional age-related transcriptional profiles and epigenetic programming enzymes in the hippocampus of 2- and 9-month-old SAMP8 female mice using the Senescent-Accelerated Resistant 1 (SAMR1) mouse strain as control. SAMP8 mice presented 1,062 genes dysregulated at 2 months of age, and 1,033 genes at 9 months, with 92 genes concurrently dysregulated at both ages compared to age-matched SAMR1. SAMP8 mice showed a significant decrease in global DNA methylation (5-mC) at 2 months while hydroxymethylation (5-hmC) levels were increased in SAMP8 mice at 2 and 9 months of age compared to SAMR1. These changes were accompanied by changes in the expression of several enzymes that regulate 5-mC and methylcytosine oxidation. Acetylated H3 and H4 histone levels were significantly diminished in SAMP8 mice at 2-month-old compared to SAMR1 and altered Histone DeACetylase (HDACs) profiles were detected in both young and old SAMP8 mice. We analyzed 84 different mouse miRNAs known to be altered in neurological diseases or involved in neuronal development. Compared with SAMR1, SAMP8 mice showed 28 and 17 miRNAs differentially expressed at 2 and 9 months of age, respectively; 6 of these miRNAs overlapped at both ages. We used several bioinformatic approaches to integrate our data in mRNA:miRNA regulatory networks and functional predictions for young and aged animals. In sum, our study reveals interplay between epigenetic mechanisms and gene networks that seems to be relevant for the progression toward a pathological aging and provides several potential markers and therapeutic candidates for Alzheimer's Disease (AD) and age-related cognitive impairment.
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Affiliation(s)
- Marta Cosín-Tomás
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Departments of Human Genetics and Pediatrics, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - María Jesús Álvarez-López
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Júlia Companys-Alemany
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Perla Kaliman
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain
| | | | - Daniel Ortuño-Sahagún
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara, Mexico
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
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25
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Liu J, Zhao W, Ware EB, Turner ST, Mosley TH, Smith JA. DNA methylation in the APOE genomic region is associated with cognitive function in African Americans. BMC Med Genomics 2018; 11:43. [PMID: 29739406 PMCID: PMC5941603 DOI: 10.1186/s12920-018-0363-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/26/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genetic variations in apolipoprotein E (APOE) and proximal genes (PVRL2, TOMM40, and APOC1) are associated with cognitive function and dementia, particularly Alzheimer's disease. Epigenetic mechanisms such as DNA methylation play a central role in the regulation of gene expression. Recent studies have found evidence that DNA methylation may contribute to the pathogenesis of dementia, but its association with cognitive function in populations without dementia remains unclear. METHODS We assessed DNA methylation levels of 48 CpG sites in the APOE genomic region in peripheral blood leukocytes collected from 289 African Americans (mean age = 67 years) from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. Using linear regression, we examined the relationship between methylation in the APOE genomic region and multiple cognitive measures including learning, memory, processing speed, concentration, language and global cognitive function. RESULTS We identified eight CpG sites in three genes (PVRL2, TOMM40, and APOE) that showed an inverse association between methylation level and delayed recall, a measure of memory, after adjusting for age and sex (False Discovery Rate q-value < 0.1). All eight CpGs are located in either CpG islands (CGIs) or CGI shelves, and six of them are in promoter regions. Education and APOE ε4 carrier status significantly modified the effect of methylation in cg08583001 (PVRL2) and cg22024783 (TOMM40), respectively. Together, methylation of the eight CpGs explained an additional 8.7% of the variance in delayed recall, after adjustment for age, sex, education, and APOE ε4 carrier status. Methylation was not significantly associated with any other cognitive measures. CONCLUSIONS Our results suggest that methylation levels at multiple CpGs in the APOE genomic region are inversely associated with delayed recall during normal cognitive aging, even after accounting for known genetic predictors for cognition. Our findings highlight the important role of epigenetic mechanisms in influencing cognitive performance, and suggest that changes in blood methylation may be an early indicator of individuals at risk for dementia as well as potential targets for intervention in asymptomatic populations.
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Affiliation(s)
- Jiaxuan Liu
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104 USA
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905 USA
| | - Thomas H. Mosley
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS 39126 USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104 USA
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26
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Cui D, Xu X. DNA Methyltransferases, DNA Methylation, and Age-Associated Cognitive Function. Int J Mol Sci 2018; 19:E1315. [PMID: 29710796 PMCID: PMC5983821 DOI: 10.3390/ijms19051315] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
Ageing, a leading cause of the decline/deficits in human learning, memory, and cognitive abilities, is a major risk factor for age-associated neurodegenerative disorders such as Alzheimer’s disease. Emerging evidence suggests that epigenetics, an inheritable but reversible biochemical process, plays a crucial role in the pathogenesis of age-related neurological disorders. DNA methylation, the best-known epigenetic mark, has attracted most attention in this regard. DNA methyltransferases (DNMTs) are key enzymes in mediating the DNA methylation process, by which a methyl group is transferred, faithfully or anew, to genomic DNA sequences. Biologically, DNMTs are important for gene imprinting. Accumulating evidence suggests that DNMTs not only play critical roles, including gene imprinting and transcription regulation, in early development stages of the central nervous system (CNS), but also are indispensable in adult learning, memory, and cognition. Therefore, the impact of DNMTs and DNA methylation on age-associated cognitive functions and neurodegenerative diseases has emerged as a pivotal topic in the field. In this review, the effects of each DNMT on CNS development and healthy and pathological ageing are discussed.
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Affiliation(s)
- Di Cui
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
| | - Xiangru Xu
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.
- Department of Anesthesiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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27
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Masser DR, Hadad N, Porter HL, Mangold CA, Unnikrishnan A, Ford MM, Giles CB, Georgescu C, Dozmorov MG, Wren JD, Richardson A, Stanford DR, Freeman WM. Sexually divergent DNA methylation patterns with hippocampal aging. Aging Cell 2017; 16:1342-1352. [PMID: 28948711 PMCID: PMC5676057 DOI: 10.1111/acel.12681] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2017] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is a central regulator of genome function, and altered methylation patterns are indicative of biological aging and mortality. Age‐related cellular, biochemical, and molecular changes in the hippocampus lead to cognitive impairments and greater vulnerability to neurodegenerative disease that varies between the sexes. The role of hippocampal epigenomic changes with aging in these processes is unknown as no genome‐wide analyses of age‐related methylation changes have considered the factor of sex in a controlled animal model. High‐depth, genome‐wide bisulfite sequencing of young (3 month) and old (24 month) male and female mouse hippocampus revealed that while total genomic methylation amounts did not change with aging, specific sites in CG and non‐CG (CH) contexts demonstrated age‐related increases or decreases in methylation that were predominantly sexually divergent. Differential methylation with age for both CG and CH sites was enriched in intergenic and intronic regions and under‐represented in promoters, CG islands, and specific enhancer regions in both sexes, suggesting that certain genomic elements are especially labile with aging, even if the exact genomic loci altered are predominantly sex‐specific. Lifelong sex differences in autosomal methylation at CG and CH sites were also observed. The lack of genome‐wide hypomethylation, sexually divergent aging response, and autosomal sex differences at CG sites was confirmed in human data. These data reveal sex as a previously unappreciated central factor of hippocampal epigenomic changes with aging. In total, these data demonstrate an intricate regulation of DNA methylation with aging by sex, cytosine context, genomic location, and methylation level.
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Affiliation(s)
- Dustin R. Masser
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Hunter L. Porter
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Colleen A. Mangold
- Department of Biochemistry and Molecular Biology Pennsylvania State University University Park PA USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Matthew M. Ford
- Division of Neuroscience Oregon National Primate Research Center Beaverton OR USA
| | - Cory B. Giles
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
| | - Constantin Georgescu
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics Virginia Commonwealth University School of Medicine Richmond VA USA
| | - Jonathan D. Wren
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
- Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma City VA Medical Center Oklahoma OK USA
| | - David R. Stanford
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
| | - Willard M. Freeman
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
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28
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Michopoulou E, Negre P, Nikita E, Kranioti EF. The auricular surface as age indicator in a modern Greek sample: A test of two qualitative methods. Forensic Sci Int 2017; 280:246.e1-246.e7. [PMID: 28965664 DOI: 10.1016/j.forsciint.2017.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022]
Abstract
The auricular surface is often found very well preserved, thus age-related changes in this anatomical area can be important for any set of human remains that require identification under different taphonomic conditions. This study tests the Buckberry and Chamberlain (2002) and Schmitt et al. (2005) methods in predicting the age of individuals in a documented sample from Crete, Greece. Both methods were used to record changes on the auricular surface in a mixed-sex sample of 74 individuals, directly as well as through photographs, by two independent observers. Cohen's kappa and intra class correlation coefficients (ICC) were used in order to assess inter-observer and intra-observer agreement. Results showed than none of the methods predicted age with sufficient accuracy, as high error rates were recorded. The Schmitt et al. (2005) method performed better, mainly because the age ranges it uses are broader. Scoring through photographs does not seem to introduce bias in predicting age, as demonstrated by the high intra-observer agreement rates. Inter-observer agreement was also high. The low intra- and inter-observer error rates suggest that the poor performance of both methods in the Cretan sample is not due to a lack of clarity in the description of the morphological changes recorded on the auricular surface; rather it should be attributed to a poor correlation between these changes and age at death in our material.
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Affiliation(s)
- Effrosyni Michopoulou
- Edinburgh Unit for Forensic Anthropology, School of History Classics and Archaeology, University of Edinburgh, 4 Teviot Place, EH8 9AG Edinburgh, UK
| | - Pierrick Negre
- Institut médico-légal, Centre Hospitalier Régional Universitaire, 191 Avenue du Doyen Gaston Giraud, 34295 Montpellier, Cedex 5, France
| | - Efthymia Nikita
- Science and Technology in Archaeology Research Center, The Cyprus Institute, Nicosia, Cyprus; Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Elena F Kranioti
- Edinburgh Unit for Forensic Anthropology, School of History Classics and Archaeology, University of Edinburgh, 4 Teviot Place, EH8 9AG Edinburgh, UK; Forensic Pathology Division Crete, Hellenic Republic Ministry of Justice, Transparency and Human Rights, Heraklion, Crete, Greece.
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29
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Ianov L, Riva A, Kumar A, Foster TC. DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment. Front Aging Neurosci 2017; 9:249. [PMID: 28824413 PMCID: PMC5539085 DOI: 10.3389/fnagi.2017.00249] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023] Open
Abstract
The current study investigates DNA methylation as a possible epigenetic regulator of transcription associated with aging and cognitive function. Young and aged male Fischer 344 rats were behaviorally characterized on a set shifting task, and whole genome bisulfite sequencing was employed to profile the DNA methylome of the medial prefrontal cortex (mPFC). DNA methylation was also compared to RNA expression in the mPFC from the same animals. Variability in methylation was mainly observed for CpG sites as opposed to CHG and CHH sites. Gene bodies, specifically introns, contain the highest levels of methylation. During aging, hypermethylation was observed for genes linked to synaptic function and GTPase activity. Furthermore, impaired cognitive flexibility during aging was associated with hypermethylation of genes linked to postsynaptic density, dendrites, the axon terminus, and Ca2+ channels. Finally, comparison with RNA expression confirmed that hypermethylation was correlated with decreased expression of synaptic genes. The results indicate that DNA methylation over the lifespan contributes to synaptic modification observed in brain aging and age-related cognitive impairment.
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Affiliation(s)
- Lara Ianov
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States.,Genetics and Genomics Program, Genetics Institute, University of Florida, GainesvilleFL, United States
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, GainesvilleFL, United States
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States
| | - Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States.,Genetics and Genomics Program, Genetics Institute, University of Florida, GainesvilleFL, United States
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30
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Kovalchuk A, Kolb B. Chemo brain: From discerning mechanisms to lifting the brain fog-An aging connection. Cell Cycle 2017; 16:1345-1349. [PMID: 28657421 DOI: 10.1080/15384101.2017.1334022] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mounting evidence indicates that cancer treatments cause numerous deleterious effects, including central nervous system (CNS) toxicity. Chemotherapy-caused CNS side effects encompass changes in cognitive function, memory, and attention, to name a few. Although chemotherapy treatment-induced side effects occur in 16-75% of all patients, the mechanisms of these effects are not well understood. We have recently proposed a new epigenetic theory of chemo brain and, in a pioneer study, determined that cytotoxic chemotherapy agents induce oxidative DNA damage and affect molecular and epigenetic processes in the brain, and may be associated with brain aging processes. In this paper, we discuss the implications of chemo brain epigenetic effects and future perspectives, as well as outline potential links with brain aging and future translational research opportunities.
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Affiliation(s)
- Anna Kovalchuk
- a Department of Neuroscience , University of Lethbridge, Lethbridge, AB Canadian Institute for Advanced Research , Toronto , ON Alberta Epigenetics Network, AB
| | - Bryan Kolb
- a Department of Neuroscience , University of Lethbridge, Lethbridge, AB Canadian Institute for Advanced Research , Toronto , ON Alberta Epigenetics Network, AB
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31
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Phillips C. Lifestyle Modulators of Neuroplasticity: How Physical Activity, Mental Engagement, and Diet Promote Cognitive Health during Aging. Neural Plast 2017; 2017:3589271. [PMID: 28695017 PMCID: PMC5485368 DOI: 10.1155/2017/3589271] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/01/2017] [Accepted: 05/28/2017] [Indexed: 12/24/2022] Open
Abstract
The number of the elderly across the globe will approximate 2.1 billion by 2050. Juxtaposed against this burgeoning segment of the population is evidence that nonpathological aging is associated with an increased risk for cognitive decline in a variety of domains, changes that can cause mild disability even before the onset of dementia. Given that pharmacological treatments that mitigate dementia are still outstanding, alternative therapeutic options are being investigated increasingly. The results from translational studies have shown that modifiable lifestyle factors-including physical activity, cognitive engagement, and diet-are a key strategy for maintaining brain health during aging. Indeed, a multiplicity of studies has demonstrated relationships between lifestyle factors, brain structure and function, and cognitive function in aging adults. For example, physical activity and diet modulate common neuroplasticity substrates (neurotrophic signaling, neurogenesis, inflammation, stress response, and antioxidant defense) in the brain whereas cognitive engagement enhances brain and cognitive reserve. The aims of this review are to evaluate the relationship between modifiable lifestyle factors, neuroplasticity, and optimal brain health during aging; to identify putative mechanisms that contribute positive brain aging; and to highlight future directions for scientists and clinicians. Undoubtedly, the translation of cutting-edge knowledge derived from the field of cognitive neuroscience will advance our understanding and enhance clinical treatment interventions as we endeavor to promote brain health during aging.
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32
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Melnik BC, Schmitz G. Milk's Role as an Epigenetic Regulator in Health and Disease. Diseases 2017; 5:diseases5010012. [PMID: 28933365 PMCID: PMC5456335 DOI: 10.3390/diseases5010012] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
It is the intention of this review to characterize milk's role as an epigenetic regulator in health and disease. Based on translational research, we identify milk as a major epigenetic modulator of gene expression of the milk recipient. Milk is presented as an epigenetic "doping system" of mammalian development. Milk exosome-derived micro-ribonucleic acids (miRNAs) that target DNA methyltransferases are implicated to play the key role in the upregulation of developmental genes such as FTO, INS, and IGF1. In contrast to miRNA-deficient infant formula, breastfeeding via physiological miRNA transfer provides the appropriate signals for adequate epigenetic programming of the newborn infant. Whereas breastfeeding is restricted to the lactation period, continued consumption of cow's milk results in persistent epigenetic upregulation of genes critically involved in the development of diseases of civilization such as diabesity, neurodegeneration, and cancer. We hypothesize that the same miRNAs that epigenetically increase lactation, upregulate gene expression of the milk recipient via milk-derived miRNAs. It is of critical concern that persistent consumption of pasteurized cow's milk contaminates the human food chain with bovine miRNAs, that are identical to their human analogs. Commercial interest to enhance dairy lactation performance may further increase the epigenetic miRNA burden for the milk consumer.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, Faculty of Human Sciences, University of Osnabrück, Am Finkenhügel 7a, D-49076 Osnabrück, Germany.
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, University of Regensburg, Franz-Josef-Strauß-Allee 11, D-93053 Regensburg, Germany.
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33
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Lin CH, Lin E, Lane HY. Genetic Biomarkers on Age-Related Cognitive Decline. Front Psychiatry 2017; 8:247. [PMID: 29209239 PMCID: PMC5702307 DOI: 10.3389/fpsyt.2017.00247] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/07/2017] [Indexed: 12/29/2022] Open
Abstract
With ever-increasing elder populations, age-related cognitive decline, which is characterized as a gradual decline in cognitive capacity in the aging process, has turned out to be a mammoth public health concern. Since genetic information has become increasingly important to explore the biological mechanisms of cognitive decline, the search for genetic biomarkers of cognitive aging has received much attention. There is growing evidence that single-nucleotide polymorphisms (SNPs) within the ADAMTS9, BDNF, CASS4, COMT, CR1, DNMT3A, DTNBP1, REST, SRR, TOMM40, circadian clock, and Alzheimer's diseases-associated genes may contribute to susceptibility to cognitive aging. In this review, we first illustrated evidence of the genetic contribution to disease susceptibility to age-related cognitive decline in recent studies ranging from approaches of candidate genes to genome-wide association studies. We then surveyed a variety of association studies regarding age-related cognitive decline with consideration of gene-gene and gene-environment interactions. Finally, we highlighted their limitations and future directions. In light of advances in precision medicine and multi-omics technologies, future research in genomic medicine promises to lead to innovative ideas that are relevant to disease prevention and novel drugs for cognitive aging.
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Affiliation(s)
- Chieh-Hsin Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center for General Education, Cheng Shiu University, Kaohsiung, Taiwan
| | - Eugene Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Electrical Engineering, University of Washington, Seattle, WA, United States.,TickleFish Systems Corporation, Seattle, WA, United States
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Department of Psychiatry, Brain Disease Research Center, China Medical University Hospital, Taichung, Taiwan
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Liu G, Ji H, Liu J, Xu C, Chang L, Cui W, Ye C, Hu H, Chen Y, Zhou X, Duan S, Wang Q. Association of OPRK1 and OPRM1 methylation with mild cognitive impairment in Xinjiang Han and Uygur populations. Neurosci Lett 2017; 636:170-176. [DOI: 10.1016/j.neulet.2016.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/13/2016] [Accepted: 11/07/2016] [Indexed: 12/01/2022]
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Effect of Regulatory Element DNA Methylation on Tissue-Type Plasminogen Activator Gene Expression. PLoS One 2016; 11:e0167588. [PMID: 27973546 PMCID: PMC5156355 DOI: 10.1371/journal.pone.0167588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/16/2016] [Indexed: 12/31/2022] Open
Abstract
Expression of the tissue-type plasminogen activator gene (t-PA; gene name PLAT) is regulated, in part, by epigenetic mechanisms. We investigated the relationship between PLAT methylation and PLAT expression in five primary human cell types and six transformed cell lines. CpG methylation was analyzed in the proximal PLAT gene promoter and near the multihormone responsive enhancer (MHRE) -7.3 kilobase pairs upstream of the PLAT transcriptional start site (TSS, -7.3 kb). In Bowes melanoma cells, the PLAT promoter and the MHRE were fully unmethylated and t-PA secretion was extremely high. In other cell types the region from -647 to -366 was fully methylated, whereas an unmethylated stretch of DNA from -121 to +94 was required but not sufficient for detectable t-PA mRNA and t-PA secretion. DNA methylation near the MHRE was not correlated with t-PA secretion. Specific methylation of the PLAT promoter region -151 to +151, inserted into a firefly luciferase reporter gene, abolished reporter gene activity. The region -121 to + 94 contains two well-described regulatory elements, a PMA-responsive element (CRE) near -106 and a GC-rich region containing an Sp1 binding site near +59. Methylation of double-stranded DNA oligonucleotides containing the CRE or the GC-rich region had little or no effect on transcription factor binding. Methylated CpGs may attract co-repressor complexes that contain histone deacetylases (HDAC). However, reporter gene activity of methylated plasmids was not restored by the HDAC inhibitor trichostatin. In conclusion, efficient PLAT gene expression requires a short stretch of unmethylated CpG sites in the proximal promoter.
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36
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Rosca A, Anton G, Ene L, Iancu I, Temereanca A, Achim CL, Ruta SM. Immunoassay and molecular methods to investigate DNA methylation changes in peripheral blood mononuclear cells in HIV infected patients on cART. J Immunoassay Immunochem 2016; 38:299-307. [PMID: 27854146 DOI: 10.1080/15321819.2016.1260587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This study aimed to investigate the influence of antiretroviral therapy on methylation markers, in a group of HIV infected, heavily treated patients. Immune and molecular methods were used to investigate potential changes in methylation profile in DNA isolated from peripheral blood mononuclear cells collected from antiretroviral-experienced HIV infected patients and healthy controls. The percentage of 5-methylcytosine was inversely correlated with proviral DNA and active replication while DNMT1 (p = 0.01) and DNMT3A (p = 0.004) independently correlated with active viral replication. DNMT3A expression increased with total treatment duration (p = 0.03), number of antiretroviral drugs ever used (p = 0.003), and cumulative exposure to protease inhibitors (p = 0.02) even in currently HIV undetectable patients.
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Affiliation(s)
- Adelina Rosca
- a Department of Virology , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania.,b Emerging Viral Diseases Department , Stefan S. Nicolau Virology Institute , Bucharest , Romania
| | - Gabriela Anton
- b Emerging Viral Diseases Department , Stefan S. Nicolau Virology Institute , Bucharest , Romania
| | - Luminita Ene
- c Infectious Diseases Department , Victor Babes Hospital for Infectious and Tropical Diseases , Bucharest , Romania
| | - Iulia Iancu
- b Emerging Viral Diseases Department , Stefan S. Nicolau Virology Institute , Bucharest , Romania
| | - Aura Temereanca
- a Department of Virology , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania.,b Emerging Viral Diseases Department , Stefan S. Nicolau Virology Institute , Bucharest , Romania
| | - Cristian L Achim
- d Department of Psychiatry , University of California , San Diego , California
| | - Simona M Ruta
- a Department of Virology , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania.,b Emerging Viral Diseases Department , Stefan S. Nicolau Virology Institute , Bucharest , Romania
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37
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Starnawska A, Tan Q, Lenart A, McGue M, Mors O, Børglum AD, Christensen K, Nyegaard M, Christiansen L. Blood DNA methylation age is not associated with cognitive functioning in middle-aged monozygotic twins. Neurobiol Aging 2016; 50:60-63. [PMID: 27889677 DOI: 10.1016/j.neurobiolaging.2016.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/23/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
The epigenetic clock, also known as DNA methylation age (DNAmAge), represents age-related changes of DNA methylation at multiple sites of the genome and is suggested to be a biomarker for biological age. Elevated blood DNAmAge is associated with all-cause mortality, with the strongest effects reported in a recent intrapair twin study where epigenetically older twins had increased mortality risk in comparison to their co-twins. In the study presented here, we hypothesize that DNAmAge in blood is associated with cross-sectional and longitudinal cognitive abilities in middle-aged individuals. In 486 monozygotic twins, we investigated the association of DNAmAge, difference between DNAmAge and chronological age and age acceleration with cognition. Despite using a powerful paired twin design, we found no evidence for association of blood DNAmAge with cognitive abilities. This observation was confirmed in unpaired analyses, where DNAmAge initially correlated with cognitive abilities, until adjusting for chronological age. Overall, our study shows that for middle-aged individuals DNAmAge calculated in blood does not correlate with cognitive abilities.
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Affiliation(s)
- A Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
| | - Q Tan
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - A Lenart
- Max Planck Odense Center on the Biodemography of Aging, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - M McGue
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - O Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - A D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - K Christensen
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - M Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - L Christiansen
- The Danish Aging Research Center, and The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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Chen C, Peng H, Huang X, Zhao M, Li Z, Yin N, Wang X, Yu F, Yin B, Yuan Y, Lu Q. Genome-wide profiling of DNA methylation and gene expression in esophageal squamous cell carcinoma. Oncotarget 2016; 7:4507-21. [PMID: 26683359 PMCID: PMC4826222 DOI: 10.18632/oncotarget.6607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/02/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the leading cause of cancer-related death worldwide. Previous studies have suggested that DNA methylation involved in the development of ESCC. However, the precise mechanisms underlying the regulation and maintenance of the methylome as well as their relationship with ESCC remain poorly understood. Herein, we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) and RNA-Seq to investigate whole-genome DNA methylation patterns and the genome expression profiles in ESCC samples. The results of MeDIP-Seq analyses identified differentially methylated regions (DMRs) covering almost the entire genome with sufficient depth and high resolution. The gene ontology (GO) analysis showed that the DMRs related genes belonged to several different ontological domains, such as cell cycle, adhesion, proliferation and apoptosis. The RNA-Seq analysis identified a total of 6150 differentially expressed genes (3423 up-regulated and 2727 down-regulated). The significant GO terms showed that these genes belonged to several molecular functions and biological pathways. Moreover, the bisulfite-sequencing of genes MLH1, CDH5, TWIST1 and CDX1 confirmed the methylation status identified by MeDIP-Seq. And the mRNA expression levels of MLH1, TWIST1 and CDX1 were consistent with their DNA methylation profiles. The DMR region of MLH1 was found to correlate with survival. The identification of whole-genome DNA methylation patterns and gene expression profiles in ESCC provides new insight into the carcinogenesis of ESCC and represents a promising avenue through which to investigate novel therapeutic targets.
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Affiliation(s)
- Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Hao Peng
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Xiaojie Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Zhi Li
- Beijing Genomics Institute at Shenzhen, Shenzhen, P.R. China
| | - Ni Yin
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Bangliang Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yunchang Yuan
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
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Ianov L, Kumar A, Foster TC. Epigenetic regulation of estrogen receptor α contributes to age-related differences in transcription across the hippocampal regions CA1 and CA3. Neurobiol Aging 2016; 49:79-85. [PMID: 27776265 DOI: 10.1016/j.neurobiolaging.2016.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
Abstract
The expression of estrogen receptor alpha (ERα) varies across brain regions and changes with age and according to the previous history of estradiol exposure. ERα is regulated by a number of mechanisms including the level of mRNA (Esr1) expression. For this study, we took advantage of regional differences in hippocampal ERα expression to investigate DNA ERα promoter methylation at CpG dinucleotide sites as a potential epigenetic mechanism for regulating gene expression. Young and aged female Fischer 344 rats were ovariectomized, and Esr1 expression and ERα promoter methylation were examined in hippocampal regions CA1 and CA3, either 3 or 14 weeks following surgery. The results indicate that reduced Esr1 expression in region CA1 relative to CA3 was associated with an increase in DNA methylation in region CA1, particularly for the first CpG site. Additionally, differential methylation of distal CpG sites, 11-17, was associated with altered Esr1 expression during aging or following long-term hormone deprivation. The results support the idea that methylation of site 1 may be the primary regulatory region for cross-regional patterns in ERα expression, while distal sites are modifiable across the life span and may act as a feedback mechanism for ERα activity.
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Affiliation(s)
- Lara Ianov
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Genetics and Genomics Program, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
| | - Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Genetics and Genomics Program, Genetics Institute, University of Florida, Gainesville, FL, USA.
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KOUKOURA OURANIA, SIFAKIS STAVROS, SPANDIDOS DEMETRIOSA. DNA methylation in endometriosis (Review). Mol Med Rep 2016; 13:2939-48. [PMID: 26934855 PMCID: PMC4805102 DOI: 10.3892/mmr.2016.4925] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 12/01/2022] Open
Abstract
Endometriosis is defined by the presence and growth of functional endometrial tissue, outside the uterine cavity, primarily in the ovaries, pelvic peritoneum and rectovaginal septum. Although it is a benign disease, it presents with malignant characteristics, such as invasion to surrounding tissues, metastasis to distant locations and recurrence following treatment. Accumulating evidence suggests that various epigenetic aberrations may play an essential role in the pathogenesis of endometriosis. Aberrant DNA methylation represents a possible mechanism repsonsible for this disease, linking gene expression alterations observed in endometriosis with hormonal and environmental factors. Several lines of evidence indicate that endometriosis may partially be due to selective epigenetic deregulations influenced by extrinsic factors. Previous studies have shed light into the epigenetic component of endometriosis, reporting variations in the epigenetic patterns of genes known to be involved in the aberrant hormonal, immunologic and inflammatory status of endometriosis. Although recent studies, utilizing advanced molecular techniques, have allowed us to further elucidate the possible association of DNA methylation with altered gene expression, whether these molecular changes represent the cause or merely the consequence of the disease is a question which remains to be answered. This review provides an overview of the current literature on the role of DNA methylation in the pathophysiology and malignant evolution of endometriosis. We also provide insight into the mechanisms through which DNA methylation-modifying agents may be the next step in the research of the pharmaceutical treatment of endometriosis.
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Affiliation(s)
- OURANIA KOUKOURA
- Department of Obstetrics and Gynecology, University Hospital of Larissa, Larissa 41500, Greece
| | - STAVROS SIFAKIS
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, Heraklion 71003, Greece
| | - DEMETRIOS A. SPANDIDOS
- Laboratory of Clinical Virology, University of Crete Medical School, Heraklion 71409, Greece
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41
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Melnik BC. Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases. J Transl Med 2015; 13:385. [PMID: 26691922 PMCID: PMC4687119 DOI: 10.1186/s12967-015-0746-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/04/2015] [Indexed: 12/14/2022] Open
Abstract
Single-nucleotide polymorphisms within intron 1 of the FTO (fat mass and obesity-associated) gene are associated with enhanced FTO expression, increased body weight, obesity and type 2 diabetes mellitus (T2DM). The N6-methyladenosine (m6A) demethylase FTO plays a pivotal regulatory role for postnatal growth and energy expenditure. The purpose of this review is to provide translational evidence that links milk signaling with FTO-activated transcription of the milk recipient. FTO-dependent demethylation of m6A regulates mRNA splicing required for adipogenesis, increases the stability of mRNAs, and affects microRNA (miRNA) expression and miRNA biosynthesis. FTO senses branched-chain amino acids (BCAAs) and activates the nutrient sensitive kinase mechanistic target of rapamycin complex 1 (mTORC1), which plays a key role in translation. Milk provides abundant BCAAs and glutamine, critical components increasing FTO expression. CpG hypomethylation in the first intron of FTO has recently been associated with T2DM. CpG methylation is generally associated with gene silencing. In contrast, CpG demethylation generally increases transcription. DNA de novo methylation of CpG sites is facilitated by DNA methyltransferases (DNMT) 3A and 3B, whereas DNA maintenance methylation is controlled by DNMT1. MiRNA-29s target all DNMTs and thus reduce DNA CpG methylation. Cow´s milk provides substantial amounts of exosomal miRNA-29s that reach the systemic circulation and target mRNAs of the milk recipient. Via DNMT suppression, milk exosomal miRNA-29s may reduce the magnitude of FTO methylation, thereby epigenetically increasing FTO expression in the milk consumer. High lactation performance with increased milk yield has recently been associated with excessive miRNA-29 expression of dairy cow mammary epithelial cells (DCMECs). Notably, the galactopoietic hormone prolactin upregulates the transcription factor STAT3, which induces miRNA-29 expression. In a retrovirus-like manner milk exosomes may transfer DCMEC-derived miRNA-29s and bovine FTO mRNA to the milk consumer amplifying FTO expression. There is compelling evidence that obesity, T2DM, prostate and breast cancer, and neurodegenerative diseases are all associated with increased FTO expression. Maximization of lactation performance by veterinary medicine with enhanced miRNA-29s and FTO expression associated with increased exosomal miRNA-29 and FTO mRNA transfer to the milk consumer may represent key epigenetic mechanisms promoting FTO/mTORC1-mediated diseases of civilization.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Sedanstrasse 115, 49090, Osnabrück, Germany.
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