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Bahabry R, Hauser RM, Sánchez RG, Jago SS, Ianov L, Stuckey RJ, Parrish RR, Hoef LV, Lubin FD. Alterations in DNA 5-hydroxymethylation Patterns in the Hippocampus of an Experimental Model of Refractory Epilepsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560698. [PMID: 37873276 PMCID: PMC10592907 DOI: 10.1101/2023.10.03.560698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Temporal lobe epilepsy (TLE) is a type of focal epilepsy characterized by spontaneous recurrent seizures originating from the hippocampus. The epigenetic reprogramming hypothesis of epileptogenesis suggests that the development of TLE is associated with alterations in gene transcription changes resulting in a hyperexcitable network in TLE. DNA 5-methylcytosine (5-mC) is an epigenetic mechanism that has been associated with chronic epilepsy. However, the contribution of 5-hydroxymethylcytosine (5-hmC), a product of 5-mC demethylation by the Ten-Eleven Translocation (TET) family proteins in chronic TLE is poorly understood. 5-hmC is abundant in the brain and acts as a stable epigenetic mark altering gene expression through several mechanisms. Here, we found that the levels of bulk DNA 5-hmC but not 5-mC were significantly reduced in the hippocampus of human TLE patients and in the kainic acid (KA) TLE rat model. Using 5-hmC hMeDIP-sequencing, we characterized 5-hmC distribution across the genome and found bidirectional regulation of 5-hmC at intergenic regions within gene bodies. We found that hypohydroxymethylated 5-hmC intergenic regions were associated with several epilepsy-related genes, including Gal , SV2, and Kcnj11 and hyperdroxymethylation 5-hmC intergenic regions were associated with Gad65 , TLR4 , and Bdnf gene expression. Mechanistically, Tet1 knockdown in the hippocampus was sufficient to decrease 5-hmC levels and increase seizure susceptibility following KA administration. In contrast, Tet1 overexpression in the hippocampus resulted in increased 5-hmC levels associated with improved seizure resiliency in response to KA. These findings suggest an important role for 5-hmC as an epigenetic regulator of epilepsy that can be manipulated to influence seizure outcomes.
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Rastin C, Schenkel LC, Sadikovic B. Complexity in Genetic Epilepsies: A Comprehensive Review. Int J Mol Sci 2023; 24:14606. [PMID: 37834053 PMCID: PMC10572646 DOI: 10.3390/ijms241914606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Epilepsy is a highly prevalent neurological disorder, affecting between 5-8 per 1000 individuals and is associated with a lifetime risk of up to 3%. In addition to high incidence, epilepsy is a highly heterogeneous disorder, with variation including, but not limited to the following: severity, age of onset, type of seizure, developmental delay, drug responsiveness, and other comorbidities. Variable phenotypes are reflected in a range of etiologies including genetic, infectious, metabolic, immune, acquired/structural (resulting from, for example, a severe head injury or stroke), or idiopathic. This review will focus specifically on epilepsies with a genetic cause, genetic testing, and biomarkers in epilepsy.
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Affiliation(s)
- Cassandra Rastin
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Laila C. Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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DNA Methylation Description of Hippocampus, Cortex, Amygdala, and Blood of Drug-Resistant Temporal Lobe Epilepsy. Mol Neurobiol 2023; 60:2070-2085. [PMID: 36602701 DOI: 10.1007/s12035-022-03180-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023]
Abstract
Epigenetic changes such as DNA methylation were observed in drug-resistant temporal lobe epilepsy (DR-TLE), a disease that affects 25-30% of epilepsy patients. The main objective is to simultaneously describe DNA methylation patterns associated with DR-TLE in hippocampus, amygdala, surrounding cortex to the epileptogenic zone (SCEZ), and peripheral blood. An Illumina Infinium MethylationEPIC BeadChip array was performed in 19 DR-TLE patients and 10 postmortem non-epileptic controls. Overall, 32, 59, and 3210 differentially methylated probes (DMPs) were associated with DR-TLE in the hippocampus, amygdala, and SCEZ, respectively. These DMP-affected genes were involved in neurotrophic and calcium signaling in the hippocampus and voltage-gated channels in SCEZ, among others. One of the hippocampus DMPs (cg26834418 (CHORDC1)) showed a strong blood-brain correlation with BECon and IMAGE-CpG, suggesting that it could be a potential surrogate peripheral biomarker of DR-TLE. Moreover, in three of the top SCEZ's DMPs (SHANK3, SBF1, and MCF2L), methylation status was verified with methylation-specific qPCR. The differentially methylated CpGs were classified in DMRs: 2 in the hippocampus, 12 in the amygdala, and 531 in the SCEZ. We identified genes that had not been associated to DR-TLE so far such as TBX5, EXOC7, and WRHN. The area with more DMPs associated with DR-TLE was the SCEZ, some of them related to voltage-gated channels. The DMPs found in the amygdala were involved in inflammatory processes. We also found a potential surrogate peripheral biomarker of DR-TLE. Thus, these results provide new insights into epigenetic modifications involved in DR-TLE.
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Martins-Ferreira R, Leal B, Chaves J, Ciudad L, Samões R, Martins da Silva A, Pinho Costa P, Ballestar E. Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy. Clin Epigenetics 2022; 14:188. [PMID: 36575526 PMCID: PMC9795776 DOI: 10.1186/s13148-022-01416-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). RESULTS We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE-HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. CONCLUSIONS Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - Bárbara Leal
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - João Chaves
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain
| | - Raquel Samões
- grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,Neurophysiology Service, HSA-CHUP, Porto, Portugal
| | - Paulo Pinho Costa
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.422270.10000 0001 2287 695XDepartment of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.22069.3f0000 0004 0369 6365Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241 China
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Younesian S, Yousefi AM, Momeny M, Ghaffari SH, Bashash D. The DNA Methylation in Neurological Diseases. Cells 2022; 11:3439. [PMID: 36359835 PMCID: PMC9657829 DOI: 10.3390/cells11213439] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is critical for the normal development and functioning of the human brain, such as the proliferation and differentiation of neural stem cells, synaptic plasticity, neuronal reparation, learning, and memory. Despite the physical stability of DNA and methylated DNA compared to other epigenetic modifications, some DNA methylation-based biomarkers have translated into clinical practice. Increasing reports indicate a strong association between DNA methylation profiles and various clinical outcomes in neurological diseases, making DNA methylation profiles valuable as novel clinical markers. In this review, we aim to discuss the latest evidence concerning DNA methylation alterations in the development of neurodegenerative, neurodevelopmental, and neuropsychiatric diseases. We also highlighted the relationship of DNA methylation alterations with the disease progression and outcome in many neurological diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and autism.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
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Pedersen S, Kverneland M, Nakken KO, Rudi K, Iversen PO, Gervin K, Selmer KK. Genome-wide decrease in DNA methylation in adults with epilepsy treated with modified ketogenic diet: A prospective study. Epilepsia 2022; 63:2413-2426. [PMID: 35762681 PMCID: PMC9796519 DOI: 10.1111/epi.17351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The aim of this study was to investigate the impact of the modified ketogenic diet on DNA methylation in adults with epilepsy. METHODS In this prospective study, we investigated the genome-wide DNA methylation in whole blood in 58 adults with epilepsy treated with the modified ketogenic for 12 weeks. Patients were recruited from the National Center for Epilepsy, Norway, from March 1, 2011 to February 28, 2017. DNA methylation was analyzed using the Illumina Infinium MethylationEPIC BeadChip array. Analysis of variance and paired t-test were used to identify differentially methylated loci after 4 and 12 weeks of dietary treatment. A false discovery rate approach with a significance threshold of <5% was used to adjust for multiple comparisons. RESULTS We observed a genome-wide decrease in DNA methylation, both globally and at specific sites, after 4 and 12 weeks of dietary treatment. A substantial share of the differentially methylated positions (CpGs) were annotated to genes associated with epilepsy (n = 7), lipid metabolism (n = 8), and transcriptional regulation (n = 10). Furthermore, five of the identified genes were related to inositol phosphate metabolism, which may represent a possible mechanism by which the ketogenic diet attenuates seizures. SIGNIFICANCE A better understanding of the modified ketogenic diet's influence at the molecular level may be the key to unraveling the mechanisms by which the diet can ameliorate seizures and possibly to identifying novel therapeutic targets for epilepsy.
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Affiliation(s)
- Sigrid Pedersen
- National Center for EpilepsyOslo University HospitalOsloNorway
| | | | | | - Knut Rudi
- Department of Chemistry, Biotechnology, and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Per Ole Iversen
- Department of NutritionUniversity of OsloOsloNorway,Department of HematologyOslo University HospitalOsloNorway
| | - Kristina Gervin
- Department of Research and InnovationOslo University HospitalOsloNorway
| | - Kaja Kristine Selmer
- National Center for EpilepsyOslo University HospitalOsloNorway,Department of Research and InnovationOslo University HospitalOsloNorway
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Berger TC, Taubøll E, Heuser K. The potential role of DNA methylation as preventive treatment target of epileptogenesis. Front Cell Neurosci 2022; 16:931356. [PMID: 35936496 PMCID: PMC9353008 DOI: 10.3389/fncel.2022.931356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacological therapy of epilepsy has so far been limited to symptomatic treatment aimed at neuronal targets, with the result of an unchanged high proportion of patients lacking seizure control. The dissection of the intricate pathological mechanisms that transform normal brain matter to a focus for epileptic seizures—the process of epileptogenesis—could yield targets for novel treatment strategies preventing the development or progression of epilepsy. While many pathological features of epileptogenesis have been identified, obvious shortcomings in drug development are now believed to be based on the lack of knowledge of molecular upstream mechanisms, such as DNA methylation (DNAm), and as well as a failure to recognize glial cell involvement in epileptogenesis. This article highlights the potential role of DNAm and related gene expression (GE) as a treatment target in epileptogenesis.
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Affiliation(s)
- Toni Christoph Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Toni Christoph Berger
| | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Kjell Heuser
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Wang ZB, Qu J, Yang ZY, Liu DY, Jiang SL, Zhang Y, Yang ZQ, Mao XY, Liu ZQ. Integrated Analysis of Expression Profile and Potential Pathogenic Mechanism of Temporal Lobe Epilepsy With Hippocampal Sclerosis. Front Neurosci 2022; 16:892022. [PMID: 35784838 PMCID: PMC9243442 DOI: 10.3389/fnins.2022.892022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To investigate the potential pathogenic mechanism of temporal lobe epilepsy with hippocampal sclerosis (TLE+HS) by analyzing the expression profiles of microRNA/ mRNA/ lncRNA/ DNA methylation in brain tissues. Methods Brain tissues of six patients with TLE+HS and nine of normal temporal or parietal cortices (NTP) of patients undergoing internal decompression for traumatic brain injury (TBI) were collected. The total RNA was dephosphorylated, labeled, and hybridized to the Agilent Human miRNA Microarray, Release 19.0, 8 × 60K. The cDNA was labeled and hybridized to the Agilent LncRNA+mRNA Human Gene Expression Microarray V3.0,4 × 180K. For methylation detection, the DNA was labeled and hybridized to the Illumina 450K Infinium Methylation BeadChip. The raw data was extracted from hybridized images using Agilent Feature Extraction, and quantile normalization was performed using the Agilent GeneSpring. P-value < 0.05 and absolute fold change >2 were considered the threshold of differential expression data. Data analyses were performed using R and Bioconductor. BrainSpan database was used to screen for signatures that were not differentially expressed in normal human hippocampus and cortex (data from BrainSpan), but differentially expressed in TLE+HS’ hippocampus and NTP’ cortex (data from our cohort). The strategy “Guilt by association” was used to predict the prospective roles of each important hub mRNA, miRNA, or lncRNA. Results A significantly negative correlation (r < −0.5) was found between 116 pairs of microRNA/mRNA, differentially expressed in six patients with TLE+HS and nine of NTP. We examined this regulation network’s intersection with target gene prediction results and built a lncRNA-microRNA-Gene regulatory network with structural, and functional significance. Meanwhile, we found that the disorder of FGFR3, hsa-miR-486-5p, and lnc-KCNH5-1 plays a key vital role in developing TLE+HS.
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Affiliation(s)
- Zhi-Bin Wang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhuan-Yi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ding-Yang Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Shi-Long Jiang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Central South University, Changsha, China
| | - Ying Zhang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhi-Quan Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Zhi-Quan Yang,
| | - Xiao-Yuan Mao
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Central South University, Changsha, China
- Xiao-Yuan Mao,
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Central South University, Changsha, China
- *Correspondence: Zhao-Qian Liu,
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Golestanian R, Barzegar A, Mianji GR, Ebrahimzadeh MA, Fatemi B. Evaluation of alternations in DNA methylation of CYP3A4 gene upstream regulatory elements in gastric cancer and in response to Diazinon treatment. Curr Drug Metab 2022; 23:242-250. [PMID: 35331105 DOI: 10.2174/1389200223666220324094645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Little is known about cytochrome P450 3A4 (CYP3A4) DNA methylation and transcription alterations in gastric cancer. OBJECTIVE In this paper, we initially aimed to address the effect of diazinon pesticide on DNA methylation and transcription changes of the CYP3A4 gene in a human gastric cell line. In the next step, we studied the methylation differences of CpG sites within the upstream regulatory regions of the CYP3A4 gene among human gastric cancerous and healthy tissues. METHODS For the in vitro assay, the methylation changes of the C/EBP response element and transcript level of the CYP3A4 gene were studied following treatment of the AGS cell line with various concentrations of diazinon pesticide. In the next phase, the methylation percentages of 24 CpG sites within or around the upstream regulatory elements including near promoter, C/EBP binding site, XREM, and CLEM4 in 11 specimens of human gastric cancer tissue were compared to their adjacent healthy tissues. RESULTS Treatment with 10 µM Diazinon significantly increased the CYP3A4 gene transcription by approximately 27-fold, which was correlated with the hypermethylation of 3 CpGs in C/EBP binding sites including -5998, -5731 and -5725 (p<0.001 for all comparisons). Results of bisulfite sequencing revealed that the CpG sites which are located in -1521 (p=0.003), -1569 (p=0.027), -10813 (p=0.003), -10851 (p=0.001) and -10895 (p=0.0) bp from transcription start site, were significantly hypermethylated in cancerous tissues comparing to their healthy cohort. CONCLUSION Hypermethylation of CLEM4 and a region near the core promoter may have a significant association with gastric cancer incidence.
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Affiliation(s)
- Ramin Golestanian
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Ghodrat Rahimi Mianji
- Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Mohammad Ali Ebrahimzadeh
- Pharmaceutical Sciences Research Center, School of Pharmacy, Mazandaran University of Medical Science, Sari, Iran
| | - Behnaz Fatemi
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
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Martins-Ferreira R, Leal B, Chaves J, Li T, Ciudad L, Rangel R, Santos A, Martins da Silva A, Pinho Costa P, Ballestar E. Epilepsy progression is associated with cumulative DNA methylation changes in inflammatory genes. Prog Neurobiol 2022; 209:102207. [DOI: 10.1016/j.pneurobio.2021.102207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 01/09/2023]
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Zhang Y, Long H, Wang S, Xiao W, Xiong M, Liu J, Chen L, Chen R, Wei X, Shu Y, Zeng Y, Zhang L. Genome-Wide DNA Methylation Pattern in Whole Blood Associated With Primary Intracerebral Hemorrhage. Front Immunol 2021; 12:702244. [PMID: 34484198 PMCID: PMC8414634 DOI: 10.3389/fimmu.2021.702244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Primary intracerebral hemorrhage (ICH) is a significant cause of morbidity and mortality throughout the world. ICH is a multifactorial disease that emerges from interactions among multiple genetic and environmental factors. DNA methylation plays an important role in the etiology of complex traits and diseases. We used the Illumina Infinium Human Methylation 850k BeadChip to detect changes in DNA methylation in peripheral blood samples from patients with ICH and healthy controls to explore DNA methylation patterns in ICH. Here, we compared genomic DNA methylation patterns in whole blood from ICH patients (n = 30) and controls (n = 34). The ICH and control groups showed significantly different DNA methylation patterns at 1530 sites (p-value < 5.92E-08), with 1377 hypermethylated sites and 153 hypomethylated sites in ICH patients compared to the methylation status in healthy controls. A total of 371 hypermethylated sites and 35 hypomethylated sites were in promoters, while 738 hypermethylated sites and 67 hypomethylated sites were in coding regions. Furthermore, the differentially methylated genes between ICH patients and controls were largely related to inflammatory pathways. Abnormalities in the DNA methylation pattern identified in the peripheral blood of ICH patients may play an important role in the development of ICH and warranted further investigation.
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Affiliation(s)
- Yupeng Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Sai Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Meishan Xiong
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianyi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ruijuan Chen
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Xueli Wei
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Shu
- Department of Neurology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Le Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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Bruxel EM, do Canto AM, Bruno DCF, Geraldis JC, Lopes-Cendes I. Multi-omic strategies applied to the study of pharmacoresistance in mesial temporal lobe epilepsy. Epilepsia Open 2021; 7 Suppl 1:S94-S120. [PMID: 34486831 PMCID: PMC9340306 DOI: 10.1002/epi4.12536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
Mesial temporal lobe epilepsy (MTLE) is the most common type of focal epilepsy in adults, and hippocampal sclerosis (HS) is a frequent histopathological feature in patients with MTLE. Pharmacoresistance is present in at least one-third of patients with MTLE with HS (MTLE+HS). Several hypotheses have been proposed to explain the mechanisms of pharmacoresistance in epilepsy, including the effect of genetic and molecular factors. In recent years, the increased knowledge generated by high-throughput omic technologies has significantly improved the power of molecular genetic studies to discover new mechanisms leading to disease and response to treatment. In this review, we present and discuss the contribution of different omic modalities to understand the basic mechanisms determining pharmacoresistance in patients with MTLE+HS. We provide an overview and a critical discussion of the findings, limitations, new approaches, and future directions of these studies to improve the understanding of pharmacoresistance in MTLE+HS. However, it is important to point out that, as with other complex traits, pharmacoresistance to anti-seizure medications is likely a multifactorial condition in which gene-gene and gene-environment interactions play an important role. Thus, studies using multidimensional approaches are more likely to unravel these intricate biological processes.
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Affiliation(s)
- Estela M Bruxel
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Amanda M do Canto
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Danielle C F Bruno
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Jaqueline C Geraldis
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Departments of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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13
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Siegel CE, Laska EM, Lin Z, Xu M, Abu-Amara D, Jeffers MK, Qian M, Milton N, Flory JD, Hammamieh R, Daigle BJ, Gautam A, Dean KR, Reus VI, Wolkowitz OM, Mellon SH, Ressler KJ, Yehuda R, Wang K, Hood L, Doyle FJ, Jett M, Marmar CR. Utilization of machine learning for identifying symptom severity military-related PTSD subtypes and their biological correlates. Transl Psychiatry 2021; 11:227. [PMID: 33879773 PMCID: PMC8058082 DOI: 10.1038/s41398-021-01324-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022] Open
Abstract
We sought to find clinical subtypes of posttraumatic stress disorder (PTSD) in veterans 6-10 years post-trauma exposure based on current symptom assessments and to examine whether blood biomarkers could differentiate them. Samples were males deployed to Iraq and Afghanistan studied by the PTSD Systems Biology Consortium: a discovery sample of 74 PTSD cases and 71 healthy controls (HC), and a validation sample of 26 PTSD cases and 36 HC. A machine learning method, random forests (RF), in conjunction with a clustering method, partitioning around medoids, were used to identify subtypes derived from 16 self-report and clinician assessment scales, including the clinician-administered PTSD scale for DSM-IV (CAPS). Two subtypes were identified, designated S1 and S2, differing on mean current CAPS total scores: S2 = 75.6 (sd 14.6) and S1 = 54.3 (sd 6.6). S2 had greater symptom severity scores than both S1 and HC on all scale items. The mean first principal component score derived from clinical summary scales was three times higher in S2 than in S1. Distinct RFs were grown to classify S1 and S2 vs. HCs and vs. each other on multi-omic blood markers feature classes of current medical comorbidities, neurocognitive functioning, demographics, pre-military trauma, and psychiatric history. Among these classes, in each RF intergroup comparison of S1, S2, and HC, multi-omic biomarkers yielded the highest AUC-ROCs (0.819-0.922); other classes added little to further discrimination of the subtypes. Among the top five biomarkers in each of these RFs were methylation, micro RNA, and lactate markers, suggesting their biological role in symptom severity.
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Affiliation(s)
- Carole E Siegel
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA.
| | - Eugene M Laska
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Ziqiang Lin
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Mu Xu
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Duna Abu-Amara
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Michelle K Jeffers
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Meng Qian
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicholas Milton
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Janine D Flory
- Department of Psychiatry, James J. Peters VA Medical Center, Bronx, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rasha Hammamieh
- Military Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Bernie J Daigle
- Departments of Biological Sciences and Computer Science, The University of Memphis, Memphis, TN, USA
| | - Aarti Gautam
- Military Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kelsey R Dean
- Department of Systems Biology, Harvard University, Cambridge, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Victor I Reus
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Owen M Wolkowitz
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Synthia H Mellon
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, CA, USA
| | | | - Rachel Yehuda
- Department of Psychiatry, James J. Peters VA Medical Center, Bronx, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Marti Jett
- Military Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Charles R Marmar
- Center for Alcohol Use Disorder and PTSD, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
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14
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Dixit AB, Srivastava A, Sharma D, Tripathi M, Paul D, Lalwani S, Doddamani R, Sharma MC, Banerjee J, Chandra PS. Integrated Genome-Wide DNA Methylation and RNAseq Analysis of Hippocampal Specimens Identifies Potential Candidate Genes and Aberrant Signalling Pathways in Patients with Hippocampal Sclerosis. Neurol India 2021; 68:307-313. [PMID: 32189710 DOI: 10.4103/0028-3886.280649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background and Aims DNA methylation and demethylation play a crucial role in the regulation of gene expression, though their interplay during pathogenesis of hippocampal scelerosis (HS) remains elusive. The present study was designed to investigate the DNA methylation regulated changes in expression of HS patients. Methods We performed integrative analysis of genome-wide CpG-DNA methylation profiling and RNA sequencing to profile global changes in promoter methylation and gene expression in HS patients. Real time PCR was performed to validate the findings of methylation and RNA sequencing. Results A total of 16040 sites showed altered DNA methylation in all the CpG islands. Of these, 3185 sites were in the promoter regions, of which 66 genes showed an inverse correlation between methylation and expression. These genes are largely related to pathways predicted to participate in axon guidance by semaphorins, MAPK, ionotropic glutamate receptor pathway, notch signaling, regulatory activities related to TFAP2A and immune response, with the most distinct ones included TFAP2A, NRP1, SEMA3B, CACNG2, MAP3K11, and ADAM17. Conclusion We performed integrated analysis of genomic methylation signature and differential gene expression patterns of hippocampal tissues resected from patients with HS for the first time. Collectively, our findings implicate DNA methylation as a critical regulator of the pathogenic mechanisms of epileptogenesis associated with HS.
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Affiliation(s)
- Aparna Banerjee Dixit
- Dr B R Ambedkar Centre for Biomedical Sciences, University of Delhi, Delhi; Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration, New Delhi, India
| | - Arpna Srivastava
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurosurgery, AIIMS, New Delhi, India
| | | | - Manjari Tripathi
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurology, AIIMS, New Delhi, India
| | | | - Sanjeev Lalwani
- Department of Forensic Medicine and Toxicology, AIIMS, New Delhi, India
| | | | - M C Sharma
- Department of Pathology, AIIMS, New Delhi, India
| | | | - P Sarat Chandra
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurosurgery, AIIMS, New Delhi, India
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15
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Upregulation of hsa-miR-196a-5p is associated with MIR196A2 methylation and affects the malignant biological behaviors of glioma. Genomics 2021; 113:1001-1010. [PMID: 33636314 DOI: 10.1016/j.ygeno.2021.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/14/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
Hsa-miR-196a-5p is involved in tumorigenesis and progression. However, the driving factors for hsa-miR-196a-5p overexpression and its correlation with the clinicopathological features and prognosis of patients remain unclear in glioma. Thus, this study aimed to investigate the prognostic value of hsa-miR-196a-5p and its correlation with MIR196A2 methylation in glioma. We observed that hsa-miR-196a-5p expression was upregulated in glioma. Next, 112 patients were divided into high (n = 56) and low (n = 56) hsa-miR-196a-5p expression groups. The chi-square test showed that hsa-miR-196a-5p expression was significantly related to age, WHO grade, histopathology, IDH mutation status, and 1p/19q codeletion. Univariate and multivariate Cox regression analyses showed that hsa-miR-196a-5p expression was an independent prognostic factor. GO and KEGG enrichment analyses showed that hsa-miR-196a-5p may be involved in the MAPK signaling, focal adhesion and cancer-related pathways. Compared with the normal astrocyte cell line, glioma cell lines had an unregulated MIR196A2 methylation level, which was confirmed by TCGA data. The hypermethylated CpG sites of MIR196A2 were mainly concentrated in the gene body region, which was significantly associated with hsa-miR-196a-5p overexpression. Kaplan-Meier curves revealed that MIR196A2 hypermethylation was a poor prognostic factor. These findings suggest that hsa-miR-196a-5p overexpression may be involved in malignant biological behaviors, and MIR196A2 hypermethylation of the gene body was significantly associated with hsa-miR-196a-5p overexpression, which was a poor prognostic factor of glioma. Therefore, MIR196A2 hypermethylation may act as an early marker of prognosis of patients with glioma.
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16
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Xiao W, Yang Z, Yan X, Feng L, Long L, Tu T, Deng N, Chen W, Xiao B, Long H, Zeng Y. iTRAQ-Based Proteomic Analysis of Dentate Gyrus in Temporal Lobe Epilepsy With Hippocampal Sclerosis. Front Neurol 2021; 11:626013. [PMID: 33569037 PMCID: PMC7868380 DOI: 10.3389/fneur.2020.626013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Temporal lobe epilepsy (TLE) is the most frequent type of focal epilepsy in adults, typically resistant to pharmacological treatment, and mostly presents with cognitive impairment and psychiatric comorbidities. The most common neuropathological hallmark in TLE patients is hippocampal sclerosis (HS). However, the underlying molecular mechanisms involved remain poorly characterized. The dentate gyrus (DG), one specific hippocampal subarea, structural and functional changes imply a key involvement of the DG in the development of TLE. In this study, a isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic technique was performed for the analysis of hippocampal DG obtained from patients with TLE-HS compared to control samples obtained from autopsy. Our proteomic data identified 5,583 proteins, of which 82 proteins were upregulated and 90 proteins were downregulated. Bioinformatics analysis indicated that differentially expressed proteins were enriched in "synaptic vesicle," "mitochondrion," "cell-cell adhesion," "regulation of synaptic plasticity," "ATP binding," and "oxidative phosphorylation." Protein-protein interaction network analysis found a pivotal module of 10 proteins that were related to "oxidative phosphorylation." This study has investigated proteomic alterations in the DG region of TLE-HS patients, and paved the way for the better understanding of epileptogenesis mechanisms and future therapeutic intervention.
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Affiliation(s)
- Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiquan Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxin Yan
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tian Tu
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Na Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Wenjuan Chen
- Department of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
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17
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Zhi D, Wu W, Xiao B, Qi S, Jiang R, Yang X, Yang J, Xiao W, Liu C, Long H, Calhoun VD, Long L, Sui J. NR4A1 Methylation Associated Multimodal Neuroimaging Patterns Impaired in Temporal Lobe Epilepsy. Front Neurosci 2020; 14:727. [PMID: 32760244 PMCID: PMC7372187 DOI: 10.3389/fnins.2020.00727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
DNA hypermethylation has been widely observed in temporal lobe epilepsy (TLE), in which NR4A1 knockdown has been reported to be able to alleviate seizure severity in mouse model, while the underlying methylation-imaging pathway modulated by aberrant methylation levels of NR4A1 remains to be clarified in patients with TLE. Here, using multi-site canonical correlation analysis with reference, methylation levels of NR4A1 in blood were used as priori to guide fusion of three MRI features: functional connectivity (FC), fractional anisotropy (FA), and gray matter volume (GMV) for 56 TLE patients and 65 healthy controls. Post-hoc correlations were further evaluated between the identified NR4A1-associated brain components and disease onset. Results suggested that higher NR4A1 methylation levels in TLE were related with impaired temporal-cerebellar and occipital-cerebellar FC strength, lower FA in cingulum (hippocampus), and reduced GMV in putamen, temporal pole, and cerebellum. Moreover, findings were also replicated well in both patient subsets with either right TLE or left TLE only. Particularly, right TLE patients showed poorer cognitive abilities and more severe brain impairment than left TLE patients, especially more reduced GMV in thalamus. In summary, this work revealed a potential imaging-methylation pathway modulated by higher NR4A1 methylation in TLE via data mining, which may impact the above-mentioned multimodal brain circuits and was also associated with earlier disease onset and more cognitive deficits.
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Affiliation(s)
- Dongmei Zhi
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenyue Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Second Affiliated Hospital, Nanchang University, Nanchang, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Shile Qi
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, Georgia State University - Emory University, Atlanta, GA, United States
| | - Rongtao Jiang
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xingdong Yang
- Department of Neurology, Beijing Haidian Hospital, Beijing, China
| | - Jian Yang
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chaorong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Vince D Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, Georgia State University - Emory University, Atlanta, GA, United States
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Sui
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, Georgia State University - Emory University, Atlanta, GA, United States.,CAS Centre for Excellence in Brain Science and Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China
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18
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Fu Y, Liu D, Guo J, Long H, Xiao W, Xiao W, Feng L, Luo Z, Xiao B. Dynamic Change of Shanks Gene mRNA Expression and DNA Methylation in Epileptic Rat Model and Human Patients. Mol Neurobiol 2020; 57:3712-3726. [PMID: 32564287 DOI: 10.1007/s12035-020-01968-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023]
Abstract
Synaptic protein shanks (SH3 and multiple ankyrin repeat domains protein, Shank) have emerged as an important mediator of synaptic remodeling. Synaptic remodeling is a common pathogenic process in various neurological disorders including epilepsy. However, the expression and function of shanks gene in epileptogenesis has not been investigated to date. Herein, we investigated the expression of shanks (shank1/2/3) mRNA expression in both epileptic rats and epilepsy patients. Furthermore, methyl target sequencing was applied to explore the relationship between shank mRNA expression and DNA methylation in both rats and human patients. In general rat model, shank1/2/3 mRNA was downregulated at acute stage, upregulated at latent stage, and returned to the basal level at chronic stage. Ten CpG sites of shank1 was found differentially methylated, out of which 6 were hypermethylated. Seventeen CpG sites of shank3 were differentially methylated, out of which 8 were hypermethylated. In human epilepsy patients, decreased shank2 mRNA was detected from the brain tissue, with DNA hypermethylation dominant from both brain (18 out of 30) and blood tissue (58 out of 80), indicating the regulation role of DNA methylation on shank2 expression. In conclusion, our finding suggests the participation of the shanks gene in the pathophysiology of seizure, out of which 2 shank3 CpG sites (Chr7: 130473419, and Chr7: 130473405) may play an important role in shank3 expression at both the acute and latent stages in the SE rat model.
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Affiliation(s)
- Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Du Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.,Department of Neurology, Taikang Tongji (Wuhan) Hospital, Wuhan, 430050, Hubei, China
| | - Jialing Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Wei Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
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19
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Xiao W, Liu C, Zhong K, Ning S, Hou R, Deng N, Xu Y, Luo Z, Fu Y, Zeng Y, Xiao B, Long H, Long L. CpG methylation signature defines human temporal lobe epilepsy and predicts drug-resistant. CNS Neurosci Ther 2020; 26:1021-1030. [PMID: 32519815 PMCID: PMC7539843 DOI: 10.1111/cns.13394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Aims Temporal lobe epilepsy (TLE) is the most common focal epilepsy syndrome in adults and frequently develops drug resistance. Studies have investigated the value of peripheral DNA methylation signature as molecular biomarker for diagnosis or prognosis. We aimed to explore methylation biomarkers for TLE diagnosis and pharmacoresistance prediction. Methods We initially conducted genome‐wide DNA methylation profiling in TLE patients, and then selected candidate CpGs in training cohort and validated in another independent cohort by employing machine learning algorithms. Furthermore, nomogram comprising DNA methylation and clinicopathological data was generated to predict the drug response in the entire patient cohort. Lastly, bioinformatics analysis for CpG‐associated genes was performed using Ingenuity Pathway Analysis. Results After screening and validation, eight CpGs were identified for diagnostic biomarker with an area under the curve (AUC) of 0.81 and six CpGs for drug‐resistant prediction biomarker with an AUC of 0.79. The nomogram for drug‐resistant prediction comprised methylation risk score, disease course, seizure frequency, and hippocampal sclerosis, with AUC as high as 0.96. Bioinformatics analysis indicated drug response–related CpGs corresponding genes closely related to DNA methylation. Conclusions This study demonstrates the ability to use peripheral DNA methylation signature as molecular biomarker for epilepsy diagnosis and drug‐resistant prediction.
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Affiliation(s)
- Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chaorong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuo Zhong
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Rui Hou
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Na Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuchen Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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20
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Wheater ENW, Stoye DQ, Cox SR, Wardlaw JM, Drake AJ, Bastin ME, Boardman JP. DNA methylation and brain structure and function across the life course: A systematic review. Neurosci Biobehav Rev 2020; 113:133-156. [PMID: 32151655 PMCID: PMC7237884 DOI: 10.1016/j.neubiorev.2020.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/01/2023]
Abstract
MRI has enhanced our capacity to understand variations in brain structure and function conferred by the genome. We identified 60 studies that report associations between DNA methylation (DNAm) and human brain structure/function. Forty-three studies measured candidate loci DNAm; seventeen measured epigenome-wide DNAm. MRI features included region-of-interest and whole-brain structural, diffusion and functional imaging features. The studies report DNAm-MRI associations for: neurodevelopment and neurodevelopmental disorders; major depression and suicidality; alcohol use disorder; schizophrenia and psychosis; ageing, stroke, ataxia and neurodegeneration; post-traumatic stress disorder; and socio-emotional processing. Consistency between MRI features and differential DNAm is modest. Sources of bias: variable inclusion of comparator groups; different surrogate tissues used; variation in DNAm measurement methods; lack of control for genotype and cell-type composition; and variations in image processing. Knowledge of MRI features associated with differential DNAm may improve understanding of the role of DNAm in brain health and disease, but caution is required because conventions for linking DNAm and MRI data are not established, and clinical and methodological heterogeneity in existing literature is substantial.
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Affiliation(s)
- Emily N W Wheater
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, United Kingdom
| | - David Q Stoye
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, United Kingdom
| | - Simon R Cox
- Department of Psychology, University of Edinburgh, United Kingdom
| | - Joanna M Wardlaw
- Centre for Clinical Brain Sciences, University of Edinburgh, United Kingdom
| | - Amanda J Drake
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
| | - Mark E Bastin
- Centre for Clinical Brain Sciences, University of Edinburgh, United Kingdom
| | - James P Boardman
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, United Kingdom; Centre for Clinical Brain Sciences, University of Edinburgh, United Kingdom.
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21
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Caramaschi D, Hatcher C, Mulder RH, Felix JF, Cecil CAM, Relton CL, Walton E. Epigenome-wide association study of seizures in childhood and adolescence. Clin Epigenetics 2020; 12:8. [PMID: 31915053 PMCID: PMC6950851 DOI: 10.1186/s13148-019-0793-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
The occurrence of seizures in childhood is often associated with neurodevelopmental impairments and school underachievement. Common genetic variants associated with epilepsy have been identified and epigenetic mechanisms have also been suggested to play a role. In this study, we analyzed the association of genome-wide blood DNA methylation with the occurrence of seizures in ~ 800 children from the Avon Longitudinal Study of Parents and Children, UK, at birth (cord blood), during childhood, and adolescence (peripheral blood). We also analyzed the association between the lifetime occurrence of any seizures before age 13 with blood DNA methylation levels. We sought replication of the findings in the Generation R Study and explored causality using Mendelian randomization, i.e., using genetic variants as proxies. The results showed five CpG sites which were associated cross-sectionally with seizures either in childhood or adolescence (1-5% absolute methylation difference at pFDR < 0.05), although the evidence of replication in an independent study was weak. One of these sites was located in the BDNF gene, which is highly expressed in the brain, and showed high correspondence with brain methylation levels. The Mendelian randomization analyses suggested that seizures might be causal for changes in methylation rather than vice-versa. In conclusion, we show a suggestive link between seizures and blood DNA methylation while at the same time exploring the limitations of conducting such study.
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Affiliation(s)
- Doretta Caramaschi
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK. .,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Charlie Hatcher
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Rosa H Mulder
- Institute of Education and Child Studies, Leiden University, Pieter de la Court building, Wassenaarseweg 52, 2333, AK, Leiden, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Caroline L Relton
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Esther Walton
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Department of Psychology, University of Bath, Bath, BA2 7AY, UK
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22
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Tan L, Chen Y, Wu W, Liu C, Fu Y, He J, Zhang M, Wang G, Wang K, Long H, Xiao W, Xiao B, Long L. Impaired Cognitive Abilities in Siblings of Patients with Temporal Lobe Epilepsy. Neuropsychiatr Dis Treat 2020; 16:3071-3079. [PMID: 33363375 PMCID: PMC7752648 DOI: 10.2147/ndt.s258074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Patients with temporal lobe epilepsy (TLE) are at high risk of cognitive impairment. In addition to persistent seizures and antiepileptic drugs (AEDs), genetic factors also play an important role in the progression of cognitive deficits in TLE patients. Defining a cognitive endophenotype for TLE can provide information on the risk of cognitive impairment in patients. This study investigated the cognitive endophenotype of TLE by comparing neuropsychological function between patients with TLE, their unaffected siblings, and healthy control subjects. PATIENTS AND METHODS A total of 46 patients with TLE, 26 siblings, and 33 control subjects were recruited. Cognitive function (ie, general cognition, short- and long-term memory, attention, visuospatial and executive functions, and working memory) was assessed with a battery of neuropsychological tests. Differences between groups were evaluated by analysis of covariance, with age and years of education as covariates. The Kruskal-Wallis test was used to evaluate data that did not satisfy the homogeneity of variance assumption. Pairwise comparisons were adjusted by Bonferroni correction, with a significance threshold of P<0.05. RESULTS Patients with TLE showed deficits in the information test (P<0.001), arithmetic test (P=0.003), digit symbol substitution test (P=0.001), block design test (BDT; P=0.005), and backward digit span test (P=0.001) and took a longer time to complete the Hayling test Part A (P=0.011) compared to controls. Left TLE patients tended to have worse executive function test scores than right TLE patients. The siblings of TLE patients showed deficits in the BDT (P=0.006, Bonferroni-corrected) relative to controls. CONCLUSION Patients with TLE exhibit cognitive impairment. Executive function is worse in patients with left TLE than in those with right TLE. Siblings show impaired visuospatial function relative to controls. Thus, cognitive deficits in TLE patients have a genetic component and are independent of seizures or AED use.
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Affiliation(s)
- Langzi Tan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yayu Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Wenyue Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Chaorong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Jialinzi He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Min Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Ge Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Kangrun Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
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23
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Berger TC, Vigeland MD, Hjorthaug HS, Etholm L, Nome CG, Taubøll E, Heuser K, Selmer KK. Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis. PLoS One 2019; 14:e0226575. [PMID: 31887157 PMCID: PMC6936816 DOI: 10.1371/journal.pone.0226575] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND AIMS Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. METHODS We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. RESULTS We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. CONCLUSION We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
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Affiliation(s)
- Toni C. Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
- * E-mail:
| | - Magnus D. Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanne S. Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Lars Etholm
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Department of Neurology, Section for Neurophysiology, Oslo University Hospital, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kaja K. Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, Oslo, Norway
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24
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Mohandas N, Loke YJ, Hopkins S, Mackenzie L, Bennett C, Berkovic SF, Vadlamudi L, Craig JM. Evidence for type-specific DNA methylation patterns in epilepsy: a discordant monozygotic twin approach. Epigenomics 2019; 11:951-968. [DOI: 10.2217/epi-2018-0136] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Epilepsy is a common neurological disorder characterized by recurrent seizures. We performed epigenetic analyses between and within 15 monozygotic (MZ) twin pairs discordant for focal or generalized epilepsy. Methods: DNA methylation analysis was performed using Illumina Infinium MethylationEPIC arrays, in blood and buccal samples. Results: Differentially methylated regions between epilepsy types associated with PM20D1 and GFPT2 genes in both tissues. Within MZ discordant twin pairs, differentially methylated regions associated with OTX1 and ARID5B genes for generalized epilepsy and TTC39C and DLX5 genes for focal epilepsy. Conclusion: This is the first epigenome-wide association study, utilizing the discordant MZ co-twin model, to deepen our understanding of the neurobiology of epilepsy.
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Affiliation(s)
- Namitha Mohandas
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
| | - Yuk Jing Loke
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
| | - Stephanie Hopkins
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- School of Medicine & Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Lisa Mackenzie
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Carmen Bennett
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, University of Melbourne, Austin Health, Victoria, Australia
| | - Lata Vadlamudi
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
- Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Jeffrey M Craig
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
- Centre for Molecular & Medical Research, School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
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25
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Luo ZH, Walid A A, Xie Y, Long H, Xiao W, Xu L, Fu Y, Feng L, Xiao B. Construction and analysis of a dysregulated lncRNA-associated ceRNA network in a rat model of temporal lobe epilepsy. Seizure 2019; 69:105-114. [PMID: 31005697 DOI: 10.1016/j.seizure.2019.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 02/09/2023] Open
Abstract
PURPOSE The aim of this work was to investigate expression and cross-talk between long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in a rat model of temporal lobe epilepsy (TLE). METHODS Noncoding RNA chips were used to explore the expression and relationship between lncRNAs and miRNAs in a rat model of TLE. The expression of different lncRNAs and mRNAs was analysed by Pearson's correlation coefficient, and the function of each lncRNA was annotated by co-expressed genes based on gene ontology classification using DAVID. MiRNA-lncRNA interactions were predicted by using StarBase v2.0, and the competing endogenous RNA (ceRNA) relationship between lncRNAs and miRNAs was built by using Cytoscape software. Real-time PCR was used to verify chip results. RESULTS According to the expression profile analysis, 54 lncRNAs, 36 miRNAs and 122 mRNAs were dysregulated in TLE rat model compared to normal controls. The functions of lncRNAs in epilepsy were annotated by their co-expressed genes based on the "guilt by association" strategy. DAVID analysis revealed that differentially expressed lncRNA functions were involved in "potassium channel activity", "metal ion transmembrane transporter activity", and "voltage-gated potassium channel activity". Based on the ceRNA theory, 13 mRNAs, 10 miRNAs and 11 lncRNAs comprise the lncRNA-miRNA-mRNA ceRNA relationship in epilepsy. CONCLUSIONS The molecular functions of the differentially expressed genes play an important role in the pathogenesis of voltage-gated potassium channel activity. Further ceRNA analyses suggest that modulation of lncRNAs could emerge as a promising therapeutic target for TLE.
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Affiliation(s)
- Zhao Hui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Alsharafi Walid A
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yuanyuan Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Liqun Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, PR China; Neurology Institute of Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.
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26
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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27
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Arpón A, Milagro FI, Ramos-Lopez O, Mansego ML, Santos JL, Riezu-Boj JI, Martínez JA. Epigenome-wide association study in peripheral white blood cells involving insulin resistance. Sci Rep 2019; 9:2445. [PMID: 30792424 PMCID: PMC6385280 DOI: 10.1038/s41598-019-38980-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
Insulin resistance (IR) is a hallmark of type 2 diabetes, metabolic syndrome and cardiometabolic risk. An epigenetic phenomena such as DNA methylation might be involved in the onset and development of systemic IR. The aim of this study was to explore the genetic DNA methylation levels in peripheral white blood cells with the objective of identifying epigenetic signatures associated with IR measured by the Homeostatic Model Assessment of IR (HOMA-IR) following an epigenome-wide association study approach. DNA methylation levels were assessed using Infinium Methylation Assay (Illumina), and were associated with HOMA-IR values of participants from the Methyl Epigenome Network Association (MENA) project, finding statistical associations for at least 798 CpGs. A stringent statistical analysis revealed that 478 of them showed a differential methylation pattern between individuals with HOMA-IR ≤ 3 and > 3. ROC curves of top four CpGs out of 478 allowed differentiating individuals between both groups (AUC≈0.88). This study demonstrated the association between DNA methylation in some specific CpGs and HOMA-IR values that will help to the understanding and in the development of new strategies for personalized approaches to predict and prevent IR-associated diseases.
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Affiliation(s)
- Ana Arpón
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - Fermín I Milagro
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
| | - Omar Ramos-Lopez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - M Luisa Mansego
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - José Luis Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José-Ignacio Riezu-Boj
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain. .,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.
| | - J Alfredo Martínez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain.,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.,Madrid Institute for Advanced Studies (IMDEA), IMDEA Food, Madrid, Spain
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28
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Mann A, Portnoy E, Han H, Inbar D, Blatch D, Shmuel M, Ben-Hur T, Eyal S, Ekstein D. Folate homeostasis in epileptic rats. Epilepsy Res 2018; 142:64-72. [PMID: 29571151 DOI: 10.1016/j.eplepsyres.2018.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 12/28/2022]
Abstract
Folate is involved in metabolic processes and it has been implicated in both aggravation and amelioration of seizures. The aim of the current work was to study the effect of chronic temporal lobe epilepsy (TLE) on the plasma and brain concentrations of folate and on its uptake carriers in the brain - the reduced folate carrier (RFC), folate receptor α (FRα) and proton coupled folate transporter (PCFT). We utilized the rat lithium pilocarpine model for TLE. Approximately two months following status epilepticus, rats with spontaneous recurrent seizures (SRS) were sacrificed for brain and plasma folate concentration analyses and folate uptake carrier expression studies. RT-PCR and western blot analyses were utilized for quantification of folate carriers' mRNAs and proteins, respectively. The distribution of folate carriers in the brain was studied using immunohistochemistry. In the SRS rats we found lower plasma concentrations (10 ± 0.9 in control vs. 6.6 ± 1.6 ng/ml in SRS, P < 0.05), but preserved cortical and increased hippocampal levels of folate (0.5 ± 0.1 in control vs. 0.9 ± 0.2 ng/mg in SRS, P = 0.055). Hippocampus - to - plasma ratio of folate concentration was 3-fold higher in the SRS group, compared with the controls (0.13 ± 0.03 vs. 0.04 ± 0.02, respectively; P < 0.01). mRNA and protein levels of the folate uptake carriers did not differ between SRS rats and controls. However, immunofluorescent staining quantification revealed that the emission intensity of both RFC and FRα was elevated 8-fold and 4-fold, respectively, in hippocampal CA1 neurons of SRS rats, compared to controls (P < 0.01). PCFT was unquantifiable. If corroborated by complementary research in humans, the findings of this study may be utilized clinically for supplemental therapy planning, in imaging the epileptic focus, and for drug delivery into the epileptic brain. Further studies are required for better elucidating the clinical and mechanistic significance of altered folate balances in the epileptic brain.
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Affiliation(s)
- Aniv Mann
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, 91120 Israel.
| | - Emma Portnoy
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, 91120 Israel.
| | - Hadas Han
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, 91120 Israel.
| | - Dorrit Inbar
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel.
| | - Dana Blatch
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel.
| | - Miriam Shmuel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, 91120 Israel.
| | - Tamir Ben-Hur
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel.
| | - Sara Eyal
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, 91120 Israel.
| | - Dana Ekstein
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel.
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29
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Jia Y, Xu H, Li Y, Wei C, Guo R, Wang F, Wu Y, Liu J, Jia J, Yan J, Qi X, Li Y, Gao X. A Modified Ficoll-Paque Gradient Method for Isolating Mononuclear Cells from the Peripheral and Umbilical Cord Blood of Humans for Biobanks and Clinical Laboratories. Biopreserv Biobank 2017; 16:82-91. [PMID: 29232525 DOI: 10.1089/bio.2017.0082] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the Ficoll-Paque method is classically used to isolate peripheral blood mononuclear cells (PBMCs), modifications in this method are required for a more rapid and economic output for biobanks and clinical laboratories, particularly in developing countries. In this study, we addressed this issue by modifying the Ficoll-Paque method for the isolation of PBMCs or mononuclear cells from the peripheral and the umbilical cord blood of healthy and diseased (infected, anemic, and chronic obstructive pulmonary disease) adult individuals. In the modified method, we initiated the cell isolation process from the buffy coat layer, which appears in the interface between the plasma and sediments after centrifugation, instead of using the whole blood as described in the classic method. Although the PBMC yield by the modified method was about 12% less than in the classic method, the number of PBMCs isolated by the modified method was more than one million, which is enough for different research/diagnostic purposes, such as multi-omics detection. Assessment of cell viability and purity by hematology analyzer and trypan blue showed no significant difference between the viability and purity of the PBMCs isolated by these two methods in almost all groups, except samples from the infected and cord blood groups, where lower PBMC purity with higher granulocyte contamination were observed. In addition, at delayed processing time points, all parameters for the two methods were decreased in a time-dependent manner, especially at 8, 12, or 24 hours after the sample collection. In summary, the performance of PBMC isolation by the classic and modified methods mainly relies on the PBMC ratio in original samples. The modified method could be preferred for PBMC isolation because of its time and cost savings, especially for the biobanks and clinical laboratories in developing countries.
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Affiliation(s)
- Yanjuan Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Hui Xu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yonghong Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Chaojun Wei
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Rui Guo
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Fang Wang
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Yu Wu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Liu
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Junwen Yan
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoming Qi
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yuanting Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoling Gao
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
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The expression of G protein-coupled receptor kinase 5 and its interaction with dendritic marker microtubule-associated protein-2 after status epilepticus. Epilepsy Res 2017; 138:62-70. [DOI: 10.1016/j.eplepsyres.2017.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/07/2017] [Accepted: 10/10/2017] [Indexed: 12/25/2022]
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Jiang J, Li S, Wang Y, Xiao X, Jin Y, Wang Y, Yang Z, Yan S, Li Y. Potential neurotoxicity of prenatal exposure to sevoflurane on offspring: Metabolomics investigation on neurodevelopment and underlying mechanism. Int J Dev Neurosci 2017; 62:46-53. [PMID: 28842206 DOI: 10.1016/j.ijdevneu.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023] Open
Affiliation(s)
- Jialong Jiang
- Department of AnesthesiologyThe First Affiliated Hospital of Anhui Medical UniversityHefei230022AnhuiPR China
| | - Shasha Li
- Guangdong Provincial Association of Chinese Medicine, Guangdong Provincial Hospital of Chinese MedicineNo. 111 Dade RoadGuangzhouGuangdong510120PR China
| | - Yiqiao Wang
- Department of AnesthesiologyThe First Affiliated Hospital of Anhui Medical UniversityHefei230022AnhuiPR China
| | - Xue Xiao
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical UniversityGuangzhou510006PR China
| | - Yi Jin
- Department of AnesthesiologyInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of MedicineShanghai200030PR China
| | - Yilong Wang
- Department of AnesthesiologyInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of MedicineShanghai200030PR China
| | - Zeyong Yang
- Department of AnesthesiologyInternational Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of MedicineShanghai200030PR China
| | - Shikai Yan
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical UniversityGuangzhou510006PR China
- School of Pharmacy, Shanghai Jiao Tong UniversityShanghai200240PR China
| | - Yuanhai Li
- Department of AnesthesiologyThe First Affiliated Hospital of Anhui Medical UniversityHefei230022AnhuiPR China
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Abstract
Epilepsy is a common and devastating neurological disorder characterized by recurrent and unprovoked spontaneous seizures. One leading hypothesis for the development and progression of epilepsy is that large-scale changes in gene transcription and protein expression contribute to aberrant network restructuring and hyperexcitability, resulting in the genesis of repeated seizures. Current research shows that epigenetic mechanisms, including posttranslational alterations to the proteins around which DNA is coiled, chemical modifications to DNA, and the activity of various noncoding RNA molecules exert important influences on these gene networks in experimental epilepsy. Key findings from animal models have been replicated in humans using brain tissue obtained from living patients at the time of neurosurgical resection for pharmacoresistant epilepsy. These findings have spurred efforts to target epigenetic processes to disrupt or modify epilepsy in experimental models with varying degrees of success. In this review, we will (1) summarize the epigenetic mechanisms implicated in epileptogenesis and epilepsy, (2) explore the influence of metabolic factors on epigenetic mechanisms, and (3) assess the potential of using epigenetic markers to support diagnosis and prognosis. Translation of these findings may guide the development of molecular biomarkers and novel therapeutics for prevention or modification of epileptic disorders.
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Affiliation(s)
- Rebecca M. Hauser
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - David C. Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Farah D. Lubin
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
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