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Bam S, Buchanan E, Mahony C, O'Ryan C. DNA Methylation of PGC-1α Is Associated With Elevated mtDNA Copy Number and Altered Urinary Metabolites in Autism Spectrum Disorder. Front Cell Dev Biol 2021; 9:696428. [PMID: 34381777 PMCID: PMC8352569 DOI: 10.3389/fcell.2021.696428] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including pathways that affect mitochondrial function. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the etiology of ASD. We measured DNA methylation of peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1α), as well as five genes involved in regulating mitochondrial homeostasis to examine mitochondrial dysfunction in an ASD cohort of South African children. Using targeted Next Generation bisulfite sequencing, we found differential methylation (p < 0.05) at six key genes converging on mitochondrial biogenesis, fission and fusion in ASD, namely PGC-1α, STOML2, MFN2, FIS1, OPA1, and GABPA. PGC-1α, the transcriptional regulator of biogenesis, was significantly hypermethylated at eight CpG sites in the gene promoter, one of which contained a putative binding site for CAMP response binding element 1 (CREB1) (p = 1 × 10–6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1α promoter and there was a positive correlation between methylation at PGC-1α CpG#1 and mtDNA copy number (Spearman’s r = 0.2, n = 49, p = 0.04) in ASD. Furthermore, DNA methylation at PGC-1α CpG#1 and mtDNA copy number correlated significantly (p < 0.05) with levels of urinary organic acids associated with mitochondrial dysfunction, oxidative stress, and neuroendocrinology. Our data show differential methylation in ASD at six key genes converging on PGC-1α-dependent regulation of mitochondrial biogenesis and function. We demonstrate that methylation at the PGC-1α promoter is associated with elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored role for DNA methylation in regulating specific pathways involved in mitochondrial biogenesis, fission and fusion contributing to mitochondrial dysfunction in ASD.
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Affiliation(s)
- Sophia Bam
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Erin Buchanan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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Tian L, Pu J, Liu Y, Gui S, Zhong X, Song X, Xu S, Zhang H, Wang H, Zhou W, Xie P. Metabolomic analysis of animal models of depression. Metab Brain Dis 2020; 35:979-990. [PMID: 32440806 DOI: 10.1007/s11011-020-00574-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/14/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Our understanding of the molecular mechanisms of depression remains largely unclear. Previous studies have shown that the prefrontal cortex (PFC) is among most important brain regions that exhibits metabolic changes in depression. A comprehensive analysis based on candidate metabolites in the PFC of animal models of depression will provide valuable information for understanding the pathogenic mechanism underlying depression. METHODS Candidate metabolites that are potentially involved in the metabolic changes of the PFC in animal models of depression were retrieved from the Metabolite Network of Depression Database. The significantly altered metabolic pathways were revealed by canonical pathway analysis, and the relationships among altered pathways were explored by pathway crosstalk analysis. Additionally, drug-associated pathways were investigated using drug-associated metabolite set enrichment analysis. The interrelationships among metabolites, proteins, and other molecules were analyzed by molecular network analysis. RESULTS Among 88 candidate metabolites, 87 altered canonical pathways were identified, and the top five ranked pathways were tRNA charging, the endocannabinoid neuronal synapse pathway, (S)-reticuline biosynthesis II, catecholamine biosynthesis, and GABA receptor signaling. Pathway crosstalk analysis revealed that these altered pathways were grouped into three interlinked modules involved in amino acid metabolism, nervous system signaling/neurotransmitters, and nucleotide metabolism. In the drug-associated metabolite set enrichment analysis, the main enriched drug pathways were opioid-related and antibiotic-related action pathways. Furthermore, the most significantly altered molecular network was involved in amino acid metabolism, molecular transport, and small molecule biochemistry. CONCLUSIONS This study provides important clues for the metabolic characteristics of the PFC in depression.
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Affiliation(s)
- Lu Tian
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Siwen Gui
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaogang Zhong
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Xuemian Song
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Shaohua Xu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Hanpin Zhang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
- College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Zhou
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Peng Xie
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016, China.
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China.
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
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Zhang Z, Wang D, Qiao S, Wu X, Cao S, Wang L, Su X, Li L. Metabolic and microbial signatures in rat hepatocellular carcinoma treated with caffeic acid and chlorogenic acid. Sci Rep 2017; 7:4508. [PMID: 28674386 PMCID: PMC5495756 DOI: 10.1038/s41598-017-04888-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) treatment remains lack of effective chemopreventive agents, therefore it is very attractive and urgent to discover novel anti-HCC drugs. In the present study, the effects of chlorogenic acid (ChA) and caffeic acid (CaA) on HCC induced by diethylnitrosamine (DEN) were evaluated. ChA or CaA could reduce the histopathological changes and liver injury markers, such as alanine transarninase, aspartate aminotransferase, alkaline phosphatase, total bile acid, total cholesterol, high density lipoprotein cholesterol and low density lipoprotein cholesterol. The underlying mechanisms were investigated by a data integration strategy based on correlation analyses of metabonomics data and 16 S rRNA gene sequencing data. ChA or CaA could inhibit the increase of Rumincoccaceae UCG-004 and reduction of Lachnospiraceae incertae sedis, and Prevotella 9 in HCC rats. The principal component analysis and partial least squares discriminant analysis were applied to reveal the metabolic differences among these groups. 28 different metabolites showed a trend to return to normal in both CaA and ChA treatment. Among them, Bilirubin, L-Tyrosine, L-Methionine and Ethanolamine were correlated increased Rumincoccaceae UCG-004 and decreased of Lachnospiraceae incertae sedis and Prevotella 9. These correlations could be identified as metabolic and microbial signatures of HCC onset and potential therapeutic targets.
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Affiliation(s)
- Zhan Zhang
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Di Wang
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Shanlei Qiao
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Xinyue Wu
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Shuyuan Cao
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Li Wang
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China
| | - Xiaojian Su
- Nanjing entry-exit inspection and quarantine bureau, 110 Jiangjun Avenue, Nanjing, 211106, Jiangsu, P.R. China
| | - Lei Li
- Department of Hygiene Analysis and Detection, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, P. R. China.
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