1
|
Imarisio A, Yahyavi I, Avenali M, Di Maio A, Buongarzone G, Galandra C, Picascia M, Filosa A, Gasparri C, Monti MC, Rondanelli M, Pacchetti C, Errico F, Valente EM, Usiello A. Blood D-serine levels correlate with aging and dopaminergic treatment in Parkinson's disease. Neurobiol Dis 2024; 192:106413. [PMID: 38253208 DOI: 10.1016/j.nbd.2024.106413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
We recently described increased D- and L-serine concentrations in the striatum of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys, the post-mortem caudate-putamen of human Parkinson's disease (PD) brains and the cerebrospinal fluid (CSF) of de novo living PD patients. However, data regarding blood D- and L-serine levels in PD are scarce. Here, we investigated whether the serum profile of D- and L-serine, as well as the other glutamate N-methyl-D-aspartate ionotropic receptor (NMDAR)-related amino acids, (i) differs between PD patients and healthy controls (HC) and (ii) correlates with clinical-demographic features and levodopa equivalent daily dose (LEDD) in PD. Eighty-three consecutive PD patients and forty-one HC were enrolled. PD cohort underwent an extensive clinical characterization. Serum levels of D- and L-serine, L-glutamate, L-glutamine, L-aspartate, L-asparagine and glycine were determined using High Performance Liquid Chromatography. In age- and sex-adjusted analyses, no differences emerged in the serum levels of D-serine, L-serine and other NMDAR-related amino acids between PD and HC. However, we found that D-serine and D-/Total serine ratio positively correlated with age in PD but not in HC, and also with PD age at onset. Moreover, we found that higher LEDD correlated with lower levels of D-serine and the other excitatory amino acids. Following these results, the addition of LEDD as covariate in the analyses disclosed a selective significant increase of D-serine in PD compared to HC (Δ ≈ 38%). Overall, these findings suggest that serum D-serine and D-/Total serine may represent a valuable biochemical signature of PD.
Collapse
Affiliation(s)
- Alberto Imarisio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Isar Yahyavi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Micol Avenali
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Anna Di Maio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Gabriele Buongarzone
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Caterina Galandra
- Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Marta Picascia
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Asia Filosa
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Clara Gasparri
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona "Istituto Santa Margherita", University of Pavia, 27100 Pavia, Italy
| | - Maria Cristina Monti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Mariangela Rondanelli
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Claudio Pacchetti
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Francesco Errico
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Agricultural Sciences, University of Naples "Federico II", 80055 Portici, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy.
| | - Alessandro Usiello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy; CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| |
Collapse
|
2
|
Di Maio A, Nuzzo T, Gilio L, Serra M, Buttari F, Errico F, De Rosa A, Bassi MS, Morelli M, Sasabe J, Sulzer D, Carta M, Centonze D, Usiello A. Homeostasis of serine enantiomers is disrupted in the post-mortem caudate putamen and cerebrospinal fluid of living Parkinson's disease patients. Neurobiol Dis 2023:106203. [PMID: 37336364 DOI: 10.1016/j.nbd.2023.106203] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023] Open
Abstract
L-serine generated in astrocytes plays a pivotal role in modulating essential neurometabolic processes, while its enantiomer, D-serine, specifically regulates NMDA receptor (NMDAR) signalling. Despite their physiological relevance in modulating cerebral activity, serine enantiomers metabolism in Parkinson's disease (PD) remains elusive. Using High-Performance Liquid Chromatography (HPLC), we measured D- and L-serine levels along with other amino acids known to modulate NMDAR function, such as L-glutamate, L-aspartate, D-aspartate, and glycine, in the post-mortem caudate putamen (CPu) and superior frontal gyrus (SFG) of PD patients. Moreover, we examined these amino acids in the cerebrospinal fluid (CSF) of de novo living PD, Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS) patients versus subjects with other neurological disorders (OND), used as control. We found higher D-serine and L-serine levels in the CPu of PD patients but not in the SFG, a cerebral region that, in contrast to the CPu, is not innervated by nigral dopaminergic terminals. We also highlighted a significant elevation of both serine enantiomers in the CSF samples from PD but not in those of AD and ALS patients, compared with control subjects. By contrast, none or only minor changes were found in the amount of other neuroactive amino acids mentioned above. Our findings identify D-serine and L-serine level upregulation as a biochemical signature associated with nigrostriatal dopaminergic degeneration in PD.
Collapse
Affiliation(s)
- Anna Di Maio
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Tommaso Nuzzo
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Luana Gilio
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy; Faculty of Psychology, Uninettuno Telematic International University, Rome, Italy; Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Marcello Serra
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Fabio Buttari
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy
| | - Francesco Errico
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Arianna De Rosa
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Micaela Morelli
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy; National Research Council of Italy, Institute of Neuroscience, Cagliari, Italy
| | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan
| | - David Sulzer
- Departments of Psychiatry, Neurology, Pharmacology, Columbia University Irving Medical Center, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Manolo Carta
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Diego Centonze
- Unit of Neurology, IRCCS Neuromed, Pozzilli (IS), Italy; Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Alessandro Usiello
- Laboratory of Translational Neuroscience, Ceinge Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy.
| |
Collapse
|
3
|
De Riso G, Sarnataro A, Scala G, Cuomo M, Della Monica R, Amente S, Chiariotti L, Miele G, Cocozza S. MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data. NAR Genom Bioinform 2022; 4:lqac096. [PMID: 36601577 PMCID: PMC9803872 DOI: 10.1093/nargab/lqac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.
Collapse
Affiliation(s)
- Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Antonella Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 21, 80126 Naples, Italy
| | - Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Gennaro Miele
- Department of Physics “E. Pancini”, University of Naples “Federico II”, Via Cinthia, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Napoli, 80126 Naples, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| |
Collapse
|
4
|
Ni X, Mori H. Complex Processes Underlying the Dynamic Changes of D-serine Levels in AD Brains. Curr Alzheimer Res 2022; 19:485-493. [PMID: 35346007 DOI: 10.2174/1567205019666220328123048] [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: 09/22/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disorder characterized by extracellular β-amyloid (Aβ) plaques and cognitive impairments. D-Serine, produced by the enzyme serine racemase (SR) in the brain, functions as an endogenous co-agonist at the glycine-binding site of N-methyl-D-aspartate receptor (NMDAR), has been implicated in the pathophysiological progression of AD. OBJECTIVES Evidence regarding the understanding of the role and dynamic modulation of D-serine during AD progression remains controversial. This literature review aims to offer novel research directions for studying the functions and metabolisms of D-serine in AD brains. METHODS We searched PubMed, using D-serine/SR and AD as keywords. Studies related to NMDAR dysfunction, neuronal excitotoxicity, D-serine dynamic changes and inflammatory response were included. RESULTS This review primarily discusses: (i) Aβ oligomers' role in NMDAR dysregulation, and the subsequent synaptic dysfunction and neuronal damage in AD, (ii) D-serine's role in NMDAR-elicited excitotoxicity, and (iii) the involvement of D-serine and SR in AD-related inflammatory pathological progression. CONCLUSION We also presented supposed metabolism and dynamic changes of D-serine during AD progression and hypothesized that: (i) the possible modulation of D-serine levels or SR expression as an effective method of alleviating neurotoxicity during AD pathophysiological progression, and (ii) the dynamic changes of D-serine levels in AD brains possibly resulting from complex processes.
Collapse
Affiliation(s)
- Xiance Ni
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-0194, Japan
| | - Hisashi Mori
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-0194, Japan.,Research Center for Idling Brain Science (RCIBS), University of Toyama, Toyama 930-0194, Japan
| |
Collapse
|
5
|
Cuomo M, Florio E, Della Monica R, Costabile D, Buonaiuto M, Di Risi T, De Riso G, Sarnataro A, Cocozza S, Visconti R, Chiariotti L. Epigenetic remodelling of Fxyd1 promoters in developing heart and brain tissues. Sci Rep 2022; 12:6471. [PMID: 35440736 PMCID: PMC9018693 DOI: 10.1038/s41598-022-10365-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
FXYD1 is a key protein controlling ion channel transport. FXYD1 exerts its function by regulating Na+/K+-ATPase activity, mainly in brain and cardiac tissues. Alterations of the expression level of the FXYD1 protein cause diastolic dysfunction and arrhythmias in heart and decreased neuronal dendritic tree and spine formation in brain. Moreover, FXYD1, a target of MeCP2, plays a crucial role in the pathogenesis of the Rett syndrome, a neurodevelopmental disorder. Thus, the amount of FXYD1 must be strictly controlled in a tissue specific manner and, likely, during development. Epigenetic modifications, particularly DNA methylation, represent the major candidate mechanism that may regulate Fxyd1 expression. In the present study, we performed a comprehensive DNA methylation analysis and mRNA expression level measurement of the two Fxyd1 transcripts, Fxyd1a and Fxyd1b, in brain and heart tissues during mouse development. We found that DNA methylation at Fxyd1a increased during brain development and decreased during heart development along with coherent changes in mRNA expression levels. We also applied ultra-deep methylation analysis to detect cell to cell methylation differences and to identify possible distinct methylation profile (epialleles) distribution between heart and brain and in different developmental stages. Our data indicate that the expression of Fxyd1 transcript isoforms inversely correlates with DNA methylation in developing brain and cardiac tissues suggesting the existence of a temporal-specific epigenetic program. Moreover, we identified a clear remodeling of epiallele profiles which were distinctive for single developmental stage both in brain and heart tissues.
Collapse
Affiliation(s)
- Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy. .,CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy.
| | - Ermanno Florio
- Department of Medicine, University of California, San Diego UCSD, Gilman Dr, La Jolla, CA, 95000, USA
| | - Rosa Della Monica
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
| | - Davide Costabile
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy.,SEMM-European School of Molecular Medicine, University of Naples, "Federico II", 80131, Naples, Italy
| | - Michela Buonaiuto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy.,CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
| | - Teodolinda Di Risi
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy.,Department of Public Health, University of Naples "Federico II", Via S. Pansini, 5, 80131, Naples, Italy
| | - Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Antonella Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Roberta Visconti
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy.,Institute of Experimental Endocrinology and Oncology, Italian National Council of Research, Via S. Pansini 5, 80131, Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy. .,CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy. .,SEMM-European School of Molecular Medicine, University of Naples, "Federico II", 80131, Naples, Italy.
| |
Collapse
|
6
|
Oh YE, Nguyen TB, Rami FZ, Karamikheirabad M, Chung YC. Impact of Social Defeat Stress on DNA Methylation in Drd2, Nr3c1, and Stmn1 in Wild-type and Stmn1 Knock-out Mice. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2022; 20:51-60. [PMID: 35078948 PMCID: PMC8813314 DOI: 10.9758/cpn.2022.20.1.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/28/2022]
Abstract
Objective Epigenetic profiles can be modified by stress. Dopamine receptor D2 (Drd2), glucocorticoid receptor gene (Nr3c1) and Stathmin 1 (Stmn1) genes are all implicated in adaptation to stress. The aim of study is to investigate impact of social defeat on DNA methylation in Drd2, Nr3c1, and Stmn1 in wild-type (WT) and Stmn1 knock-out (KO) mice. Methods The WT and Stmn1 KO mice were subjected to chronic social defeat. Brain tissues of the prefrontal cortex (PFC), amygdala (AMY) and hippocampus (HIP) were obtained. We measured DNA methylation levels of the Drd2, Nr3c1, and Stmn1 genes in the PFC, AMY, and HIP using pyrosequencing. Results In WT mice, social defeat stress did not induce any changes in Drd2 methylation, whereas significant hypermethylation occurred in Nr3c1 and Stmn1 in the susceptible and unsusceptible groups, respectively, compared to the control group. The methylation responses in the Stmn1 KO mice differed from those seen in the WT mice, such that hypermethylation was evident in all three genes in the susceptible and unsusceptible groups compared to control group. Comparison of the Stmn1 KO and WT mice revealed the same pattern of hypermethylation for all three genes. Conclusion Social defeat stress induced different epigenetic modifications in three genes among control, unsusceptible, and susceptible groups of WT and Stmn1 KO mice. In particular, hypermethylation of Nr3c1 in the HIP of the susceptible group, and of Stmn1 in the AMY of the unsusceptible group in WT mice, could serve as epigenetic biomarkers of stress susceptibility and stress resilience, respectively.
Collapse
Affiliation(s)
- Young-Eun Oh
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Thong Ba Nguyen
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Fatima Zahra Rami
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Maryam Karamikheirabad
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Young-Chul Chung
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| |
Collapse
|
7
|
Endutkin AV, Yatsenko DD, Zharkov DO. Effect of DNA Methylation on the 3'→5' Exonuclease Activity of Major Human Abasic Site Endonuclease APEX1. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:10-20. [PMID: 35491018 DOI: 10.1134/s0006297922010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Apurinic/apyrimidinic (AP) endonucleases are the key enzymes in the DNA base excision repair, as they hydrolyze the phosphodiester bond in the AP site formed after removal of the damaged base. Major human AP endonuclease APEX1 also possesses the 3'-phosphodiesterase and 3'→5' exonuclease activities. The biological role of the latter has not been established yet; it is assumed that it corrects DNA synthesis errors during DNA repair. If DNA is damaged at the 3'-side of 5-methylcytosine (mC) residue, the 3'→5' exonuclease activity can change the epigenetic methylation status of the CpG dinucleotide. It remains unclear whether the 3'→5' exonuclease activity of APEX1 contributes to the active epigenetic demethylation or, on the contrary, is limited in the case of methylated CpG dinucleotides in order to preserve the epigenetic status upon repair of accidental DNA damage. Here, we report the results of the first systematic study on the efficiency of removal of 3'-terminal nucleotides from the substrates modeling DNA repair intermediates in the CpG dinucleotides. The best substrates for the 3'→5' exonuclease activity of APEX1 were oligonucleotides with the 3'-terminal bases non-complementary to the template, while the worst substrates contained mC. The presence of mC in the complementary strand significantly reduced the reaction rate even for the non-complementary 3'-ends. Therefore, the efficiency of the 3'→5' exonuclease reaction catalyzed by APEX1 is limited in the case of the methylated CpG dinucleotides, which likely reflects the need to preserve the epigenetic status during DNA repair.
Collapse
Affiliation(s)
- Anton V Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Darya D Yatsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| |
Collapse
|
8
|
Pollegioni L, Molla G, Sacchi S, Murtas G. Human D-aspartate Oxidase: A Key Player in D-aspartate Metabolism. Front Mol Biosci 2021; 8:689719. [PMID: 34250021 PMCID: PMC8260693 DOI: 10.3389/fmolb.2021.689719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/09/2021] [Indexed: 11/15/2022] Open
Abstract
In recent years, the D-enantiomers of amino acids have been recognized as natural molecules present in all kingdoms, playing a variety of biological roles. In humans, d-serine and d-aspartate attracted attention for their presence in the central nervous system. Here, we focus on d-aspartate, which is involved in glutamatergic neurotransmission and the synthesis of various hormones. The biosynthesis of d-aspartate is still obscure, while its degradation is due to the peroxisomal flavin adenine dinucleotide (FAD)-containing enzyme d-aspartate oxidase. d-Aspartate emergence is strictly controlled: levels decrease in brain within the first days of life while increasing in endocrine glands postnatally and through adulthood. The human d-aspartate oxidase (hDASPO) belongs to the d-amino acid oxidase-like family: its tertiary structure closely resembles that of human d-amino acid oxidase (hDAAO), the enzyme that degrades neutral and basic d-amino acids. The structure-function relationships of the physiological isoform of hDASPO (named hDASPO_341) and the regulation of gene expression and distribution and properties of the longer isoform hDASPO_369 have all been recently elucidated. Beyond the substrate preference, hDASPO and hDAAO also differ in kinetic efficiency, FAD-binding affinity, pH profile, and oligomeric state. Such differences suggest that evolution diverged to create two different ways to modulate d-aspartate and d-serine levels in the human brain. Current knowledge about hDASPO is shedding light on the molecular mechanisms underlying the modulation of d-aspartate levels in human tissues and is pushing novel, targeted therapeutic strategies. Now, it has been proposed that dysfunction in NMDA receptor-mediated neurotransmission is caused by disrupted d-aspartate metabolism in the nervous system during the onset of various disorders (such as schizophrenia): the design of suitable hDASPO inhibitors aimed at increasing d-aspartate levels thus represents a novel and useful form of therapy.
Collapse
Affiliation(s)
- Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| |
Collapse
|
9
|
Epigenome Chaos: Stochastic and Deterministic DNA Methylation Events Drive Cancer Evolution. Cancers (Basel) 2021; 13:cancers13081800. [PMID: 33918773 PMCID: PMC8069666 DOI: 10.3390/cancers13081800] [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: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Cancer is a group of diseases characterized by abnormal cell growth with a high potential to invade other tissues. Genetic abnormalities and epigenetic alterations found in tumors can be due to high levels of DNA damage and repair. These can be transmitted to daughter cells, which assuming other alterations as well, will generate heterogeneous and complex populations. Deciphering this complexity represents a central point for understanding the molecular mechanisms of cancer and its therapy. Here, we summarize the genomic and epigenomic events that occur in cancer and discuss novel approaches to analyze the epigenetic complexity of cancer cell populations. Abstract Cancer evolution is associated with genomic instability and epigenetic alterations, which contribute to the inter and intra tumor heterogeneity, making genetic markers not accurate to monitor tumor evolution. Epigenetic changes, aberrant DNA methylation and modifications of chromatin proteins, determine the “epigenome chaos”, which means that the changes of epigenetic traits are randomly generated, but strongly selected by deterministic events. Disordered changes of DNA methylation profiles are the hallmarks of all cancer types, but it is not clear if aberrant methylation is the cause or the consequence of cancer evolution. Critical points to address are the profound epigenetic intra- and inter-tumor heterogeneity and the nature of the heterogeneity of the methylation patterns in each single cell in the tumor population. To analyze the methylation heterogeneity of tumors, new technological and informatic tools have been developed. This review discusses the state of the art of DNA methylation analysis and new approaches to reduce or solve the complexity of methylated alleles in DNA or cell populations.
Collapse
|
10
|
Di Risi T, Vinciguerra R, Cuomo M, Della Monica R, Riccio E, Cocozza S, Imbriaco M, Duro G, Pisani A, Chiariotti L. DNA methylation impact on Fabry disease. Clin Epigenetics 2021; 13:24. [PMID: 33531072 PMCID: PMC7852133 DOI: 10.1186/s13148-021-01019-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Fabry disease (FD) is a rare X-linked disease caused by mutations in GLA gene with consequent lysosomal accumulation of globotriaosylceramide (Gb3). Women with FD often show highly heterogeneous symptoms that can manifest from mild to severe phenotype. MAIN BODY The phenotypic variability of the clinical manifestations in heterozygous women with FD mainly depends on the degree and direction of inactivation of the X chromosome. Classical approaches to measure XCI skewness might be not sufficient to explain disease manifestation in women. In addition to unbalanced XCI, allele-specific DNA methylation at promoter of GLA gene may influence the expression levels of the mutated allele, thus impacting the onset and the outcome of FD. In this regard, analyses of DNA methylation at GLA promoter, performed by approaches allowing distinction between mutated and non-mutated allele, may be much more informative. The aim of this review is to critically evaluate recent literature articles addressing the potential role of DNA methylation in the context of FD. Although up to date relatively few works have addressed this point, reviewing all pertinent studies may help to evaluate the importance of DNA methylation analysis in FD and to develop new research and technologies aimed to predict whether the carrier females will develop symptoms. CONCLUSIONS Relatively few studies have addressed the complexity of DNA methylation landscape in FD that remains poorly investigated. The hope for the future is that ad hoc and ultradeep methylation analyses of GLA gene will provide epigenetic signatures able to predict whether pre-symptomatic female carriers will develop symptoms thus helping timely interventions.
Collapse
Affiliation(s)
- Teodolinda Di Risi
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
- Department of Public Health, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Roberta Vinciguerra
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
- Department of Public Health, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Mariella Cuomo
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Rosa Della Monica
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy
| | - Eleonora Riccio
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB CNR), Palermo, Italy
| | - Sirio Cocozza
- Department of Advanced Biomedical Sciences, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Massimo Imbriaco
- Department of Advanced Biomedical Sciences, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Giovanni Duro
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB CNR), Palermo, Italy
| | - Antonio Pisani
- Department of Public Health, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy
| | - Lorenzo Chiariotti
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145, Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnology, University Federico II of Naples, Via S. Pansini, 5, 80131, Naples, Italy.
| |
Collapse
|
11
|
Cuomo M, Borrelli L, Della Monica R, Coretti L, De Riso G, D’Angelo Lancellotti di Durazzo L, Fioretti A, Lembo F, Dinan TG, Cryan JF, Cocozza S, Chiariotti L. DNA Methylation Profiles of Tph1A and BDNF in Gut and Brain of L. Rhamnosus-Treated Zebrafish. Biomolecules 2021; 11:biom11020142. [PMID: 33499115 PMCID: PMC7911505 DOI: 10.3390/biom11020142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
The bidirectional microbiota–gut–brain axis has raised increasing interest over the past years in the context of health and disease, but there is a lack of information on molecular mechanisms underlying this connection. We hypothesized that change in microbiota composition may affect brain epigenetics leading to long-lasting effects on specific brain gene regulation. To test this hypothesis, we used Zebrafish (Danio Rerio) as a model system. As previously shown, treatment with high doses of probiotics can modulate behavior in Zebrafish, causing significant changes in the expression of some brain-relevant genes, such as BDNF and Tph1A. Using an ultra-deep targeted analysis, we investigated the methylation state of the BDNF and Tph1A promoter region in the brain and gut of probiotic-treated and untreated Zebrafishes. Thanks to the high resolution power of our analysis, we evaluated cell-to-cell methylation differences. At this resolution level, we found slight DNA methylation changes in probiotic-treated samples, likely related to a subgroup of brain and gut cells, and that specific DNA methylation signatures significantly correlated with specific behavioral scores.
Collapse
Affiliation(s)
- Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (M.C.); (G.D.R.); (L.D.L.d.D.); (S.C.)
- CEINGE Biotecnologie Avanzate, via Gaetano Salvatore 482, 80145 Naples, Italy;
| | - Luca Borrelli
- Department of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, Via Delpino 1, 80137 Naples, Italy; (L.B.); (A.F.)
- Task Force on Microbiota Studies University of Naples “Federico II” of Naples, 80131 Naples, Italy; (L.C.); (F.L.)
| | - Rosa Della Monica
- CEINGE Biotecnologie Avanzate, via Gaetano Salvatore 482, 80145 Naples, Italy;
| | - Lorena Coretti
- Task Force on Microbiota Studies University of Naples “Federico II” of Naples, 80131 Naples, Italy; (L.C.); (F.L.)
- Department of Pharmacy, University “Federico II” of Naples, via Domenico Montesano, 80131 Naples, Italy
| | - Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (M.C.); (G.D.R.); (L.D.L.d.D.); (S.C.)
| | - Luna D’Angelo Lancellotti di Durazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (M.C.); (G.D.R.); (L.D.L.d.D.); (S.C.)
| | - Alessandro Fioretti
- Department of Veterinary Medicine and Animal Productions, University of Naples “Federico II”, Via Delpino 1, 80137 Naples, Italy; (L.B.); (A.F.)
- Task Force on Microbiota Studies University of Naples “Federico II” of Naples, 80131 Naples, Italy; (L.C.); (F.L.)
| | - Francesca Lembo
- Task Force on Microbiota Studies University of Naples “Federico II” of Naples, 80131 Naples, Italy; (L.C.); (F.L.)
- Department of Pharmacy, University “Federico II” of Naples, via Domenico Montesano, 80131 Naples, Italy
| | - Timothy G. Dinan
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland; (T.G.D.); (J.F.C.)
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland; (T.G.D.); (J.F.C.)
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (M.C.); (G.D.R.); (L.D.L.d.D.); (S.C.)
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131 Naples, Italy; (M.C.); (G.D.R.); (L.D.L.d.D.); (S.C.)
- CEINGE Biotecnologie Avanzate, via Gaetano Salvatore 482, 80145 Naples, Italy;
- Task Force on Microbiota Studies University of Naples “Federico II” of Naples, 80131 Naples, Italy; (L.C.); (F.L.)
- Correspondence:
| |
Collapse
|
12
|
Orzylowski M, Fujiwara E, Mousseau DD, Baker GB. An Overview of the Involvement of D-Serine in Cognitive Impairment in Normal Aging and Dementia. Front Psychiatry 2021; 12:754032. [PMID: 34707525 PMCID: PMC8542907 DOI: 10.3389/fpsyt.2021.754032] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/02/2021] [Indexed: 12/14/2022] Open
Abstract
Dementia, of which Alzheimer's disease (AD) is the most common form, is characterized by progressive cognitive deterioration, including profound memory loss, which affects functioning in many aspects of life. Although cognitive deterioration is relatively common in aging and aging is a risk factor for AD, the condition is not necessarily a part of the aging process. The N-methyl-D-aspartate glutamate receptor (NMDAR) and its co-agonist D-serine are currently of great interest as potential important contributors to cognitive function in normal aging and dementia. D-Serine is necessary for activation of the NMDAR and in maintenance of long-term potentiation (LTP) and is involved in brain development, neuronal connectivity, synaptic plasticity and regulation of learning and memory. In this paper, we review evidence, from both preclinical and human studies, on the involvement of D-serine (and the enzymes involved in its metabolism) in regulation of cognition. Potential mechanisms of action of D-serine are discussed in the context of normal aging and in dementia, as is the potential for using D-serine as a potential biomarker and/or therapeutic agent in dementia. Although there is some controversy in the literature, it has been proposed that in normal aging there is decreased expression of serine racemase and decreased levels of D-serine and down-regulation of NMDARs, resulting in impaired synaptic plasticity and deficits in learning and memory. In contrast, in AD there appears to be activation of serine racemase, increased levels of D-serine and overstimulation of NMDARs, resulting in cytotoxicity, synaptic deficits, and dementia.
Collapse
Affiliation(s)
- Magdalena Orzylowski
- Villa Caritas Geriatric Psychiatry Hospital, Edmonton, AB, Canada.,Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Esther Fujiwara
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Darrell D Mousseau
- Department of Psychiatry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Glen B Baker
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
13
|
Grimaldi M, Marino C, Buonocore M, Santoro A, Sommella E, Merciai F, Salviati E, De Rosa A, Nuzzo T, Errico F, Campiglia P, Usiello A, D'Ursi AM. Prenatal and Early Postnatal Cerebral d-Aspartate Depletion Influences l-Amino Acid Pathways, Bioenergetic processes, and Developmental Brain Metabolism. J Proteome Res 2020; 20:727-739. [PMID: 33274941 DOI: 10.1021/acs.jproteome.0c00622] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
d-Amino acids were believed to occur only in bacteria and invertebrates. Today, it is well known that d-amino acids are also present in mammalian tissues in a considerable amount. In particular, high levels of free d-serine (d-Ser) and d-aspartate (d-Asp) are found in the brain. While the functions of d-Ser are well known, many questions remain unanswered regarding the role of d-Asp in the central nervous system. d-Asp is very abundant at the embryonic stage, while it strongly decreases after birth because of the expression of d-aspartate oxidase (Ddo) enzyme, which catalyzes the oxidation of this d-amino acid into oxaloacetate, ammonium, and hydrogen peroxide. Pharmacologically, d-Asp acts as an endogenous agonist of N-methyl d-aspartate and mGlu5 receptors, which are known to control fundamental brain processes, including brain development, synaptic plasticity, and cognition. In this work, we studied a recently generated knockin mouse model (R26ddo/ddo), which was designed to express DDO beginning at the zygotic stage. This strategy enables d-Asp to be almost eliminated in both prenatal and postnatal lives. To understand which biochemical pathways are affected by depletion of d-Asp, in this study, we carried out a metabolomic and lipidomic study of ddo knockin brains at different stages of embryonic and postnatal development, combining nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS) techniques. Our study shows that d-Asp deficiency in the brain influences amino acid pathways such as threonine, glycine, alanine, valine, and glutamate. Interestingly, d-Asp is also correlated with metabolites involved in brain development and functions such as choline, creatine, phosphocholine (PCho), glycerophosphocholine (GPCho), sphingolipids, and glycerophospholipids, as well as metabolites involved in brain energy metabolism, such as GPCho, glucose, and lactate.
Collapse
Affiliation(s)
| | - Carmen Marino
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Michela Buonocore
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Angelo Santoro
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | | | - Fabrizio Merciai
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Emanuela Salviati
- PhD Program in Drug Discovery and Development, University of Salerno, 84084 Fisciano, Salerno, Italy
| | - Arianna De Rosa
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Science and Technologies (DISTABIF), University of Campania, L. Vanvitelli, 81100 Caserta, Italy
| | - Tommaso Nuzzo
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Science and Technologies (DISTABIF), University of Campania, L. Vanvitelli, 81100 Caserta, Italy
| | - Francesco Errico
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università, 100-80055 Portici, Italy
| | - Pietro Campiglia
- European Biomedical Research Institute of Salerno, Via De Renzi 50, 84125 Salerno, Italy
| | - Alessandro Usiello
- Laboratory of Behavioural Neuroscience, Ceinge Biotecnologie Avanzate, 80145 Naples, Italy.,Department of Environmental, Biological and Pharmaceutical Science and Technologies (DISTABIF), University of Campania, L. Vanvitelli, 81100 Caserta, Italy
| | | |
Collapse
|
14
|
Pezone A, Tramontano A, Scala G, Cuomo M, Riccio P, De Nicola S, Porcellini A, Chiariotti L, Avvedimento E. Tracing and tracking epiallele families in complex DNA populations. NAR Genom Bioinform 2020; 2:lqaa096. [PMID: 33575640 PMCID: PMC7671405 DOI: 10.1093/nargab/lqaa096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/14/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a stable epigenetic modification, extremely polymorphic and driven by stochastic and deterministic events. Most of the current techniques used to analyse methylated sequences identify methylated cytosines (mCpGs) at a single-nucleotide level and compute the average methylation of CpGs in the population of molecules. Stable epialleles, i.e. CpG strings with the same DNA sequence containing a discrete linear succession of phased methylated/non-methylated CpGs in the same DNA molecule, cannot be identified due to the heterogeneity of the 5'-3' ends of the molecules. Moreover, these are diluted by random unstable methylated CpGs and escape detection. We present here MethCoresProfiler, an R-based tool that provides a simple method to extract and identify combinations of methylated phased CpGs shared by all components of epiallele families in complex DNA populations. The methylated cores are stable over time, evolve by acquiring or losing new methyl sites and, ultimately, display high information content and low stochasticity. We have validated this method by identifying and tracing rare epialleles and their families in synthetic or in vivo complex cell populations derived from mouse brain areas and cells during postnatal differentiation. MethCoresProfiler is written in R language. The software is freely available at https://github.com/84AP/MethCoresProfiler/.
Collapse
Affiliation(s)
- Antonio Pezone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Alfonso Tramontano
- Department of Precision Medicine, University of Campania ‘L. Vanvitelli’, 80138 Naples, Italy
| | - Giovanni Scala
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Mariella Cuomo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Patrizia Riccio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Sergio De Nicola
- Department of Physics, Università Federico II Napoli, 80126 Naples, Italy
| | - Antonio Porcellini
- Department of Biology, Università Federico II Napoli, 80126 Naples, Italy
| | - Lorenzo Chiariotti
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| | - Enrico V Avvedimento
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II Napoli, 80131 Naples, Italy
| |
Collapse
|
15
|
Usiello A, Di Fiore MM, De Rosa A, Falvo S, Errico F, Santillo A, Nuzzo T, Chieffi Baccari G. New Evidence on the Role of D-Aspartate Metabolism in Regulating Brain and Endocrine System Physiology: From Preclinical Observations to Clinical Applications. Int J Mol Sci 2020; 21:E8718. [PMID: 33218144 PMCID: PMC7698810 DOI: 10.3390/ijms21228718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
The endogenous amino acids serine and aspartate occur at high concentrations in free D-form in mammalian organs, including the central nervous system and endocrine glands. D-serine (D-Ser) is largely localized in the forebrain structures throughout pre and postnatal life. Pharmacologically, D-Ser plays a functional role by acting as an endogenous coagonist at N-methyl-D-aspartate receptors (NMDARs). Less is known about the role of free D-aspartate (D-Asp) in mammals. Notably, D-Asp has a specific temporal pattern of occurrence. In fact, free D-Asp is abundant during prenatal life and decreases greatly after birth in concomitance with the postnatal onset of D-Asp oxidase expression, which is the only enzyme known to control endogenous levels of this molecule. Conversely, in the endocrine system, D-Asp concentrations enhance after birth during its functional development, thereby suggesting an involvement of the amino acid in the regulation of hormone biosynthesis. The substantial binding affinity for the NMDAR glutamate site has led us to investigate the in vivo implications of D-Asp on NMDAR-mediated responses. Herein we review the physiological function of free D-Asp and of its metabolizing enzyme in regulating the functions of the brain and of the neuroendocrine system based on recent genetic and pharmacological human and animal studies.
Collapse
Affiliation(s)
- Alessandro Usiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Napoli, Italy;
| | - Maria Maddalena Di Fiore
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
| | - Arianna De Rosa
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Napoli, Italy;
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Sara Falvo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
| | - Francesco Errico
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Via Università, 100, 80055 Portici, Italy;
| | - Alessandra Santillo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
| | - Tommaso Nuzzo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Napoli, Italy;
| | - Gabriella Chieffi Baccari
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania «L. Vanvitelli», Via Vivaldi 43, 81100 Caserta, Italy; (M.M.D.F.); (S.F.); (A.S.); (T.N.)
| |
Collapse
|
16
|
Ploux E, Freret T, Billard JM. d-serine in physiological and pathological brain aging. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140542. [PMID: 32950692 DOI: 10.1016/j.bbapap.2020.140542] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 01/24/2023]
Abstract
Among aging-induced impairments, those affecting cognitive functions certainly represent one the most major challenge to face to improve elderly quality of life. In last decades, our knowledge on changes in the morphology and function of neuronal networks associated with normal and pathological brain aging has rapidly progressed, initiating the development of different pharmacological and behavioural strategies to alleviate cognitive aging. In particular, experimental evidences have accumulated indicating that the communication between neurons and its plasticity gradually weakens with aging. Because of its pivotal role for brain functional plasticity, the N-Methyl‑d-Aspartate receptor subtype of glutamate receptors (NMDAr) has gathered much of the experimental interest. NMDAr activation is regulated by many mechanisms. Among is the mandatory binding of a co-agonist, such as the amino acid d-serine, in order to activate NMDAr. This mini-review presents the most recent information indicating how d-serine could contribute to mechanisms of physiological cognitive aging and also considers the divergent views relative of the role of the NMDAr co-agonist in Alzheimer's disease.
Collapse
Affiliation(s)
- E Ploux
- Normandie Univ, UNICAEN, INSERM, CYCERON, COMETE, 14000 Caen, France.
| | - T Freret
- Normandie Univ, UNICAEN, INSERM, CYCERON, COMETE, 14000 Caen, France
| | - J-M Billard
- Normandie Univ, UNICAEN, INSERM, CYCERON, COMETE, 14000 Caen, France.
| |
Collapse
|
17
|
Errico F, Cuomo M, Canu N, Caputo V, Usiello A. New insights on the influence of free d-aspartate metabolism in the mammalian brain during prenatal and postnatal life. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140471. [PMID: 32561430 DOI: 10.1016/j.bbapap.2020.140471] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023]
Abstract
Free d-aspartate is abundant in the mammalian embryonic brain. However, following the postnatal onset of the catabolic d-aspartate oxidase (DDO) activity, cerebral d-aspartate levels drastically decrease, remaining constantly low throughout life. d-Aspartate stimulates both glutamatergic NMDA receptors (NMDARs) and metabotropic Glu5 receptors. In rodents, short-term d-aspartate exposure increases spine density and synaptic plasticity, and improves cognition. Conversely, persistently high d-Asp levels produce NMDAR-dependent neurotoxic effects, leading to precocious neuroinflammation and cell death. These pieces of evidence highlight the dichotomous impact of d-aspartate signaling on NMDAR-dependent processes and, in turn, unveil a neuroprotective role for DDO in preventing the detrimental effects of excessive d-aspartate stimulation during aging. Here, we will focus on the in vivo influence of altered d-aspartate metabolism on the modulation of glutamatergic functions and its involvement in translational studies. Finally, preliminary data on the role of embryonic d-aspartate in the mouse brain will also be reviewed.
Collapse
Affiliation(s)
- Francesco Errico
- Department of Agricultural Sciences, University of Naples "Federico II", 80055 Portici, Italy.
| | - Mariella Cuomo
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131 Naples, Italy
| | - Nadia Canu
- Department of System Medicine, University of Rome "Tor Vergata", 00133 Rome, Italy; Institute of Biochemistry and Cell Biology, National Research Council (CNR), 00015, Monterotondo Scalo, Rome, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandro Usiello
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; Department of Environmental, Biological and Pharmaceutical Science and Technologies, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| |
Collapse
|
18
|
Ultra-Deep DNA Methylation Analysis of X-Linked Genes: GLA and AR as Model Genes. Genes (Basel) 2020; 11:genes11060620. [PMID: 32512878 PMCID: PMC7349208 DOI: 10.3390/genes11060620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Recessive X-linked disorders may occasionally evolve in clinical manifestations of variable severity also in female carriers. For some of such diseases, the frequency of the symptoms’ appearance during women’s life may be particularly relevant. This phenomenon has been largely attributed to the potential skewness of the X-inactivation process leading to variable phenotypes. Nonetheless, in many cases, no correlation with X-inactivation unbalance was demonstrated. However, methods for analyzing skewness have been mainly limited to Human Androgen Receptor methylation analysis (HUMARA). Recently, the X-inactivation process has been largely revisited, highlighting the heterogeneity existing among loci in the epigenetic state within inactive and, possibly, active X-chromosomes. We reasoned that gene-specific and ultra-deep DNA methylation analyses could greatly help to unravel details of the X-inactivation process and the roles of specific X genes inactivation in disease manifestations. We recently provided evidence that studying DNA methylation at specific autosomic loci at a single-molecule resolution (epiallele distribution analysis) allows one to analyze cell-to-cell methylation differences in a given cell population. We here apply the epiallele analysis at two X-linked loci to investigate whether females show allele-specific epiallelic patterns. Due to the high potential of this approach, the method allows us to obtain clearly distinct allele-specific epiallele profiles.
Collapse
|
19
|
Prenatal expression of d-aspartate oxidase causes early cerebral d-aspartate depletion and influences brain morphology and cognitive functions at adulthood. Amino Acids 2020; 52:597-617. [DOI: 10.1007/s00726-020-02839-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022]
|