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Flores JC, Zito K. A synapse-specific refractory period for plasticity at individual dendritic spines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595787. [PMID: 38826343 PMCID: PMC11142223 DOI: 10.1101/2024.05.24.595787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
How newly formed memories are preserved while brain plasticity is ongoing has been a source of debate. One idea is that synapses which experienced recent plasticity become resistant to further plasticity, a type of metaplasticity often referred to as saturation. Here, we probe the local dendritic mechanisms that limit plasticity at recently potentiated synapses. We show that recently potentiated individual synapses exhibit a synapse-specific refractory period for further potentiation. We further found that the refractory period is associated with reduced postsynaptic CaMKII signaling; however, stronger synaptic activation only partially restored the ability for further plasticity. Importantly, the refractory period is released after one hour, a timing that coincides with the enrichment of several postsynaptic proteins to pre-plasticity levels. Notably, increasing the level of the postsynaptic scaffolding protein, PSD95, but not of PSD93, overcomes the refractory period. Our results support a model in which potentiation at a single synapse is sufficient to initiate a synapse-specific refractory period that persists until key postsynaptic proteins regain their steady-state synaptic levels.
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Affiliation(s)
- Juan C. Flores
- Center for Neuroscience, University of California, Davis, CA 95618
| | - Karen Zito
- Center for Neuroscience, University of California, Davis, CA 95618
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Ahmed S, Polis B, Jamwal S, Sanganahalli BG, Kaswan ZM, Islam R, Kim D, Bowers C, Giuliano L, Biederer T, Hyder F, Kaffman A. Transient Impairment in Microglial Function Causes Sex-Specific Deficits in Synaptic and Hippocampal Function in Mice Exposed to Early Adversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580284. [PMID: 38405887 PMCID: PMC10888912 DOI: 10.1101/2024.02.14.580284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Abnormal development and function of the hippocampus are two of the most consistent findings in humans and rodents exposed to early life adversity, with males often being more affected than females. Using the limited bedding (LB) paradigm as a rodent model of early life adversity, we found that male adolescent mice that had been exposed to LB exhibit significant deficits in contextual fear conditioning and synaptic connectivity in the hippocampus, which are not observed in females. This is linked to altered developmental refinement of connectivity, with LB severely impairing microglial-mediated synaptic pruning in the hippocampus of male and female pups on postnatal day 17 (P17), but not in adolescent P33 mice when levels of synaptic engulfment by microglia are substantially lower. Since the hippocampus undergoes intense synaptic pruning during the second and third weeks of life, we investigated whether microglia are required for the synaptic and behavioral aberrations observed in adolescent LB mice. Indeed, transient ablation of microglia from P13-21, in normally developing mice caused sex-specific behavioral and synaptic abnormalities similar to those observed in adolescent LB mice. Furthermore, chemogenetic activation of microglia during the same period reversed the microglial-mediated phagocytic deficits at P17 and restored normal contextual fear conditioning and synaptic connectivity in adolescent LB male mice. Our data support an additional contribution of astrocytes in the sex-specific effects of LB, with increased expression of the membrane receptor MEGF10 and enhanced synaptic engulfment in hippocampal astrocytes of 17-day-old LB females, but not in LB male littermates. This finding suggests a potential compensatory mechanism that may explain the relative resilience of LB females. Collectively, these studies highlight a novel role for glial cells in mediating sex-specific hippocampal deficits in a mouse model of early-life adversity.
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Affiliation(s)
- Sahabuddin Ahmed
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Baruh Polis
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Sumit Jamwal
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Basavaraju G. Sanganahalli
- Department of Radiology & Biomedical Imaging and Magnetic Resonance Research Center, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06519, USA
| | - Zoe MacDowell Kaswan
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Rafiad Islam
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Dana Kim
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Christian Bowers
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Lauryn Giuliano
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
| | - Thomas Biederer
- Department of Neurology, Yale School of Medicine, 100 College Street, New Haven, CT 06510, USA
| | - Fahmeed Hyder
- Department of Radiology & Biomedical Imaging and Magnetic Resonance Research Center, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06519, USA
| | - Arie Kaffman
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, Suite 901, New Haven CT, 06511, USA
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Li J, Wang J, Lin Z. SGCAST: symmetric graph convolutional auto-encoder for scalable and accurate study of spatial transcriptomics. Brief Bioinform 2023; 25:bbad490. [PMID: 38171928 PMCID: PMC10782917 DOI: 10.1093/bib/bbad490] [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: 05/21/2023] [Revised: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Recent advances in spatial transcriptomics (ST) have enabled comprehensive profiling of gene expression with spatial information in the context of the tissue microenvironment. However, with the improvements in the resolution and scale of ST data, deciphering spatial domains precisely while ensuring efficiency and scalability is still challenging. Here, we develop SGCAST, an efficient auto-encoder framework to identify spatial domains. SGCAST adopts a symmetric graph convolutional auto-encoder to learn aggregated latent embeddings via integrating the gene expression similarity and the proximity of the spatial spots. This framework in SGCAST enables a mini-batch training strategy, which makes SGCAST memory-efficient and scalable to high-resolution spatial transcriptomic data with a large number of spots. SGCAST improves the overall accuracy of spatial domain identification on benchmarking data. We also validated the performance of SGCAST on ST datasets at various scales across multiple platforms. Our study illustrates the superior capacity of SGCAST on analyzing spatial transcriptomic data.
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Affiliation(s)
- Jinzhao Li
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
| | - Jiong Wang
- School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, 518172, China
| | - Zhixiang Lin
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China
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Mathew BA, Katta M, Ludhiadch A, Singh P, Munshi A. Role of tRNA-Derived Fragments in Neurological Disorders: a Review. Mol Neurobiol 2023; 60:655-671. [PMID: 36348262 DOI: 10.1007/s12035-022-03078-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022]
Abstract
tRFs are small tRNA derived fragments that are emerging as novel therapeutic targets and regulatory molecules in the pathophysiology of various neurological disorders. These are derived from precursor or mature tRNA, forming different subtypes that have been reported to be involved in neurological disorders like stroke, Alzheimer's, epilepsy, Parkinson's, MELAS, autism, and Huntington's disorder. tRFs were earlier believed to be random degradation debris of tRNAs. The significant variation in the expression level of tRFs in disease conditions indicates their salient role as key players in regulation of these disorders. Various animal studies are being carried out to decipher their exact role; however, more inputs are required to transform this research knowledge into clinical application. Future investigations also call for high-throughput technologies that could help to bring out the other hidden aspects of these entities. However, studies on tRFs require further research efforts to overcome the challenges posed in quantifying tRFs, their interactions with other molecules, and the exact mechanism of function. In this review, we are abridging the current understanding of tRFs, including their biogenesis, function, relevance in clinical therapies, and potential as diagnostic and prognostic biomarkers of these neurological disorders.
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Affiliation(s)
- Blessy Aksa Mathew
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Madhumitha Katta
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Paramdeep Singh
- Department of Radiology, All India Institute of Medical Sciences, Bathinda, Punjab, India, 151001
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401.
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Kim B, Sasaki A, Murphy K, Matthews SG. DNA methylation signatures in human neonatal blood following maternal antenatal corticosteroid treatment. Transl Psychiatry 2022; 12:132. [PMID: 35354798 PMCID: PMC8967826 DOI: 10.1038/s41398-022-01902-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
Antenatal corticosteroids (ACS) are used to treat women at risk of preterm birth to improve neonatal survival. Though affected children may be at long-term risk of neurobehavioural disorders, the driving mechanisms remain unknown. Animal studies have shown that ACS exposure can lead to overlapping changes in DNA methylation between the blood and the brain, identifying gene pathways for neurodevelopment, which highlights the potential to examine peripheral blood as a surrogate for inaccessible human brain tissue. We hypothesized that differential methylation will be identified in blood of term-born neonates following ACS. Mother-infant dyads that received ACS were retrospectively identified through the Ontario Birth Study at Sinai Health Complex and matched to untreated controls for maternal age, BMI, parity and foetal sex (n = 14/group). Genome-wide methylation differences were examined at single-nucleotide resolution in DNA extracted from dried bloodspot cards using reduced representative bisulfite sequencing approaches. 505 differentially methylated CpG sites (DMCs) were identified, wherein 231 were hypermethylated and 274 were hypomethylated. These sites were annotated to 219 genes, of which USP48, SH3PXD2A, NTM, CAMK2N2, MAP6D1 were five of the top ten genes with known neurological function. Collectively, the set of hypermethylated genes were enriched for pathways of transcription regulation, while pathways of proteasome activity were enriched among the set of hypomethylated genes. This study is the first to identify DNA methylation changes in human neonatal blood following ACS. Understanding the epigenetic changes that occur in response to ACS will support future investigations to delineate the effects of prenatal glucocorticoid exposure on human development.
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Affiliation(s)
- Bona Kim
- Department of Physiology, University of Toronto, Toronto, ON, Canada. .,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
| | - Aya Sasaki
- grid.17063.330000 0001 2157 2938Department of Physiology, University of Toronto, Toronto, ON Canada ,grid.250674.20000 0004 0626 6184Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada
| | - Kellie Murphy
- grid.17063.330000 0001 2157 2938Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada
| | - Stephen G. Matthews
- grid.17063.330000 0001 2157 2938Department of Physiology, University of Toronto, Toronto, ON Canada ,grid.250674.20000 0004 0626 6184Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada
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Vergara P, Pino G, Vera J, Arancibia F, Sanhueza M. Heterogeneous CaMKII-Dependent Synaptic Compensations in CA1 Pyramidal Neurons From Acute Hippocampal Slices. Front Cell Neurosci 2022; 16:821088. [PMID: 35431809 PMCID: PMC9005847 DOI: 10.3389/fncel.2022.821088] [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: 11/23/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Prolonged changes in neural activity trigger homeostatic synaptic plasticity (HSP) allowing neuronal networks to operate within functional ranges. Cell-wide or input-specific adaptations can be induced by pharmacological or genetic manipulations of activity, and by sensory deprivation. Reactive functional changes caused by deafferentation may partially share mechanisms with HSP. Acute hippocampal slices are a suitable model to investigate relatively rapid (hours) modifications occurring after denervation and explore the underlying mechanisms. As during slicing many afferents are cut, we conducted whole-cell recordings of miniature excitatory postsynaptic currents (mEPSCs) in CA1 pyramidal neurons to evaluate changes over the following 12 h. As Schaffer collaterals constitute a major glutamatergic input to these neurons, we also dissected CA3. We observed an average increment in mEPSCs amplitude and a decrease in decay time, suggesting synaptic AMPA receptor upregulation and subunit content modifications. Sorting mEPSC by rise time, a correlate of synapse location along dendrites, revealed amplitude raises at two separate domains. A specific frequency increase was observed in the same domains and was accompanied by a global, unspecific raise. Amplitude and frequency increments were lower at sites initially more active, consistent with local compensatory processes. Transient preincubation with a specific Ca2+/calmodulin-dependent kinase II (CaMKII) inhibitor either blocked or occluded amplitude and frequency upregulation in different synapse populations. Results are consistent with the concurrent development of different known CaMKII-dependent HSP processes. Our observations support that deafferentation causes rapid and diverse compensations resembling classical slow forms of adaptation to inactivity. These results may contribute to understand fast-developing homeostatic or pathological events after brain injury.
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Wei Z, Fei Y, Wang Q, Hou J, Cai X, Yang Y, Chen T, Xu Q, Wang Y, Li YG. Loss of Camk2n1 aggravates cardiac remodeling and malignant ventricular arrhythmia after myocardial infarction in mice via NLRP3 inflammasome activation. Free Radic Biol Med 2021; 167:243-257. [PMID: 33746041 DOI: 10.1016/j.freeradbiomed.2021.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/18/2022]
Abstract
AIMS Inflammation response and subsequent ventricular remodeling are critically involved in the development of ventricular arrhythmia post myocardial infarction (MI). However, as the vital endogenous inhibitor of calcium/calmodulin-dependent protein kinase II (CaMKII), the effects of CaMKII inhibitor 1 (Camk2n1) on the process of arrhythmia substrate generation following MI remains unclear. In this study, we investigated the role of Camk2n1 in ventricular arrhythmia post-MI and the underlying mechanisms. METHODS AND RESULTS Camk2n1 was mainly expressed in cardiomyocytes and inhibited the phosphorylation of CaMKIIδ in the infarcted border zone. Compared to wild type (WT) littermates mice, Camk2n1 knockout mice (Camk2n1-/-) manifested exacerbated cardiac dysfunction, larger fibrosis area, higher incidence of premature ventricular contractions (PVCs) and higher vulnerability to ventricular tachycardia (VT) or ventricular fibrillation (VF) after MI. The results of RNA sequencing (RNA-seq) identified that excessive activation of NLRP3 inflammasome was responsible for aggravated inflammation response which led to adverse cardiac remodeling in Camk2n1-/- mice subjected to MI. More importantly, both in vivo and in vitro experiments verified that aggravated NLRP3 inflammasome activation occurred via CaMKIIδ-p38/JNK pathway in Camk2n1-/- mice. CONCLUSIONS Collectively, our results highlight the importance of Camk2n1 in alleviating ventricular remodeling and malignant ventricular arrhythmia post-MI by reducing cardiomyocytes inflammation activation via CaMKIIδ-p38/JNK-NLRP3 inflammasome pathway, targeting Camk2n1 might serve as a novel therapeutic strategy after MI.
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Affiliation(s)
- Zhixing Wei
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yudong Fei
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Wang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianwen Hou
- Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xingxing Cai
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuli Yang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Taizhong Chen
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quanfu Xu
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuepeng Wang
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Gang Li
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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