scholarly journals A survey of RNA editing at single cell resolution links interneurons to schizophrenia and autism

RNA ◽  
2021 ◽  
pp. rna.078804.121
Author(s):  
Brendan Robert E. Ansell ◽  
Simon N Thomas ◽  
Roberto Bonelli ◽  
Jacob E Munro ◽  
Saskia Freytag ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Structure ◽  
Serotonin Receptor ◽  
Target Genes ◽  
Linear Models ◽  
Inhibitory Neurons ◽  
Neuronal Nuclei ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cortical Regions

BACKGROUND: Conversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is essential for healthy brain development. This editing process is dysregulated in many neuropsychiatric diseases, but has not yet been investigated at the level of individual neurons. METHODS: We quantified RNA editing sites in full-length capture nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical post-mortem female donor. Putative editing sites were intersected with sites in bulk human tissue transcriptomes including healthy and neuropsychiatric brain tissue, and sites identified in single nuclei from unrelated brain donors. Differential editing between cell types and cortical regions, and individual sites and genes therein, was quantified using linear models. Associations between gene abundance and editing were also tested. RESULTS: We identified 41,930 RNA editing sites with robust read coverage in at least ten neuronal nuclei. Most sites were located within Alu repeats in introns or 3’ UTRs, and approximately 80% were catalogued in published RNA editing databases. We identified 9285 putative novel RNA editing sites, 29% of which were also detectable in neuronal transcriptomes from unrelated donors. Among the strongest correlates of global editing rates were snoRNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2. Autism related genes were enriched with editing sites predicted to modify RNA structure. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons. Additionally, we identified 29 genes preferentially edited in excitatory neurons and 43 genes edited more heavily in inhibitory neurons including RBFOX1, its target genes, and small nucleolar RNA-associated genes in the autism-associated Prader-Willi locus 15q11. These results provide cell-type and spatial context for 1730 sites that are differentially edited in the brains of schizophrenic patients, and 910 sites in autistic patients. CONCLUSIONS: RNA editing, including thousands of previously unreported sites, is robustly detectable in single neuronal nuclei, where gene editing differences are stronger between cell subtypes than between cortical regions. Insufficient editing of autism-related genes in inhibitory neurons may manifest in the specific perturbation of these cells in autism.

scholarly journals Whole-transcriptome RNA editing analysis in single cortical neurons links locus 15q11 with psychiatric illness

2019 ◽  
Author(s):  
Brendan Robert E. Ansell ◽  
Simon N. Thomas ◽  
Roberto Bonelli ◽  
Jacob E. Munro ◽  
Saskia Freytag ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cortical Neurons ◽  
Serotonin Receptor ◽  
Target Genes ◽  
Linear Models ◽  
Inhibitory Neurons ◽  
Neuronal Nuclei ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cortical Regions

ABSTRACTBACKGROUNDConversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is essential for healthy brain development. This ‘RNA editing’ process is dysregulated in many neuropsychiatric diseases, but is little understood at the level of individual neurons.METHODSWe quantified RNA editing sites in full-length capture nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical post-mortem female donor. Putative editing sites were intersected with sites in bulk human tissue transcriptomes including healthy and neuropsychiatric brain tissue, and sites identified in single nuclei from unrelated brain donors. Differential editing between cell types and cortical regions, and individual sites and genes therein, was quantified using linear models. Associations between gene expression and editing were also tested.RESULTSWe identified 41,930 RNA editing sites with robust read coverage in at least ten neuronal nuclei. Most sites were located within Alu repeats in introns or 3’ UTRs, and approximately 80% were catalogued in published RNA editing databases. We identified 9285 putative novel RNA editing sites, 29% of which were also detectable neuronal transcriptomes from unrelated donors. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons. Among the strongest correlates of global editing rates were snoRNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2. We identified 29 genes preferentially edited in excitatory neurons and 44 genes edited more heavily in inhibitory neurons including RBFOX1, its target genes and small nucleolar RNA-associated genes in the autism-associated Prader-Willi locus 15q11. These results provide cell-type and spatial context for 1730 and 910 sites that are also edited in the brains of schizophrenic and autistic patients respectively, and a reference for future studies of RNA editing in single brain cells from these cohorts.CONCLUSIONSRNA editing, including thousands of previously unreported sites, is robustly detectable in single neuronal nuclei, where gene editing differences are stronger between cell subtypes than between cortical regions. Insufficient editing of ASD-related genes in inhibitory neurons may manifest in the specific perturbation of these cells in autism.

scholarly journals A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

2018 ◽  
Vol 4 (9) ◽  
pp. eaau6190 ◽  
Author(s):  
Alexey Kozlenkov ◽  
Junhao Li ◽  
Pasha Apontes ◽  
Yasmin L. Hurd ◽  
William M. Byne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Brain Cell ◽  
Inhibitory Neurons ◽  
Brain Diseases ◽  
Unique Role ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cell Type Specific

Brain function depends on interaction of diverse cell types whose gene expression and identity are defined, in part, by epigenetic mechanisms. Neuronal DNA contains two major epigenetic modifications, methylcytosine (mC) and hydroxymethylcytosine (hmC), yet their cell type–specific landscapes and relationship with gene expression are poorly understood. We report high-resolution (h)mC analyses, together with transcriptome and histone modification profiling, in three major cell types in human prefrontal cortex: glutamatergic excitatory neurons, medial ganglionic eminence–derived γ-aminobutyric acid (GABA)ergic inhibitory neurons, and oligodendrocytes. We detected a unique association between hmC and gene expression in inhibitory neurons that differed significantly from the pattern in excitatory neurons and oligodendrocytes. We also found that risk loci associated with neuropsychiatric diseases were enriched near regions of reduced hmC in excitatory neurons and reduced mC in inhibitory neurons. Our findings indicate differential roles for mC and hmC in regulation of gene expression in different brain cell types, with implications for the etiology of human brain diseases.

scholarly journals Implications of Extended Inhibitory Neuron Development

2021 ◽  
Vol 22 (10) ◽  
pp. 5113
Author(s):  
Jae-Yeon Kim ◽  
Mercedes F. Paredes
Keyword(s):  
Neural Circuit ◽  
Inhibitory Neuron ◽  
Postnatal Period ◽  
Specific Pattern ◽  
Inhibitory Neurons ◽  
Gabaergic Interneuron ◽  
Gabaergic Interneurons ◽  
Neuron Development ◽  
Cortical Regions ◽  
Circuit Formation

A prolonged developmental timeline for GABA (γ-aminobutyric acid)-expressing inhibitory neurons (GABAergic interneurons) is an amplified trait in larger, gyrencephalic animals. In several species, the generation, migration, and maturation of interneurons take place over several months, in some cases persisting after birth. The late integration of GABAergic interneurons occurs in a region-specific pattern, especially during the early postnatal period. These changes can contribute to the formation of functional connectivity and plasticity, especially in the cortical regions responsible for higher cognitive tasks. In this review, we discuss GABAergic interneuron development in the late gestational and postnatal forebrain. We propose the protracted development of interneurons at each stage (neurogenesis, neuronal migration, and network integration), as a mechanism for increased complexity and cognitive flexibility in larger, gyrencephalic brains. This developmental feature of interneurons also provides an avenue for environmental influences to shape neural circuit formation.

scholarly journals Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rebecca Rani Das Gupta ◽  
Louis Scheurer ◽  
Pawel Pelczar ◽  
Hendrik Wildner ◽  
Hanns Ulrich Zeilhofer
Keyword(s):  
Spinal Cord ◽  
Dorsal Horn ◽  
Functional Organization ◽  
Affinity Purification ◽  
Expression Patterns ◽  
Inhibitory Neurons ◽  
Dorsal Horn Neurons ◽  
Expression Of Genes ◽  
Excitatory Neurons ◽  
Genes Encoding

AbstractThe spinal dorsal horn harbors a sophisticated and heterogeneous network of excitatory and inhibitory neurons that process peripheral signals encoding different sensory modalities. Although it has long been recognized that this network is crucial both for the separation and the integration of sensory signals of different modalities, a systematic unbiased approach to the use of specific neuromodulatory systems is still missing. Here, we have used the translating ribosome affinity purification (TRAP) technique to map the translatomes of excitatory glutamatergic (vGluT2+) and inhibitory GABA and/or glycinergic (vGAT+ or Gad67+) neurons of the mouse spinal cord. Our analyses demonstrate that inhibitory and excitatory neurons are not only set apart, as expected, by the expression of genes related to the production, release or re-uptake of their principal neurotransmitters and by genes encoding for transcription factors, but also by a differential engagement of neuromodulator, especially neuropeptide, signaling pathways. Subsequent multiplex in situ hybridization revealed eleven neuropeptide genes that are strongly enriched in excitatory dorsal horn neurons and display largely non-overlapping expression patterns closely adhering to the laminar and presumably also functional organization of the spinal cord grey matter.

scholarly journals Mechanisms underlying contrast-dependent orientation selectivity in mouse V1

2018 ◽  
Vol 115 (45) ◽  
pp. 11619-11624 ◽  
Author(s):  
Wei P. Dai ◽  
Douglas Zhou ◽  
David W. McLaughlin ◽  
David Cai
Keyword(s):  
Large Scale ◽  
Feedback Inhibition ◽  
Orientation Selectivity ◽  
Inhibitory Neurons ◽  
Orientation Tuning ◽  
Response Properties ◽  
Firing Rates ◽  
Excitatory Neurons ◽  
Cortical Excitation ◽  
Contrast Invariance

Recent experiments have shown that mouse primary visual cortex (V1) is very different from that of cat or monkey, including response properties—one of which is that contrast invariance in the orientation selectivity (OS) of the neurons’ firing rates is replaced in mouse with contrast-dependent sharpening (broadening) of OS in excitatory (inhibitory) neurons. These differences indicate a different circuit design for mouse V1 than that of cat or monkey. Here we develop a large-scale computational model of an effective input layer of mouse V1. Constrained by experiment data, the model successfully reproduces experimentally observed response properties—for example, distributions of firing rates, orientation tuning widths, and response modulations of simple and complex neurons, including the contrast dependence of orientation tuning curves. Analysis of the model shows that strong feedback inhibition and strong orientation-preferential cortical excitation to the excitatory population are the predominant mechanisms underlying the contrast-sharpening of OS in excitatory neurons, while the contrast-broadening of OS in inhibitory neurons results from a strong but nonpreferential cortical excitation to these inhibitory neurons, with the resulting contrast-broadened inhibition producing a secondary enhancement on the contrast-sharpened OS of excitatory neurons. Finally, based on these mechanisms, we show that adjusting the detailed balances between the predominant mechanisms can lead to contrast invariance—providing insights for future studies on contrast dependence (invariance).

scholarly journals Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse

2020 ◽  
Author(s):  
Ziheng Zhou ◽  
Shuguang Wang ◽  
Dengwei Zhang ◽  
Xiaosen Jiang ◽  
Jie Li ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Single Cell ◽  
Developmental Trajectories ◽  
Expression Patterns ◽  
Development Stage ◽  
Inhibitory Neurons ◽  
Projection Neurons ◽  
Cerebral Cortex Development ◽  
Excitatory Neurons ◽  
Human And Mouse

AbstractBackgroundThe specification and differentiation of neocortical projection neurons is a complex process under precise molecular regulation; however, little is known about the similarities and differences in cerebral cortex development between human and mouse at single-cell resolution.ResultsHere, using single-cell RNA-seq (scRNA-seq) data we explore the divergence and conservation of human and mouse cerebral cortex development using 18,446 and 7,610 neocortical cells. Systematic cross-species comparison reveals that the overall transcriptome profile in human cerebral cortex is similar to that in mouse such as cell types and their markers genes. By single-cell trajectories analysis we find human and mouse excitatory neurons have different developmental trajectories of neocortical projection neurons, ligand-receptor interactions and gene expression patterns. Further analysis reveals a refinement of neuron differentiation that occurred in human but not in mouse, suggesting that excitatory neurons in human undergo refined transcriptional states in later development stage. By contrast, for glial cells and inhibitory neurons we detected conserved developmental trajectories in human and mouse.ConclusionsTaken together, our study integrates scRNA-seq data of cerebral cortex development in human and mouse, and uncovers distinct developing models in neocortical projection neurons. The earlier activation of cognition -related genes in human may explain the differences in behavior, learning or memory abilities between the two species.

scholarly journals Psychiatric pharmacogenomic testing in clinical practice

2010 ◽  
Vol 12 (1) ◽  
pp. 69-76 ◽  
Keyword(s):  
Cytochrome P450 ◽  
Clinical Practice ◽  
Serotonin Receptor ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Target Genes ◽  
European Ancestry ◽  
Cytochrome P450 2D6 ◽  
Drug Metabolizing Enzyme ◽  
Ultrarapid Metabolizers ◽  
P450 2D6

The clinical adoption of psychiatric pharmacogenomic testing has taken place rapidly over the past 7 years. Initially, drug-metabolizing enzyme genes, such as the cytochrome P450 2D6 gene (CYP2D6), were identified. Genotyping the highly variable cytochrome P450 2D6 gene now provides clinicians with the opportunity to identify both poor metabolizers and ultrarapid metabolizers of 2D6 substrate medications. Subsequently, genes influencing the pharmacodynamic response of medications have been made available for clinical practice. Among the earliest "target genes" was the serotonin transporter gene (SLC6A4) which has variants that have been shown to influence the clinical response of patients of European ancestry when they are treated with selective serotonin reuptake inhibitors. Genotyping of some of the serotonin receptor genes is also available to guide clinical practice. The quantification of the clinical utility of pharmacogenomic testing is evolving, and ethical considerations for testing have been established. Given the increasingly clear cost-effectiveness of genotyping, it has recently been predicted that pharmacogenomic testing will routinely be ordered to guide the selection and dosing of psychotropic medications.

scholarly journals Functional selectivity and specific connectivity of inhibitory neurons in primary visual cortex

2018 ◽  
Author(s):  
Petr Znamenskiy ◽  
Mean-Hwan Kim ◽  
Dylan R. Muir ◽  
Maria Florencia Iacaruso ◽  
Sonja B. Hofer ◽  
...  
Keyword(s):  
Visual Cortex ◽  
Primary Visual Cortex ◽  
Pyramidal Cells ◽  
Fine Tuning ◽  
Inhibitory Neurons ◽  
Local Network ◽  
Cortical Circuits ◽  
Sensory Stimuli ◽  
Excitatory Neurons ◽  
Strong Excitation

In the cerebral cortex, the interaction of excitatory and inhibitory synaptic inputs shapes the responses of neurons to sensory stimuli, stabilizes network dynamics1 and improves the efficiency and robustness of the neural code2–4. Excitatory neurons receive inhibitory inputs that track excitation5–8. However, how this co-tuning of excitation and inhibition is achieved by cortical circuits is unclear, since inhibitory interneurons are thought to pool the inputs of nearby excitatory cells and provide them with non-specific inhibition proportional to the activity of the local network9–13. Here we show that although parvalbumin-expressing (PV) inhibitory cells in mouse primary visual cortex make connections with the majority of nearby pyramidal cells, the strength of their synaptic connections is structured according to the similarity of the cells’ responses. Individual PV cells strongly inhibit those pyramidal cells that provide them with strong excitation and share their visual selectivity. This fine-tuning of synaptic weights supports co-tuning of inhibitory and excitatory inputs onto individual pyramidal cells despite dense connectivity between inhibitory and excitatory neurons. Our results indicate that individual PV cells are preferentially integrated into subnetworks of inter-connected, co-tuned pyramidal cells, stabilising their recurrent dynamics. Conversely, weak but dense inhibitory connectivity between subnetworks is sufficient to support competition between them, de-correlating their output. We suggest that the history and structure of correlated firing adjusts the weights of both inhibitory and excitatory connections, supporting stable amplification and selective recruitment of cortical subnetworks.

Epileptiform activity in microcultures containing one excitatory hippocampal neuron

1991 ◽  
Vol 65 (4) ◽  
pp. 761-770 ◽  
Author(s):  
M. M. Segal
Keyword(s):  
Action Potentials ◽  
Epileptiform Activity ◽  
Inhibitory Neuron ◽  
Excitatory Neuron ◽  
Inhibitory Neurons ◽  
Gamma Aminobutyric Acid ◽  
Intracellular Recordings ◽  
Voltage Fluctuations ◽  
Excitatory Neurons ◽  
Small Voltage

1. Paroxysmal depolarizing shifts (PDSs) occur during interictal epileptiform activity. Sustained depolarizations are characteristic of ictal activity, and events resembling PDSs also occur during the sustained depolarizations. To study these elements of epileptiform activity in a simpler context, I used the in vitro chronic-excitatory-block model of epilepsy of Furshpan and Potter and the microculture technique of Segal and Furshpan. 2. Intracellular recordings were made from 93 single-neuron microcultures. Forty of these solitary neurons were excitatory, their action potentials were replaced by PDS-like events or sustained depolarizations as kynurenate was removed from the perfusion solution. PDS-like events were similar to PDSs in intact cortex, mass cultures, and microcultures with more than one neuron. Small voltage fluctuations were also seen in solitary excitatory neurons in the absence of recorded action potentials. Sustained depolarizations developed in 5 of the 40 excitatory neurons. Forty-eight of the 93 solitary neurons were inhibitory, with bicuculline-sensitive hyperpolarizations after the action potential (ascribable to gamma-aminobutyric acid-A autapses). None of the solitary inhibitory neurons displayed sustained depolarizations. Five of the 93 neurons were insensitive to both kynurenate and bicuculline and were not placed in either the excitatory or the inhibitory category. 3. Both N-methyl-D-aspartate (NMDA) and non-NMDA glutamate receptors contributed to the PDS-like events and sustained depolarizations. Only a non-NMDA glutamate receptor component was evident for the small voltage fluctuations. 4. Intracellular recordings were also made from two-neuron microcultures, each containing one excitatory neuron and one inhibitory neuron. Sustained depolarizations developed in five microcultures, in each case only in the excitatory neuron.

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