Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-Species Single-cell Comparative Analysis of Amygdala

ABSTRACT: The amygdala or amygdala-like structure in the brain are found in all vertebrates, and plays a critical role for emotional processing. But the cellular architecture of amygdala and how they evolved are still elusive. Here, we generated single-nucleus RNA-sequencing data for more than 200,000 cells in human, macaque, mouse and chicken amygdala. Abundant neuronal cell types derived from different subnuclei of amygdala were identified in all datasets. Cross-species analyses revealed GABAergic neurons and GABAergic neuron-enriched subnuclei of amygdala were well-conserved in cellular composition and marker gene expression, whereas glutamatergic neuron-enriched subnuclei were relatively divergent. Furthermore, we discovered that LAMP5+ interneurons were much more numerous in primates, while DRD2+ GABAergic neurons, LAMP5+ and SATB2+ glutamatergic neurons were predominant in the human central amygdalar nucleus (CEA) and basolateral amygdala complex (BLA), respectively. In addition, we also identified GABAergic neuron-enriched subnuclei of amygdala in the chicken. Altogether, our study highlight extremely cell-type diversity in the amygdala across species and their species-specifc adaptations.

ORGANISM(S): Mus musculus Gallus gallus Homo sapiens Macaca mulatta

PROVIDER: GSE195445 | GEO | 2022/12/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gephyrin interacts with the K-Cl co-transporter KCC2 to regulate its surface expression and function in cortical neurons

Project description:The K+-Cl- co-transporter KCC2, encoded by the Slc12a5 gene, is a neuron-specific chloride extruder that tunes the strength and polarity of GABAA receptor-mediated transmission. Besides its canonical ion-transport function, KCC2 also regulates spinogenesis and excitatory synaptic function through interaction with a variety of molecular partners. KCC2 is enriched in the vicinity of both glutamatergic and GABAergic synapses, the activity of which in turn regulates its membrane stability and function. KCC2 interaction with submembrane actin cytoskeleton via 4.1N is known to control its anchoring in the vicinity of glutamatergic synapses on dendritic spines. However, the molecular determinants of KCC2 clustering near GABAergic synapses remain unknown. Here, we use proteomics to identify novel KCC2 interacting proteins in adult rat cortex. We identify both known and novel candidate KCC2 partners, including some involved in neuronal development and synaptic transmission. These include gephyrin, the main scaffolding molecule at GABAergic synapses. Gephyrin interaction with endogenous KCC2 was confirmed by immunoprecipitation from rat brain extracts. We show that gephyrin stabilizes plasmalemmal KCC2 and promotes its clustering, notably but not exclusively near GABAergic synapses, thereby controlling KCC2-mediated chloride extrusion. This study identifies gephyrin as a novel KCC2 anchoring molecule that regulates its membrane expression and function in cortical neurons.

2021-11-29 | PXD022412 | Pride

Cell-type based analysis of microRNA profiles in the mouse brain

Project description:MicroRNAs (miRNA) are implicated in brain development and function but the underlying mechanisms have been difficult to study in part due to cellular heterogeneity in neural circuits. To systematically analyze miRNA expression in neurons, we have established a miRNA tagging and affinity purification (miRAP) method that is targeted to cell types through the Cre-loxP binary system in mice. Our studies of the neocortex and cerebellum reveal the expression of a large fraction of known miRNAs with distinct profiles in glutamatergic and GABAergic neurons, and subtypes of GABAergic neurons. We further detected putative novel miRNAs, tissue or cell type-specific strand selection of miRNAs, and miRNA editing. Our method thus will facilitate a systematic analysis of miRNA expression and regulation in specific neuron types in the context of neuronal development, physiology, plasticity, pathology and disease models, and is generally applicable to other cell types and tissues. RNA was extracted from miRNA tagging samples(Ago2 IP or Myc IP), processed and sequenced on Illumina genome analyzer

2011-06-29 | E-GEOD-30286 | biostudies-arrayexpress

Axonal mRNA in human embryonic stem cell derived neurons

Project description:The identification of axonal mRNAs in model organisms has led to the discovery of many axonally translated proteins required for axon guidance and injury response. The extent to which these axonal mRNAs are conserved in humans is unknown. Here we report on the axonal transcriptome of glutamatergic neurons derived from human embryonic stem cells (hESC-neurons) grown in axon isolating microfluidic chambers. We identified mRNAs enriched in axons, representing a functionally unique local transcriptome as compared to the whole neuron transcriptome. Further, we found that the enriched functional categories within high confidence axonal transcripts resemble those in the axonal transcriptome of rat cortical neurons. Comparing our list of human axonal transcripts to similar datasets generated from embryonic and adult rat dorsal root ganglia and rat cortical neurons we found 60 mRNAs common to all four neuron types. We found that over half of these genes are associated with neurological phenotypes or diseases in model organisms and human. This data provides an important resource for studying local mRNA translation in human axons and has the potential to reveal both conserved and unique axonal mechanisms across species and neuronal types. We analyzed the axonal and whole hESC-neuron transcriptome in triplicate using the Affymetrix Human Gene 2.0 ST Array platform.

2016-07-29 | E-GEOD-84975 | biostudies-arrayexpress

ERK1/2 signaling and cortical interneuron development

Project description:We used RNA sequencing to profile the translatome of GABAergic neurons in P7.5 cortices in wildtype and Cre-directed ERK1/2 mutated animals. Using a Cre-dependent RiboTag approach, we enriched IP samples for cortical GABAergic neuron transcripts.

2022-06-25 | GSE206633 | GEO

EZH2-mediated H3K27me3 targets transcriptional circuits of neuronal differentiation ChIP-seq

Project description:Our work describes novel roles for EZH2 in the specification of cortical neurons. Previous reports established the current model of EZH2-mediated control of neuronal progenitors differentiation through the regulation of their proliferation and developmental transitions. We built on these findings and studied the role of EZH2 in post-mitotic glutamatergic neurons differentiated from embryonic stem cells, a particularly relevant cell type where the impact of its regulation has thus far remained elusive. Briefly, our key results can be summarized as follows: 1. The conditional deletion of EZH2 at the moment of cell cycle exit in neural progenitors allowed us to study the role of EZH2 selectively in post-mitotic glutamatergic neurons. 2. Time course transcriptomic and epigenomic analyses of H3K27me3 in absence of EZH2 revealed a significant dysregulation of transcriptional networks affecting synaptic plasticity, in particular long term depression. 3. These analyses also revealed potential novel roles of EZH2 in controlling the regulation between the glutamatergic signature and the GABAergic one, suggesting a mechanism entailing failure of Prdm13 repression, a histone methyltransferase with a known role in determining GABAergic neurons specification.

2022-03-28 | E-MTAB-11363 | biostudies-arrayexpress

EZH2-mediated H3K27me3 targets transcriptional circuits of neuronal differentiation

2022-04-18 | E-MTAB-11387 | biostudies-arrayexpress

Single cell RNA-sequencing in the mouse central amygdala (CEA)

Project description:The central amygdala (CEA) is a brain region that consists of primarily GABAergic neurons. It has been widely investigated for its role in many innate and adaptive behaviors, such as appetitive and defensive behaviors. Despite the complex functions of CEA, the molecular diversity of CEA neurons has not been systemically examined. Here, we performed single-cell RNA-sequencing (scRNA-Seq) in the CEA to classify the molecularly defined neuron types in this region.

2023-02-03 | GSE213828 | GEO

Translational Insights from Cell-type variation across Amygdala Subnuclei in Rhesus Monkeys and Humans

Project description:Theories of amygdala function are central to our understanding of psychiatric and neurodevelopmental disorders. However, our limited knowledge of the molecular and cellular composition of the amygdala impedes translational research aimed at developing new treatments and interventions. Here, we use single-nucleus RNA-sequencing from multiple amygdala subnuclei in both humans (n=3, Male) and rhesus macaques (n=3, Male) to begin to bridge the gap between preclinical rodent models and human disorders. Our results reveal substantial heterogeneity between regions, even when restricted to inhibitory or excitatory neurons. Consistent with prior work, our data highlight the complexities of individual marker genes for uniquely targeting specific cell-types. Cross-species analyses suggest the rhesus monkey model to be well-suited to understanding the human amygdala, but also identify limitations. For example, we identified a cell-cluster in the ventral lateral nucleus (vLA) of the amygdala that is enriched in humans, relative to rhesus macaques. Additionally, we identify specific cell-clusters with relative enrichment of disorder-related genes. These analyses point to the human-enriched vLa cell-cluster as relevant to ASD, potentially highlighting a vulnerability to neurodevelopmental disorders that has emerged in recent primate evolution. Further, we identified a cluster of cells expressing markers for intercalated cells (ITCs) that is enriched for genes reported in human genome-wide association studies of neuroticism, anxiety disorders, and depressive disorders. Together, these data shed light on the composition of the amygdala and identify specific cell-types that can be prioritized in basic science research to better understand human psychopathology and guide the development of potential treatments

2024-04-05 | GSE262905 | GEO

Single-nucleus transcriptional profiling of Gad2-positive neurons from the mouse lateral habenula with distinct expression of neurotransmitter-related genes

Project description:Glutamatergic projection neurons of the lateral habenula (LHb) effect behavioral statemodulation by regulating the activity of midbrain monoaminergic neurons. Identifying circuit mechanisms that control LHb output is of interest for understanding motivated behaviors. A small population of neurons within the medial subnucleus of the mouse LHb express the GABAergic synthesizing enzyme GAD2 and are capable of inhibiting nearby LHb projection neurons. However, these neurons lack most markers of classic inhibitory interneurons, and they co-express the vesicular glutamate transporter VGLUT2. To determine the molecular phenotype of these neurons, we genetically tagged the nuclei of GAD2-positive cells and used fluorescence-activated nuclear sorting followed by single nuclear RNA sequencing (FANS-snRNAseq) to determine the full transcriptional profile of GAD2+ neurons isolated from LHb. Our data demonstrate that LHb GAD2+ neurons co-express markers of both glutamatergic and GABAergic transmission and that they are transcriptionally distinct from GABAergic interneurons or habenular glutamatergic neurons. We show sex-specific differences in gene expression in this neuronal population and find that these gene sets are enriched for genes involved in depression. Finally, we identify the Ntng2 gene encoding the cell adhesion protein Netrin-G2 as a selective marker of LHb GAD2+ neurons that may contribute to their target projections. These data show the value of using genetic enrichment of rare cell types for transcriptome studies, and they advance understanding of the molecular composition of a functionally important class of neurons in the LHb.

2022-11-08 | GSE179198 | GEO

Mutation of a schizophrenia risk gene SETD1A alters neuronal network activity in human neurons through cAMP/PKA pathway

Project description:Using CRISPR/Cas9 to generate an hiPSC line with SETD1A haploinsufficiency and differentiating it into glutamatergic and GABAergic neurons, we found that SETD1A haploinsufficiency resulted in altered neuronal network activity, which was predominantly defined by increased network burst frequency, whereas unchanged global firing activity. In individual neurons, this network phenotype was reflected functionally by increased synchronized synaptic inputs and structurally by increased somatodendritic complexity in both glutamatergic and GABAergic neurons. The transcriptome profile in SETD1A haploinsufficient neurons demonstrated perturbations in gene sets associated with schizophrenia, synaptic transmission, and glutamatergic synaptic function. In addition, transcriptomic data suggested cAMP/PKA pathway might be disturbed in SETD1A haploinsufficient networks, which was further verified by pharmacological experiments.

2021-07-23 | GSE180648 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data