scholarly journals Deciphering how specialized interneuron-specific cell types contribute to circuit function

2020 ◽  
Author(s):  
Alexandre Guet-McCreight ◽  
Frances K Skinner
Keyword(s):  
Computational Models ◽  
Brain Area ◽  
Pyramidal Cells ◽  
Cell Types ◽  
Specific Cell ◽  
Cell Type ◽  
Inhibitory Cell ◽  
Cell Firing ◽  
The Brain

AbstractThe wide diversity of inhibitory cells across the brain makes them fit to contribute to network dynamics in specialized fashions. However, the contributions of a particular inhibitory cell type in a behaving animal is challenging to decipher as one needs to both record cellular activities and identify the cell type being recorded. Thus, using computational modeling to explore cell-specific contributions so as to predict and hypothesize functional contributions is desirable. Here we examine potential contributions of interneuron-specific 3 (I-S3) cells - a type of inhibitory interneuron found in CA1 hippocampus that only targets other inhibitory interneurons - during simulated theta rhythms. We use previously developed multi-compartment models of oriens lacunosum-moleculare (OLM) cells, the main target of I-S3 cells, and explore how I-S3 cell inputs during in vitro and in vivo scenarios contribute to theta. We find that I-S3 cells suppress OLM cell spiking, rather than engender its spiking via post-inhibitory rebound mechanisms. To elicit recruitment similar to experiment, the inclusion of disinhibited pyramidal cell inputs is necessary, suggesting that I-S3 cell firing can broaden the window for disinhibiting pyramidal cells. Using in vivo virtual networks, we show that I-S3 cells can contribute to a sharpening of OLM cell recruitment at theta frequencies. Further, a shifting of the timing of I-S3 cell spiking due to external modulation can shift the timing of the OLM cell firing and thus disinhibitory windows. We thus propose a specialized contribution of I-S3 cells to create temporally precise coordination of modulation pathways.Significance StatementHow information is processed across different brain structures is an important question that relates to the different functions that the brain performs. In this work we use computational models that focus on a particular inhibitory cell type that only inhibits other inhibitory cell types – the I-S3 cell in the hippocampus. We show that this cell type is able to broaden the window for disinhibition of excitatory cells. We further illustrate that this broadening presents itself as a mechanism for input pathway switching and modulation over the timing of inhibitory cell spiking. Overall, this work contributes to our knowledge of how coordination between sensory and memory consolidation information is attained in a brain area that is involved in memory formation.

scholarly journals A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 103-110 ◽  
Author(s):  
Zizhen Yao ◽  
Hanqing Liu ◽  
Fangming Xie ◽  
Stephan Fischer ◽  
Ricky S. Adkins ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Primary Motor Cortex ◽  
Neuronal Cell ◽  
Pyramidal Cells ◽  
Cell Types ◽  
Regulatory Elements ◽  
Marker Genes ◽  
Specific Cell ◽  
Cell Type ◽  
The Brain

AbstractSingle-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1–3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas—containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities—is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.

scholarly journals Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition

2019 ◽  
Author(s):  
Laura E. Sanman ◽  
Ina W. Chen ◽  
Jake M. Bieber ◽  
Veronica Steri ◽  
Byron Hann ◽  
...  
Keyword(s):  
Quantitative Imaging ◽  
Cell Types ◽  
Culture Conditions ◽  
Tissue Cell ◽  
Specific Cell ◽  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Coordinate Changes

AbstractRenewing tissues have the remarkable ability to continually produce both proliferative progenitor and specialized differentiated cell-types. How are complex milieus of microenvironmental signals interpreted to coordinate tissue cell-type composition? Here, we develop a high-throughput approach that combines organoid technology and quantitative imaging to address this question in the context of the intestinal epithelium. Using this approach, we comprehensively survey enteroid responses to individual and paired perturbations to eight epithelial signaling pathways. We uncover culture conditions that enrich for specific cell-types, including Lgr5+ stem and enteroendocrine cells. We analyze interactions between perturbations and dissect mechanisms underlying an unexpected mutual antagonism between EGFR and IL-4 signals. Finally, we show that, across diverse perturbations, modulating proliferation of transit-amplifying cells also consistently changes the composition of differentiated secretory and absorptive cell-types. This property is conserved in vivo and can arise from differential amplification of secretory and absorptive progenitor cells. Taken together, the observations highlight an underappreciated role for transit-amplifying cells in which proliferation of these short-lived progenitors provides a lineage-based mechanism for tuning differentiated cell-type composition.

scholarly journals Cell type-specific biotin labeling in vivo resolves regional neuronal proteomic differences in mouse brain

2021 ◽  
Author(s):  
Sruti Rayaprolu ◽  
Sara Bitarafan ◽  
Ranjita Betarbet ◽  
Sydney N Sunna ◽  
Lihong Cheng ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Neurological Diseases ◽  
Neuronal Cell ◽  
Cell Types ◽  
Proteomic Profiling ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific ◽  
The Brain

Isolation and proteomic profiling of brain cell types, particularly neurons, pose several technical challenges which limit our ability to resolve distinct cellular phenotypes in neurological diseases. Therefore, we generated a novel mouse line that enables cell type-specific expression of a biotin ligase, TurboID, via Cre-lox strategy for in vivo proximity-dependent biotinylation of proteins. Using adenoviral-based and transgenic approaches, we show striking protein biotinylation in neuronal cell bodies and axons throughout the mouse brain. We quantified more than 2,000 neuron-derived proteins following enrichment that mapped to numerous subcellular compartments. Synaptic, transmembrane transporters, ion channel subunits, and disease-relevant druggable targets were among the most significantly enriched proteins. Remarkably, we resolved brain region-specific proteomic profiles of Camk2a neurons with distinct functional molecular signatures and disease associations that may underlie regional neuronal vulnerability. Leveraging the neuronal specificity of this in vivo biotinylation strategy, we used an antibody-based approach to uncover regionally unique patterns of neuron-derived signaling phospho-proteins and cytokines, particularly in the cortex and cerebellum. Our work provides a proteomic framework to investigate cell type-specific mechanisms driving physiological and pathological states of the brain as well as complex tissues beyond the brain.

scholarly journals Transposon-mediated, cell type-specific transcription factor recording in the mouse brain

2019 ◽  
Author(s):  
Alexander J. Cammack ◽  
Arnav Moudgil ◽  
Tomas Lagunas ◽  
Michael J. Vasek ◽  
Mark Shabsovich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Mouse Tissue ◽  
Specific Cell ◽  
Cell Type ◽  
Cell Fate Decisions ◽  
Cell Type Specific ◽  
The Brain

AbstractTranscription factors (TFs) play a central role in the regulation of gene expression, controlling everything from cell fate decisions to activity dependent gene expression. However, widely-used methods for TF profiling in vivo (e.g. ChIP-seq) yield only an aggregated picture of TF binding across all cell types present within the harvested tissue; thus, it is challenging or impossible to determine how the same TF might bind different portions of the genome in different cell types, or even to identify its binding events at all in rare cell types in a complex tissue such as the brain. Here we present a versatile methodology, FLEX Calling Cards, for the mapping of TF occupancy in specific cell types from heterogenous tissues. In this method, the TF of interest is fused to a hyperactive piggyBac transposase (hypPB), and this bipartite gene is delivered, along with donor transposons, to mouse tissue via a Cre-dependent adeno-associated virus (AAV). The fusion protein is expressed in Cre-expressing cells where it inserts transposon “Calling Cards” near to TF binding sites. These transposons permanently mark TF binding events and can be mapped using high-throughput sequencing. Alternatively, unfused hypPB interacts with and records the binding of the super enhancer (SE)-associated bromodomain protein, Brd4. To demonstrate the FLEX Calling Card method, we first show that donor transposon and transposase constructs can be efficiently delivered to the postnatal day 1 (P1) mouse brain with AAV and that insertion profiles report TF occupancy. Then, using a Cre-dependent hypPB virus, we show utility of this tool in defining cell type-specific TF profiles in multiple cell types of the brain. This approach will enable important cell type-specific studies of TF-mediated gene regulation in the brain and will provide valuable insights into brain development, homeostasis, and disease.

scholarly journals Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing

2017 ◽  
Author(s):  
Mari Mito ◽  
Mitsutaka Kadota ◽  
Kaori Tanaka ◽  
Yasuhide Furuta ◽  
Kuniya Abe ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Cortical Neurons ◽  
Expression Profiles ◽  
Cell Types ◽  
Epigenetic Modifications ◽  
Specific Cell ◽  
Cell Type ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Cell Type Specific

AbstractBackgroundThe nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq).ResultsFLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3—an active promoter mark—allowed us to survey neuron-specific coding and non-coding transcripts. Indeed, tChIP-Seq identified hundreds of genes associated with neuronal functions and genes with unknown functions expressed in cortical neurons.ConclusionstChIP-Seq thus provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.

scholarly journals Combined Effects of Surface Morphology and Mechanical Straining Magnitudes on the Differentiation of Mesenchymal Stem Cells without Using Biochemical Reagents

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Ji-Yeon Jang ◽  
Shi Woo Lee ◽  
So Hee Park ◽  
Ji Won Shin ◽  
ChiWoong Mun ◽  
...  
Keyword(s):  
Tensile Strain ◽  
Cell Types ◽  
Residual Effects ◽  
Specific Cell ◽  
Combined Effects ◽  
Cell Type ◽  
Surface Geometry ◽  
Strain Magnitude ◽  
Msc Differentiation

Existing studies examining the control of mesenchymal stem cell (MSC) differentiation into desired cell types have used a variety of biochemical reagents such as growth factors despite possible side effects. Recently, the roles of biomimetic microphysical environments have drawn much attention in this field. We studied MSC differentiation and changes in gene expression in relation to osteoblast-like cell and smooth muscle-like cell type resulting from various microphysical environments, including differing magnitudes of tensile strain and substrate geometries for 8 days. In addition, we also investigated the residual effects of those selected microphysical environment factors on the differentiation by ceasing those factors for 3 days. The results of this study showed the effects of the strain magnitudes and surface geometries. However, the genes which are related to the same cell type showed different responses depending on the changes in strain magnitude and surface geometry. Also, different responses were observed three days after the straining was stopped. These data confirm that controlling microenvironments so that they mimic those in vivo contributes to the differentiation of MSCs into specific cell types. And duration of straining engagement was also found to play important roles along with surface geometry.

scholarly journals Cellular Targeting of Oligonucleotides by Conjugation with Small Molecules

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5963
Author(s):  
Manuel Hawner ◽  
Christian Ducho
Keyword(s):  
Small Molecules ◽  
Cell Types ◽  
Target Cells ◽  
Specific Cell ◽  
Cell Type ◽  
Drug Candidates ◽  
Cellular Targeting ◽  
Related Proteins ◽  
High Polarity

Drug candidates derived from oligonucleotides (ON) are receiving increased attention that is supported by the clinical approval of several ON drugs. Such therapeutic ON are designed to alter the expression levels of specific disease-related proteins, e.g., by displaying antigene, antisense, and RNA interference mechanisms. However, the high polarity of the polyanionic ON and their relatively rapid nuclease-mediated cleavage represent two major pharmacokinetic hurdles for their application in vivo. This has led to a range of non-natural modifications of ON structures that are routinely applied in the design of therapeutic ON. The polyanionic architecture of ON often hampers their penetration of target cells or tissues, and ON usually show no inherent specificity for certain cell types. These limitations can be overcome by conjugation of ON with molecular entities mediating cellular ‘targeting’, i.e., enhanced accumulation at and/or penetration of a specific cell type. In this context, the use of small molecules as targeting units appears particularly attractive and promising. This review provides an overview of advances in the emerging field of cellular targeting of ON via their conjugation with small-molecule targeting structures.

scholarly journals Linking minimal and detailed models of CA1 microcircuits reveals how theta rhythms emerge and how their frequencies are controlled

2020 ◽  
Author(s):  
Alexandra P Chatzikalymniou ◽  
Melisa Gumus ◽  
Anton R Lunyov ◽  
Scott Rich ◽  
Jeremie Lefebvre ◽  
...  
Keyword(s):  
Pyramidal Cell ◽  
Theta Rhythm ◽  
Computational Models ◽  
Pyramidal Cells ◽  
Cell Types ◽  
Minimal Models ◽  
Detailed Model ◽  
Theta Frequency ◽  
Hippocampal Theta

AbstractThe wide variety of cell types and their inherent biophysical complexities pose a challenge to our understanding of oscillatory activities produced by cellular-based computational models. This challenge stems from the high-dimensional and multi-parametric nature of these systems. To overcome this issue, we implement systematic comparisons of minimal and detailed models of CA1 microcircuits that generate intra-hippocampal theta rhythms (3-12 Hz). We leverage insights from minimal models to guide detailed model explorations and obtain a cellular perspective of theta generation. Our findings distinguish the pyramidal cells as the theta rhythm initiators and reveal that their activity is regularized by the inhibitory cell populations, supporting an ‘inhibition-based tuning’ mechanism. We find a strong correlation between the pyramidal cell input current and the resulting LFP theta frequency, establishing that the intrinsic pyramidal cell properties underpin network frequency characteristics. This work provides a cellular-based foundation from which in vivo theta activities can be explored.

scholarly journals An intein-split transactivator for intersectional neural imaging and optogenetic manipulation

2021 ◽  
Author(s):  
Hao-Shan Chen ◽  
Xiao-Long Zhang ◽  
Rong-Rong Yang ◽  
Guang-Ling Wang ◽  
Xin-Yue Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Types ◽  
Specific Cell ◽  
Control Gene ◽  
Cell Type ◽  
Neural Imaging ◽  
Control Gene Expression ◽  
Numerous Cell ◽  
Marker Location

The complexity of brain circuitry is manifested by numerous cell types based on genetic marker, location and neural connectivity. Cell-type specific recording and manipulation is essential to disentangle causal neural mechanisms in physiology and behavior; however, many current approaches are largely limited by number of intersectional features, incompatibility of common effectors and insufficient gene expression. To tackle these limitations, we devise an intein-based intersectional synthesis of transactivator (IBIST) to selectively control gene expression of common effectors in specific cell types defined by a combination of multiple features. We validate the specificity and sufficiency of IBIST to control common effectors including fluorophores, optogenetic opsins and Ca2+ indicators in various intersectional conditions in vivo. Using IBIST-based Ca2+ imaging, we show that the IBIST can intersect up to five features, and that hippocampal cells tune differently to distinct emotional valences depending on the pattern of projection targets. Collectively, the IBIST multiplexes the capability to intersect cell-type features and is compatible with common effectors to effectively control gene expression, monitor and manipulate neural activities.

scholarly journals A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data

2020 ◽  
Author(s):  
Francoise Mazet ◽  
Marcus J. Tindall ◽  
Jonathan M. Gibbins ◽  
Michael J. Fry
Keyword(s):  
Experimental Data ◽  
Rate Constants ◽  
Computational Models ◽  
Cell Types ◽  
Specific Cell ◽  
Cell Type ◽  
Kinetic Rate ◽  
Kinetic Rate Constants ◽  
Model Predictions ◽  
Single Cell Type

AbstractThe phosphatidylinositol (PI) cycle is central to eukaryotic cell signaling. Its complexity, due to the number of reactions and lipid and inositol phosphate intermediates involved makes it difficult to analyze experimentally. Computational modelling approaches are seen as a way forward to elucidate complex biological regulatory mechanisms when this cannot be achieved solely through experimental approaches. Whilst mathematical modelling is well established in informing biological systems, many models are often informed by data sourced from different cell types (mosaic data), to inform model parameters. For instance, kinetic rate constants are often determined from purified enzyme data in vitro or use experimental concentrations obtained from multiple unrelated cell types. Thus they do not represent any specific cell type nor fully capture cell specific behaviours. In this work, we develop a model of the PI cycle informed by in-vivo omics data taken from a single cell type, namely platelets. Our model recapitulates the known experimental dynamics before and after stimulation with different agonists and demonstrates the importance of lipid- and protein-binding proteins in regulating second messenger outputs. Furthermore, we were able to make a number of predictions regarding the regulation of PI cycle enzymes and the importance of the number of receptors required for successful GPCR signaling. We then consider how pathway behavior differs, when fully informed by data for HeLa cells and show that model predictions remain relatively consistent. However, when informed by mosaic experimental data model predictions greatly vary. Our work illustrates the risks of using mosaic datasets from unrelated cell types which leads to over 75% of outputs not fitting with expected behaviors.Authors summaryComputational models of cellular complexity offer much in terms of understanding cell behaviors and in informing experimental design, but their usefulness is limited in them being built with mosaic data not representing specific cell types and tested against limited experimental outputs. In this work we demonstrate an approach using quantitative proteomic datasets and temporal experimental data from a single cell type (platelets) to inform kinetic rate constants and protein concentrations for a mathematical model of a key signaling pathway - the phosphatidylinositol (PI) cycle; known for its central role in numerous cell functions and diseases. After using our model to make novel predictions regarding how aspects of the pathway are regulated, we demonstrate its versatile nature by utilising proteomic data from other cell types to generate similar predictions for those cells while highlighting the pitfalls of using mosaic data when constructing computational models.

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