scholarly journals Sensory coding mechanisms revealed by optical tagging of physiologically defined neuronal types

Science ◽  
2019 ◽  
Vol 366 (6471) ◽  
pp. 1384-1389 ◽  
Author(s):  
Donghoon Lee ◽  
Maiko Kume ◽  
Timothy E. Holy
Keyword(s):  
Neural Circuit ◽  
Ectopic Expression ◽  
Cell Types ◽  
Specific Cell ◽  
Sensory Coding ◽  
Cell Type ◽  
Neuronal Types ◽  
A Cell ◽  
Circuit Function

Neural circuit analysis relies on having molecular markers for specific cell types. However, for a cell type identified only by its circuit function, the process of identifying markers remains laborious. We developed physiological optical tagging sequencing (PhOTseq), a technique for tagging and expression profiling of cells on the basis of their functional properties. PhOTseq was capable of selecting rare cell types and enriching them by nearly 100-fold. We applied PhOTseq to the challenge of mapping receptor-ligand pairings among pheromone-sensing neurons in mice. Together with in vivo ectopic expression of vomeronasal chemoreceptors, PhOTseq identified the complete combinatorial receptor code for a specific set of ligands.

scholarly journals A molecular logic of sensory coding revealed by optical tagging of physiologically-defined neuronal types

2019 ◽  
Author(s):  
Donghoon Lee ◽  
Maiko Kume ◽  
Timothy E Holy
Keyword(s):  
Neural Circuit ◽  
Strong Predictor ◽  
Ectopic Expression ◽  
Cell Types ◽  
Specific Cell ◽  
Molecular Logic ◽  
Neuronal Types ◽  
A Cell ◽  
Circuit Function

Neural circuit analysis relies on having molecular markers for specific cell types. However, for a cell type identified only by its circuit function, the process of identifying markers remains laborious. Here, we report physiological optical tagging sequencing (PhOTseq), a technique for tagging and expression-profiling cells based on their functional properties. We demonstrate that PhOTseq is capable of selecting rare cell types and enriching them by nearly one hundred-fold. We applied PhOTseq to the challenge of mapping receptor-ligand pairings among vomeronasal pheromone-sensing neurons in mice. Together with in vivo ectopic expression of vomeronasal chemoreceptors, PhOTseq identified the complete combinatorial receptor code for a specific set of ligands, and revealed that the primary sequence of a chemoreceptor was an unexpectedly strong predictor of functional similarity.

scholarly journals Rational reprogramming of cellular states by combinatorial perturbation

2018 ◽  
Author(s):  
Jialei Duan ◽  
Boxun Li ◽  
Minoti Bhakta ◽  
Shiqi Xie ◽  
Pei Zhou ◽  
...  
Keyword(s):  
Computational Analysis ◽  
Ectopic Expression ◽  
Cell Types ◽  
Specific Cell ◽  
Cell Type ◽  
Epicardial Cells ◽  
Organ Specific ◽  
A Cell ◽  
Cardiac System ◽  
Combinatorial Space

AbstractEctopic expression of transcription factors (TFs) can reprogram cell state. However, due to the large combinatorial space of possible TF cocktails, it remains difficult to identify TFs that reprogram specific cell types. Here, we develop Reprogram-Seq to experimentally screen thousands of TF cocktails for reprogramming performance. Reprogram-Seq leverages organ-specific cell atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Focusing on the cardiac system, we perform Reprogram-Seq on MEFs using an undirected library of 48 cardiac factors and separately on a directed library of 10 epicardial-related TFs. We identify a novel combination of 3 TFs which efficiently reprogram MEFs to epicardial-like cells that are transcriptionally, molecularly, morphologically, and functionally similar to primary epicardial cells. Reprogram-Seq holds promise to accelerate the generation of specific cell types for regenerative medicine.

scholarly journals Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens

2021 ◽  
Author(s):  
Hee-Dae Kim ◽  
Jing Wei ◽  
Tanessa Call ◽  
Nicole Teru Quintus ◽  
Alexander J. Summers ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Current Treatment ◽  
Specific Cell ◽  
Excitatory Synapses ◽  
Cell Type ◽  
Cell Type Specific ◽  
Specific Regulation ◽  
Circuit Function

AbstractDepression is the leading cause of disability and produces enormous health and economic burdens. Current treatment approaches for depression are largely ineffective and leave more than 50% of patients symptomatic, mainly because of non-selective and broad action of antidepressants. Thus, there is an urgent need to design and develop novel therapeutics to treat depression. Given the heterogeneity and complexity of the brain, identification of molecular mechanisms within specific cell-types responsible for producing depression-like behaviors will advance development of therapies. In the reward circuitry, the nucleus accumbens (NAc) is a key brain region of depression pathophysiology, possibly based on differential activity of D1- or D2- medium spiny neurons (MSNs). Here we report a circuit- and cell-type specific molecular target for depression, Shisa6, recently defined as an AMPAR component, which is increased only in D1-MSNs in the NAc of susceptible mice. Using the Ribotag approach, we dissected the transcriptional profile of D1- and D2-MSNs by RNA sequencing following a mouse model of depression, chronic social defeat stress (CSDS). Bioinformatic analyses identified cell-type specific genes that may contribute to the pathogenesis of depression, including Shisa6. We found selective optogenetic activation of the ventral tegmental area (VTA) to NAc circuit increases Shisa6 expression in D1-MSNs. Shisa6 is specifically located in excitatory synapses of D1-MSNs and increases excitability of neurons, which promotes anxiety- and depression-like behaviors in mice. Cell-type and circuit-specific action of Shisa6, which directly modulates excitatory synapses that convey aversive information, identifies the protein as a potential rapid-antidepressant target for aberrant circuit function in depression.

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 CD300LF Polymorphisms of Inbred Mouse Strains Confer Resistance to Murine Norovirus Infection in a Cell Type-Dependent Manner

2020 ◽  
Vol 94 (17) ◽  
Author(s):  
Kevin Furlong ◽  
Scott B. Biering ◽  
Jayoung Choi ◽  
Craig B. Wilen ◽  
Robert C. Orchard ◽  
...  
Keyword(s):  
Cell Types ◽  
Host Cells ◽  
Mouse Strains ◽  
Specific Cell ◽  
Dependent Manner ◽  
Murine Norovirus ◽  
Cell Type ◽  
Human Norovirus ◽  
A Cell ◽  
Cell Type Specific

ABSTRACT Human norovirus is the leading cause of gastroenteritis worldwide, yet basic questions about its life cycle remain unanswered due to an historical lack of robust experimental systems. Recent studies on the closely related murine norovirus (MNV) have identified CD300LF as an indispensable entry factor for MNV. We compared the MNV susceptibilities of cells from different mouse strains and identified polymorphisms in murine CD300LF which are critical for its function as an MNV receptor. Bone marrow-derived macrophages (BMDMs) from I/LnJ mice were resistant to infection from multiple MNV strains which readily infect BMDMs from C57BL/6J mice. The resistance of I/LnJ BMDMs was specific to MNV, since the cells supported infection of other viruses comparably to C57BL/6J BMDMs. Transduction of I/LnJ BMDMs with C57BL/6J CD300LF made the cells permissible to MNV infection, suggesting that the cause of resistance lies in the entry step of MNV infection. In fact, we mapped this phenotype to a 4-amino-acid difference at the CC′ loop of CD300LF; swapping of these amino acids between C57BL/6J and I/LnJ CD300LF proteins made the mutant C57BL/6J CD300LF functionally impaired and the corresponding mutant of I/LnJ CD300LF functional as an MNV entry factor. Surprisingly, expression of the I/LnJ CD300LF in other cell types made the cells infectible by MNV, even though the I/LnJ allele did not function as an MNV receptor in macrophage-like cells. Correspondingly, I/LnJ CD300LF bound MNV virions in permissive cells but not in nonpermissive cells. Collectively, our data suggest the existence of a cell type-specific modifier of MNV entry. IMPORTANCE MNV is a prevalent model system for studying human norovirus, which is the leading cause of gastroenteritis worldwide and thus a sizeable public health burden. Elucidating mechanisms underlying susceptibility of host cells to MNV infection can lead to insights on the roles that specific cell types play during norovirus pathogenesis. Here, we show that different alleles of the proteinaceous receptor for MNV, CD300LF, function in a cell type-dependent manner. In contrast to the C57BL/6J allele, which functions as an MNV entry factor in all tested cell types, including human cells, I/LnJ CD300LF does not function as an MNV entry factor in macrophage-like cells but does allow MNV entry in other cell types. Together, these observations indicate the existence of cell type-specific modifiers of CD300LF-dependent MNV entry.

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 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 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.

Contact guidance on microfabricated substrata: the response of teleost fin mesenchyme cells to repeating topographical patterns

1988 ◽  
Vol 90 (4) ◽  
pp. 667-681 ◽  
Author(s):  
A. Wood
Keyword(s):  
Cell Types ◽  
Cell Type ◽  
Fibroblastic Cell ◽  
Tissue Component ◽  
Flat Surfaces ◽  
Mesenchymal Tissue ◽  
Computer Aided Analysis ◽  
A Cell ◽  
Mesenchyme Cells

The mesenchymal tissue component of the teleost pectoral fin bud has been explanted onto microfabricated quartz discs containing patterns of regular grooves of dimensions similar to those encountered by contact-guided cells in the intact fin system. Computer-aided analysis of cell migration on five separate patterns, from 1.8 to 7.4 microns repeat spacing, revealed that migration was predominantly aligned parallel to the long axis of the grooves, with individual cells becoming highly polarized, and the highest index of alignment (3.7) produced on the widest repeat spacings. When these cells are cultured on planar quartz, which is both chemically and physically isotropic, they flatten and adopt a morphology similar to that shown by cultured fibroblastic cell types on flat surfaces, suggesting that fin mesenchymal cells are not intrinsically predisposed to adopt an arborized morphology, like that observed in the intact fin bud. These results clearly demonstrate a directional migration in response to substratum topography, from a cell type known to be contact guided in vivo, and in the complete absence of adhesive heterogeneities.

scholarly journals Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina

Development ◽  
2020 ◽  
Vol 147 (14) ◽  
pp. dev187922 ◽  
Author(s):  
Candace S. Y. Chan ◽  
Nicolas Lonfat ◽  
Rong Zhao ◽  
Alexander E. Davis ◽  
Liang Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Cell Types ◽  
Retinal Cell ◽  
Mouse Retina ◽  
Cell Type ◽  
Specific Expression ◽  
Regulatory Modules ◽  
A Cell

ABSTRACTTranscription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.

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