scholarly journals Molecular and genetic approaches for assaying human cell type synaptic connectivity

2020 ◽  
Author(s):  
Mean-Hwan Kim ◽  
Cristina Radaelli ◽  
Elliot R. Thomsen ◽  
Joseph T. Mahoney ◽  
Brian Long ◽  
...  
Keyword(s):  
Brain Slice ◽  
Cell Type ◽  
Functional Studies ◽  
Brain Circuits ◽  
Genetic Labeling ◽  
Post Hoc ◽  
Excised Tissue ◽  
Specific Neuron ◽  
Cortical Slices ◽  
Local Brain

ABSTRACTProspective and post-hoc molecular identification of specific neuron types is essential for functional studies of cellular and synaptic properties. We demonstrate a thick brain slice mFISH technique applied to multi-patch-clamp recordings in human cortical slices obtained from neurosurgical-excised tissue to reveal the molecular and morpho-electric properties of synaptically connected neurons, both with and without prospective AAV based genetic labeling. This “quadruple modality” methodology should be extensible to other local brain circuits in many organisms.

scholarly journals Cell type-specific pharmacology of NMDA receptors using masked MK801

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Yunlei Yang ◽  
Peter Lee ◽  
Scott M Sternson
Keyword(s):  
Synaptic Plasticity ◽  
Ion Channels ◽  
Signaling Pathways ◽  
Drug Addiction ◽  
Neuronal Population ◽  
Dopamine Neurons ◽  
Synaptic Potentiation ◽  
Cell Type ◽  
Brain Circuits ◽  
Cell Type Specific

N-Methyl-D-aspartate receptors (NMDA-Rs) are ion channels that are important for synaptic plasticity, which is involved in learning and drug addiction. We show enzymatic targeting of an NMDA-R antagonist, MK801, to a molecularly defined neuronal population with the cell-type-selectivity of genetic methods and the temporal control of pharmacology. We find that NMDA-Rs on dopamine neurons are necessary for cocaine-induced synaptic potentiation, demonstrating that cell type-specific pharmacology can be used to dissect signaling pathways within complex brain circuits.

scholarly journals Highly efficient and super-bright neurocircuit tracing using vector mixing-based virus cocktail

2019 ◽  
Author(s):  
Pei Sun ◽  
Sen Jin ◽  
Sijue Tao ◽  
Junjun Wang ◽  
Anan Li ◽  
...  
Keyword(s):  
Brain Function ◽  
Individual Cell ◽  
Brain Regions ◽  
Cell Type ◽  
Current Standard ◽  
Functional Studies ◽  
Highly Efficient ◽  
Order Of Magnitude ◽  
Cell Type Specific ◽  
Dependent Vector

ABSTRACTMapping the detailed cell-type-specific input networks and neuronal projectomes are essential to understand brain function in normal and pathological states. However, several properties of current tracing systems, including labeling sensitivity, trans-synaptic efficiencies, reproducibility among different individuals and different Cre-driver animals, still remained unsatisfactory. Here, we developed MAP-ENVIVIDERS, a recombinase system-dependent vector mixing-based strategy for highly efficient neurocircuit tracing. MAP-ENVIVIDERS enhanced tracing efficiency of input networks across the whole brain, with over 10-fold improvement in diverse previously poor-labeled input brain regions and particularly, up to 70-fold enhancement in brainstem compared with the current standard rabies-virus-mediated systems. MAP-ENVIVIDERS was over 10-fold more sensitive for cell-type-specific labeling than previous strategies, enabling us to capture individual cell-type-specific neurons with extremely complex axonal branches and presynaptic axonal boutons, both about one order of magnitude than previously reported and considered. MAP-ENVIVIDERS provides powerful tools for deconstructing novel input/output circuitry towards functional studies and disorders-related mechanisms.

scholarly journals Light Up the Brain: The Application of Optogenetics in Cell-Type Specific Dissection of Mouse Brain Circuits

2020 ◽  
Vol 14 ◽  
Author(s):  
Candice Lee ◽  
Andreanne Lavoie ◽  
Jiashu Liu ◽  
Simon X. Chen ◽  
Bao-hua Liu
Keyword(s):  
Mouse Brain ◽  
Cell Type ◽  
Brain Circuits ◽  
Cell Type Specific ◽  
The Brain

scholarly journals Cardiac cell type–specific gene regulatory programs and disease risk association

2021 ◽  
Vol 7 (20) ◽  
pp. eabf1444
Author(s):  
James D. Hocker ◽  
Olivier B. Poirion ◽  
Fugui Zhu ◽  
Justin Buchanan ◽  
Kai Zhang ◽  
...  
Keyword(s):  
Disease Risk ◽  
Cell Types ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Dependent Manner ◽  
Cardiac Cell ◽  
Limited Information ◽  
Cell Type ◽  
Functional Studies ◽  
Cell Type Specific

Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease–associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type–specific gene regulation in human hearts during health and disease.

scholarly journals Transcriptional Studies on Trypanosoma cruzi – Host Cell Interactions: A Complex Puzzle of Variables

2021 ◽  
Vol 11 ◽  
Author(s):  
María Gabriela Libisch ◽  
Natalia Rego ◽  
Carlos Robello
Keyword(s):  
Trypanosoma Cruzi ◽  
Host Cell ◽  
Protozoan Parasite ◽  
Cell Interactions ◽  
Host Cells ◽  
Molecular Signaling ◽  
Cell Type ◽  
Experimental Conditions ◽  
Functional Studies ◽  
Host Cell Interactions

Chagas Disease, caused by the protozoan parasite Trypanosoma cruzi, affects nearly eight million people in the world. T. cruzi is a complex taxon represented by different strains with particular characteristics, and it has the ability to infect and interact with almost any nucleated cell. The T. cruzi-host cell interactions will trigger molecular signaling cascades in the host cell that will depend on the particular cell type and T. cruzi strain, and also on many different experimental variables. In this review we collect data from multiple transcriptomic and functional studies performed in different infection models, in order to highlight key differences between works that in our opinion should be addressed when comparing and discussing results. In particular, we focus on changes in the respiratory chain and oxidative phosphorylation of host cells in response to infection, which depends on the experimental model of T. cruzi infection. Finally, we also discuss host cell responses which reiterate independently of the strain, cell type and experimental conditions.

scholarly journals RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications

2019 ◽  
Author(s):  
Ali Cetin ◽  
Shenqin Yao ◽  
Ben Ouellette ◽  
Pooja Balaram ◽  
Thomas Zhou ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Viral Vectors ◽  
Molecular Tools ◽  
Morphological Reconstruction ◽  
Functional Studies ◽  
Two Photon ◽  
Brain Circuits ◽  
Physiological Properties ◽  
Inducible Protein ◽  
And Function

AbstractBrain circuits are composed of vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow highly specific targeting of individual neurons for structural and functional studies, we modified three site-specific DNA recombinases, Cre, Dre and Flp, by combining them with a fungal light-inducible protein, Vivid, so that their recombinase activities can be driven by blue light. We generated viral vectors to express these light-inducible recombinases and demonstrated that they can induce genomic modifications in dense or sparse populations of neurons in live mouse brains controlled by one-photon or two-photon light induction. As an important application, we showed that light-inducible recombinases can produce highly targeted, sparse and strong labeling of individual neurons thereby enabling whole-brain morphological reconstruction to identify their axonal projection specificity. In addition to targeting cortical brain areas, we applied the method in deep targets, with a demonstration of functional calcium imaging. These molecular tools enable spatiotemporally-precise, targeted genomic modifications that will greatly facilitate detailed analysis of neural circuits and linking genetic identity, morphology, connectivity and function.

scholarly journals Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Marta Florio ◽  
Michael Heide ◽  
Anneline Pinson ◽  
Holger Brandl ◽  
Mareike Albert ◽  
...  
Keyword(s):  
Human Evolution ◽  
Expression Profiles ◽  
Neural Progenitor Cell ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Protein Coding ◽  
Functional Studies ◽  
Basal Progenitor ◽  
Stem And Progenitor Cells ◽  
Human Specific

Understanding the molecular basis that underlies the expansion of the neocortex during primate, and notably human, evolution requires the identification of genes that are particularly active in the neural stem and progenitor cells of the developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. We show that 15 human-specific genes exhibit such expression, and many of them evolved distinct neural progenitor cell-type expression profiles and levels compared to their ancestral paralogs. Functional studies on one such gene, NOTCH2NL, demonstrate its ability to promote basal progenitor proliferation in mice. An additional 35 human genes with progenitor-enriched expression are shown to have orthologs only in primates. Our study provides a resource of genes that are promising candidates to exert specific, and novel, roles in neocortical development during primate, and notably human, evolution.

scholarly journals scReClassify: post hoc cell type classification of single-cell rNA-seq data

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Taiyun Kim ◽  
Kitty Lo ◽  
Thomas A. Geddes ◽  
Hani Jieun Kim ◽  
Jean Yee Hwa Yang ◽  
...  
Keyword(s):  
Single Cell ◽  
Supervised Learning ◽  
Current Knowledge ◽  
Cell Types ◽  
Computational Techniques ◽  
Biological Knowledge ◽  
Marker Genes ◽  
Cell Type ◽  
Post Hoc ◽  
Type Classification

Abstract Background Single-cell RNA-sequencing (scRNA-seq) is a fast emerging technology allowing global transcriptome profiling on the single cell level. Cell type identification from scRNA-seq data is a critical task in a variety of research such as developmental biology, cell reprogramming, and cancers. Typically, cell type identification relies on human inspection using a combination of prior biological knowledge (e.g. marker genes and morphology) and computational techniques (e.g. PCA and clustering). Due to the incompleteness of our current knowledge and the subjectivity involved in this process, a small amount of cells may be subject to mislabelling. Results Here, we propose a semi-supervised learning framework, named scReClassify, for ‘post hoc’ cell type identification from scRNA-seq datasets. Starting from an initial cell type annotation with potentially mislabelled cells, scReClassify first performs dimension reduction using PCA and next applies a semi-supervised learning method to learn and subsequently reclassify cells that are likely mislabelled initially to the most probable cell types. By using both simulated and real-world experimental datasets that profiled various tissues and biological systems, we demonstrate that scReClassify is able to accurately identify and reclassify misclassified cells to their correct cell types. Conclusions scReClassify can be used for scRNA-seq data as a post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure. It is implemented as an R package and is freely available from https://github.com/SydneyBioX/scReClassify

scholarly journals Immune regulation by glucocorticoids can be linked to cell type–dependent transcriptional responses

2019 ◽  
Vol 216 (2) ◽  
pp. 384-406 ◽  
Author(s):  
Luis M. Franco ◽  
Manasi Gadkari ◽  
Katherine N. Howe ◽  
Jing Sun ◽  
Lela Kardava ◽  
...  
Keyword(s):  
Cell Types ◽  
Cell Receptor ◽  
Cell Type ◽  
Transcriptional Responses ◽  
Functional Studies ◽  
Specific Effects ◽  
Genes Encoding ◽  
Inflammatory Drugs ◽  
The Individual ◽  
Transcriptional Output

Glucocorticoids remain the most widely used immunosuppressive and anti-inflammatory drugs, yet substantial gaps exist in our understanding of glucocorticoid-mediated immunoregulation. To address this, we generated a pathway-level map of the transcriptional effects of glucocorticoids on nine primary human cell types. This analysis revealed that the response to glucocorticoids is highly cell type dependent, in terms of the individual genes and pathways affected, as well as the magnitude and direction of transcriptional regulation. Based on these data and given their importance in autoimmunity, we conducted functional studies with B cells. We found that glucocorticoids impair upstream B cell receptor and Toll-like receptor 7 signaling, reduce transcriptional output from the three immunoglobulin loci, and promote significant up-regulation of the genes encoding the immunomodulatory cytokine IL-10 and the terminal-differentiation factor BLIMP-1. These findings provide new mechanistic understanding of glucocorticoid action and emphasize the multifactorial, cell-specific effects of these drugs, with potential implications for designing more selective immunoregulatory therapies.

scholarly journals Axonal Na+ channels detect and transmit levels of input synchrony in local brain circuits

2019 ◽  
Author(s):  
Mickaёl Zbili ◽  
Sylvain Rama ◽  
Pierre Yger ◽  
Yanis Inglebert ◽  
Norah Boumedine-Guignon ◽  
...  
Keyword(s):  
Sodium Channels ◽  
Sensory Processing ◽  
Coincidence Detection ◽  
Network Activity ◽  
Spike Threshold ◽  
Brain Circuits ◽  
Presynaptic Spike ◽  
Cortical Synapses ◽  
Powerful Mechanism ◽  
Local Brain

AbstractSensory processing requires mechanisms of fast coincidence-detection to discriminate synchronous from asynchronous inputs. Spike-threshold adaptation enables such a discrimination but is ineffective in transmitting this information to the network. We show here that presynaptic axonal sodium channels read and transmit precise levels of input synchrony to the postsynaptic cell by modulating the presynaptic action potential (AP) amplitude. As a consequence, synaptic transmission is facilitated at cortical synapses when the presynaptic spike is produced by synchronous inputs. Using dual soma-axon recordings, imaging, and modeling, we show that this facilitation results from enhanced AP amplitude in the axon due to minimized inactivation of axonal sodium-channels. Quantifying local circuit activity and using network modeling, we found that spikes induced by synchronous inputs produced a larger effect on network activity than spikes induced by asynchronous inputs. Therefore, this input-synchrony dependent facilitation (ISF) may constitute a powerful mechanism regulating spike transmission.

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