scholarly journals High-throughput mapping of single-cell molecular and projection architecture of neurons by retrograde barcoded labelling

2021 ◽  
Author(s):  
Peibo Xu ◽  
Jian Peng ◽  
Tingli Yuan ◽  
Zhaoqin Chen ◽  
Ziyan Wu ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Neuron ◽  
Neural Circuit ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Projection Neurons ◽  
Proof Of Concept ◽  
Sequencing Technology ◽  
Modal Data ◽  
Projection Pattern

Deciphering mesoscopic connectivity of the mammalian brain is a pivotal step in neuroscience. Most imaging-based conventional neuroanatomical tracing methods identify area-to-area or sparse single neuronal labeling information. Although recently developed barcode-based connectomics has been able to map a large number of single-neuron projections efficiently, there is a missing link in single-cell connectome and transcriptome. Here, combining single-cell RNA sequencing technology, we established a retro-AAV barcode-based multiplexed tracing method called MEGRE-seq (Multiplexed projEction neuRons retroGrade barcodE), which can resolve projectome and transcriptome of source neurons simultaneously. Using the ventromedial prefrontal cortex (vmPFC) as a proof-of-concept neocortical region, we investigated projection patterns of its excitatory neurons targeting five canonical brain regions, as well as corresponding transcriptional profiles. Dedicated, bifurcated or collateral projection patterns were inferred by digital projectome. In combination with simultaneously recovered transcriptome, we find that certain projection pattern has a preferential layer or neuron subtype bias. Further, we fitted single-neuron two-modal data into a machine learning-based model and delineated gene importance by each projection target. In summary, we anticipate that the new multiplexed digital connectome technique is potential to understand the organizing principle of the neural circuit by linking projectome and transcriptome.

scholarly journals Resolving brain organoid heterogeneity by mapping single cell genomic data to a spatial reference

2020 ◽  
Author(s):  
Jonas Simon Fleck ◽  
Zhisong He ◽  
Michael James Boyle ◽  
J. Gray Camp ◽  
Barbara Treutlein
Keyword(s):  
Single Cell ◽  
Developmental State ◽  
Brain Regions ◽  
Cellular Heterogeneity ◽  
Brain Atlas ◽  
Mammalian Brain ◽  
Human Stem Cells ◽  
Cell Composition ◽  
Brain Organoid

ABSTRACTSelf-organizing tissues resembling brain regions grown in vitro from human stem cells (so-called organoids or spheroids) offer exciting possibilities to study human brain development, disease, and evolution. Brain organoids or spheroids are complex and can contain cells at various stages of differentiation from different brain structures. Single-cell genomic methods provide powerful approaches to explore cell composition, differentiation trajectories, gene regulation, and genetic perturbations in brain organoid systems. However, it remains a major challenge to understand the cellular heterogeneity observed within and between individual organoids. Here, we have developed a computational approach (VoxHunt) to assess brain organoid patterning, developmental state, and cell composition through systematic comparisons to three-dimensional in situ hybridization data from the Allen Brain Atlas. Cellular transcriptomes as well as accessible chromatin landscapes can be compared to spatial transcript patterns in the developing mammalian brain, which enables characterization and visualization of organoid cell compositions. VoxHunt will be useful to assess novel organoid engineering protocols and to annotate cell fates that emerge in organoids during genetic and environmental perturbation experiments.

scholarly journals Functional dissection of neural circuitry using a genetic reporter for fMRI

2020 ◽  
Author(s):  
Souparno Ghosh ◽  
Nan Li ◽  
Benjamin B. Bartelle ◽  
Tianshu Xie ◽  
Jade I. Daher ◽  
...  
Keyword(s):  
Neural Circuit ◽  
Viral Vector ◽  
Retrograde Transport ◽  
Cytosolic Calcium ◽  
Brain Regions ◽  
Neural Systems ◽  
Mammalian Brain ◽  
Formidable Challenge ◽  
Mechanistic Analysis ◽  
Stimulation Paradigm

ABSTRACTThe complex connectivity of the mammalian brain underlies its function, but understanding how interconnected brain regions interact in neural processing remains a formidable challenge. Here we address this problem by introducing a genetic probe that permits selective functional imaging of neural circuit elements defined by their synaptic interrelationships throughout the brain. The probe is an engineered enzyme that transduces cytosolic calcium dynamics of probe-expressing cells into localized hemodynamic responses that can be selectively visualized by functional magnetic resonance imaging. Using a viral vector that undergoes retrograde transport, we apply the probe to characterize a brain-wide network of monosynaptic inputs to the striatum activated in a deep brain stimulation paradigm in rats. The results reveal engagement of surprisingly diverse projection sources and inform an integrated model of striatal function relevant to reward behavior and therapeutic neurostimulation approaches. Our work thus establishes a potent strategy for mechanistic analysis of distributed neural systems.

scholarly journals Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

2017 ◽  
Author(s):  
Vincent Croset ◽  
Christoph D Treiber ◽  
Scott Waddell
Keyword(s):  
Single Cell ◽  
Neural Circuit ◽  
Cell Types ◽  
Brain Regions ◽  
Neurotransmitter Receptor ◽  
Neural Processes ◽  
Subunit Expression ◽  
Circuit Function ◽  
Fast Acting ◽  
The Brain

AbstractTo understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes.

Nanostimulation: Manipulation of Single Neuron Activity by Juxtacellular Current Injection

2010 ◽  
Vol 103 (3) ◽  
pp. 1696-1704 ◽  
Author(s):  
Arthur R. Houweling ◽  
Guy Doron ◽  
Birgit C. Voigt ◽  
Lucas J. Herfst ◽  
Michael Brecht
Keyword(s):  
Single Cell ◽  
Single Neuron ◽  
Close Contact ◽  
Fold Increase ◽  
Mammalian Brain ◽  
Neuron Activity ◽  
Single Neurons ◽  
Cell Stimulation ◽  
Pipette Tip ◽  
Sensory Responses

In the mammalian brain, many thousands of single-neuron recording studies have been performed but less than 10 single-cell stimulation studies. This paucity of single-cell stimulation data reflects a lack of easily applicable single-cell stimulation techniques. We provide a detailed description of the procedures involved in nanostimulation, a single-cell stimulation method derived from the juxtacellular labeling technique. Nanostimulation is easy to apply and can be directed to a wide variety of identifiable neurons in anesthetized and awake animals. We describe the recording approach and the parameters of the electric configuration underlying nanostimulation. We use glass pipettes with a DC resistance of 4–7 MΩ. Obtaining the juxtacellular configuration requires a close contact between pipette tip and neuron and is associated with a several-fold increase in resistance to values ≥20 MΩ. The recorded action potential (AP) amplitude grows to ≥2 mV, and neurons can be activated with currents in the nanoampere range—hence the term nanostimulation. While exact AP timing has not been achieved, AP frequency and AP number can be parametrically controlled. We demonstrate that nanostimulation can also be used to selectively inhibit sensory responses in identifiable neurons. Nanostimulation is biophysically similar to electroporation, and based on this assumption, we argue that nanostimulation operates on membranes in the micrometer area directly below the pipette tip, where membrane pores are induced by high transmembrane voltage. There is strong evidence to suggest that nanostimulation selectively activates single neurons and that the evoked effects are cell-specific. Nanostimulation therefore holds great potential for elucidating how single neurons contribute to behavior.

scholarly journals Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Vincent Croset ◽  
Christoph D Treiber ◽  
Scott Waddell
Keyword(s):  
Single Cell ◽  
Neural Circuit ◽  
Cell Types ◽  
Brain Regions ◽  
Neurotransmitter Receptor ◽  
Neural Processes ◽  
Subunit Expression ◽  
Circuit Function ◽  
Fast Acting ◽  
The Brain

To understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes.

scholarly journals Single-cell analysis of Foxp1-driven mechanisms essential for striatal development

2019 ◽  
Author(s):  
Ashley G. Anderson ◽  
Ashwinikumar Kulkarni ◽  
Matthew Harper ◽  
Genevieve Konopka
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Single Cell Analysis ◽  
Cell Types ◽  
Brain Regions ◽  
Projection Neurons ◽  
Loss Of Function ◽  
Cell Type ◽  
Motor Information ◽  
Cell Type Specific

AbstractThe striatum is a critical forebrain structure for integrating cognitive, sensory, and motor information from diverse brain regions into meaningful behavioral output. However, the transcriptional mechanisms that underlie striatal development and organization at single-cell resolution remain unknown. Here, we show that Foxp1, a transcription factor strongly linked to autism and intellectual disability, regulates organizational features of striatal circuitry in a cell-type-dependent fashion. Using single-cell RNA-sequencing, we examine the cellular diversity of the early postnatal striatum and find that cell-type-specific deletion ofFoxp1in striatal projection neurons alters the cellular composition and neurochemical architecture of the striatum. Importantly, using this approach, we identify the non-cell autonomous effects produced by disruptingFoxp1in one cell-type and the molecular compensation that occurs in other populations. Finally, we identify Foxp1-regulated target genes within distinct cell-types and connect these molecular changes to functional and behavioral deficits relevant to phenotypes described in patients withFOXP1loss-of-function mutations. These data reveal cell-type-specific transcriptional mechanisms underlying distinct features of striatal circuitry and identify Foxp1 as a key regulator of striatal development.

scholarly journals Benchmarking of tools for axon length measurement in individually-labeled projection neurons

2021 ◽  
Vol 17 (12) ◽  
pp. e1009051
Author(s):  
Mario Rubio-Teves ◽  
Sergio Díez-Hermano ◽  
César Porrero ◽  
Abel Sánchez-Jiménez ◽  
Lucía Prensa ◽  
...  
Keyword(s):  
Single Neuron ◽  
Estimation Method ◽  
Brain Regions ◽  
Projection Neurons ◽  
Stereological Method ◽  
Tissue Sections ◽  
Length Estimation ◽  
Human Effort ◽  
Neuronal Type ◽  
Selection Of

Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools—design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length—in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. The evaluated reliability of each axon length estimation method was then balanced with the required human effort, experience and know-how, and economic affordability. Subsequently, computational results were contrasted with measurements performed on actual brain tissue sections. We show that the plane-based stereological method balances acceptable errors (~5%) with robustness to biases, whereas the projection-based method, despite its accuracy, is prone to inherent biases when implemented in the laboratory. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research.

scholarly journals Benchmarking of tools for axon length measurement in individually-labeled projection neurons

2021 ◽  
Author(s):  
Mario Rubio-Teves ◽  
Sergio Díez-Hermano ◽  
César Porrero ◽  
Abel Sánchez-Jiménez ◽  
Lucía Prensa ◽  
...  
Keyword(s):  
Single Neuron ◽  
Estimation Method ◽  
Brain Regions ◽  
Projection Neurons ◽  
Tissue Sections ◽  
Length Estimation ◽  
Direct Measurements ◽  
Human Effort ◽  
Neuronal Type ◽  
Selection Of

Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools - design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length - in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. Additionally, the computational results were compared with estimated and direct measurements of individual axon lengths performed on actual brain tissue sections, to analyze the practical difficulties and biases arising in real cases. The evaluated reliability of each axon length estimation method is then balanced with the required human effort, experience and know-how, and economic affordability. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research.

scholarly journals High-throughput mapping of single neuron projections by sequencing of barcoded RNA

2016 ◽  
Author(s):  
Justus M Kebschull ◽  
Pedro Garcia da Silva ◽  
Ashlan P Reid ◽  
Ian D Peikon ◽  
Dinu F Albeanu ◽  
...  
Keyword(s):  
High Throughput ◽  
Single Neuron ◽  
Brain Regions ◽  
Projection Area ◽  
Single Neurons ◽  
Sequencing Technology ◽  
Rna Sequences ◽  
Axonal Projections ◽  
Large Sets ◽  
Brain Circuits

SummaryNeurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area isdissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionallyviewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits.

scholarly journals An architectonic type principle in the development of laminar patterns of cortico-cortical connections

2021 ◽  
Author(s):  
Sarah F. Beul ◽  
Alexandros Goulas ◽  
Claus C. Hilgetag
Keyword(s):  
Structural Connectivity ◽  
Macaque Monkey ◽  
Brain Regions ◽  
Adult Brain ◽  
Mammalian Brain ◽  
Cortical Connections ◽  
Cortical Projections ◽  
Structural Connections ◽  
High Degree ◽  
The Brain

AbstractStructural connections between cortical areas form an intricate network with a high degree of specificity. Many aspects of this complex network organization in the adult mammalian cortex are captured by an architectonic type principle, which relates structural connections to the architectonic differentiation of brain regions. In particular, the laminar patterns of projection origins are a prominent feature of structural connections that varies in a graded manner with the relative architectonic differentiation of connected areas in the adult brain. Here we show that the architectonic type principle is already apparent for the laminar origins of cortico-cortical projections in the immature cortex of the macaque monkey. We find that prenatal and neonatal laminar patterns correlate with cortical architectonic differentiation, and that the relation of laminar patterns to architectonic differences between connected areas is not substantially altered by the complete loss of visual input. Moreover, we find that the degree of change in laminar patterns that projections undergo during development varies in proportion to the relative architectonic differentiation of the connected areas. Hence, it appears that initial biases in laminar projection patterns become progressively strengthened by later developmental processes. These findings suggest that early neurogenetic processes during the formation of the brain are sufficient to establish the characteristic laminar projection patterns. This conclusion is in line with previously suggested mechanistic explanations underlying the emergence of the architectonic type principle and provides further constraints for exploring the fundamental factors that shape structural connectivity in the mammalian brain.

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