Ascertaining cells' synaptic connections and RNA expression simultaneously with massively barcoded rabies virus libraries

Brain function depends on forming and maintaining connections between neurons of specific types, ensuring neural function while allowing the plasticity necessary for cellular and behavioral dynamics. However, systematic descriptions of how brain cell types organize into synaptic networks and which molecules instruct these relationships are not readily available. Here, we introduce SBARRO (Synaptic Barcode Analysis by Retrograde Rabies ReadOut), a method that uses single-cell RNA sequencing to reveal directional, monosynaptic relationships based on the paths of a barcoded rabies virus from its "starter" postsynaptic cell to that cell's presynaptic partners1. Thousands of these partner relationships can be ascertained in a single experiment, alongside genome-wide RNA profiles - and thus cell identities and molecular states - of each host cell. We used SBARRO to describe synaptic networks formed by diverse mouse brain cell types in vitro, leveraging a system similar to those used to identify synaptogenic molecules. We found that the molecular identity (cell type/subtype) of the starter cell predicted the number and types of cells that had synapsed onto it. Rabies transmission tended to occur into cells with RNA-expression signatures related to developmental maturation and synaptic transmission. The estimated size of a cell's presynaptic network, relative to that of other cells of the same type, associated with increased expression of Arpp21 and Cdh13. By tracking individual virions and their clonal progeny as they travel among host cells, single-cell, single-virion genomic technologies offer new opportunities to map the synaptic organization of neural circuits in health and disease.

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Localization of migraine susceptibility genes in human brain by single-cell RNA sequencing

Cephalalgia ◽

10.1177/0333102418762476 ◽

2018 ◽

Vol 38 (13) ◽

pp. 1976-1983 ◽

Cited By ~ 5

Author(s):

William Renthal

Keyword(s):

Human Brain ◽

Single Cell ◽

Rna Sequencing ◽

Expression Profiles ◽

Cell Types ◽

Susceptibility Genes ◽

Brain Cell ◽

Cell Type ◽

Single Cell Rna Sequencing ◽

Brain Cell Types

Background Migraine is a debilitating disorder characterized by severe headaches and associated neurological symptoms. A key challenge to understanding migraine has been the cellular complexity of the human brain and the multiple cell types implicated in its pathophysiology. The present study leverages recent advances in single-cell transcriptomics to localize the specific human brain cell types in which putative migraine susceptibility genes are expressed. Methods The cell-type specific expression of both familial and common migraine-associated genes was determined bioinformatically using data from 2,039 individual human brain cells across two published single-cell RNA sequencing datasets. Enrichment of migraine-associated genes was determined for each brain cell type. Results Analysis of single-brain cell RNA sequencing data from five major subtypes of cells in the human cortex (neurons, oligodendrocytes, astrocytes, microglia, and endothelial cells) indicates that over 40% of known migraine-associated genes are enriched in the expression profiles of a specific brain cell type. Further analysis of neuronal migraine-associated genes demonstrated that approximately 70% were significantly enriched in inhibitory neurons and 30% in excitatory neurons. Conclusions This study takes the next step in understanding the human brain cell types in which putative migraine susceptibility genes are expressed. Both familial and common migraine may arise from dysfunction of discrete cell types within the neurovascular unit, and localization of the affected cell type(s) in an individual patient may provide insight into to their susceptibility to migraine.

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Brain Microenvironment Heterogeneity: Potential Value for Brain Tumors

Frontiers in Oncology ◽

10.3389/fonc.2021.714428 ◽

2021 ◽

Vol 11 ◽

Author(s):

Laura Álvaro-Espinosa ◽

Ana de Pablos-Aragoneses ◽

Manuel Valiente ◽

Neibla Priego

Keyword(s):

Brain Tumors ◽

Single Cell ◽

Brain Injuries ◽

Clinical Work ◽

Cell Types ◽

Brain Cell ◽

Brain Disorders ◽

Brain Connectome ◽

The Brain ◽

Brain Cell Types

Uncovering the complexity of the microenvironment that emerges in brain disorders is key to identify potential vulnerabilities that might help challenging diseases affecting this organ. Recently, genomic and proteomic analyses, especially at the single cell level, have reported previously unrecognized diversity within brain cell types. The complexity of the brain microenvironment increases during disease partly due to the immune infiltration from the periphery that contributes to redefine the brain connectome by establishing a new crosstalk with resident brain cell types. Within the rewired brain ecosystem, glial cell subpopulations are emerging hubs modulating the dialogue between the Immune System and the Central Nervous System with important consequences in the progression of brain tumors and other disorders. Single cell technologies are crucial not only to define and track the origin of disease-associated cell types, but also to identify their molecular similarities and differences that might be linked to specific brain injuries. These altered molecular patterns derived from reprogramming the healthy brain into an injured organ, might provide a new generation of therapeutic targets to challenge highly prevalent and lethal brain disorders that remain incurable with unprecedented specificity and limited toxicities. In this perspective, we present the most relevant clinical and pre-clinical work regarding the characterization of the heterogeneity within different components of the microenvironment in the healthy and injured brain with a special interest on single cell analysis. Finally, we discuss how understanding the diversity of the brain microenvironment could be exploited for translational purposes, particularly in primary and secondary tumors affecting the brain.

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Leveraging single-cell ATAC-seq to identify disease-critical fetal and adult brain cell types

10.1101/2021.05.20.445067 ◽

2021 ◽

Author(s):

Samuel S Kim ◽

Karthik Jagadeesh ◽

Kushal K Dey ◽

Amber Z Shen ◽

Soumya Raychaudhuri ◽

...

Keyword(s):

Single Cell ◽

Ganglion Cells ◽

Association Studies ◽

Photoreceptor Cells ◽

Cell Types ◽

Chromatin Accessibility ◽

Brain Cell ◽

Adult Brain ◽

Genome Wide Association Studies ◽

Brain Cell Types

Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at high resolution, and early work on integrating GWAS with scRNA-seq has shown promise, but work on integrating GWAS with scATAC-seq has been limited. Here, we identify disease-critical fetal and adult brain cell types by integrating GWAS summary statistics from 28 brain-related diseases and traits (average N=298K) with 3.2 million scATAC-seq and scRNA-seq profiles from 83 cell types. We identified disease-critical fetal (resp. adult) brain cell types for 22 (resp. 23) of 28 traits using scATAC-seq data, and for 8 (resp. 17) of 28 traits using scRNA-seq data. Notable findings using scATAC-seq data included highly significant enrichments of fetal photoreceptor cells for major depressive disorder, fetal ganglion cells for BMI, fetal astrocytes for ADHD, and adult VGLUT2 excitatory neurons for schizophrenia. Our findings improve our understanding of brain-related diseases and traits, and inform future analyses of other diseases/traits.

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Innovations in Primate Interneuron Repertoire

10.1101/709501 ◽

2019 ◽

Cited By ~ 24

Author(s):

Fenna M. Krienen ◽

Melissa Goldman ◽

Qiangge Zhang ◽

Ricardo del Rosario ◽

Marta Florio ◽

...

Keyword(s):

Expression Patterns ◽

Cell Types ◽

Brain Cell ◽

Cognitive Capacity ◽

Evolutionary Divergence ◽

Rna Expression ◽

Mouse Hippocampus ◽

Striatal Interneurons ◽

Brain Cell Types ◽

Expression Gradients

ABSTRACTPrimates and rodents, which descended from a common ancestor more than 90 million years ago, exhibit profound differences in behavior and cognitive capacity. Modifications, specializations, and innovations to brain cell types may have occurred along each lineage. We used Drop-seq to profile RNA expression in more than 184,000 individual telencephalic interneurons from humans, macaques, marmosets, and mice. Conserved interneuron types varied significantly in abundance and RNA expression between mice and primates, but varied much more modestly among primates. In adult primates, the expression patterns of dozens of genes exhibited spatial expression gradients among neocortical interneurons, suggesting that adult neocortical interneurons are imprinted by their local cortical context. In addition, we found that an interneuron type previously associated with the mouse hippocampus—the “ivy cell”, which has neurogliaform characteristics—has become abundant across the neocortex of humans, macaques, and marmosets. The most striking innovation was subcortical: we identified an abundant striatal interneuron type in primates that had no molecularly homologous cell population in mouse striatum, cortex, thalamus, or hippocampus. These interneurons, which expressed a unique combination of transcription factors, receptors, and neuropeptides, including the neuropeptide TAC3, constituted almost 30% of striatal interneurons in marmosets and humans. Understanding how gene and cell-type attributes changed or persisted over the evolutionary divergence of primates and rodents will guide the choice of models for human brain disorders and mutations and help to identify the cellular substrates of expanded cognition in humans and other primates.

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Single-cell mapping of focused ultrasound-transfected brain

Gene Therapy ◽

10.1038/s41434-021-00226-0 ◽

2021 ◽

Author(s):

A. S. Mathew ◽

C. M. Gorick ◽

R. J. Price

Keyword(s):

Single Cell ◽

Focused Ultrasound ◽

Cell Types ◽

Brain Cell ◽

Therapeutic Modality ◽

Full Potential ◽

Stress Genes ◽

Multiple Cell ◽

Differential Gene

AbstractGene delivery via focused ultrasound (FUS) mediated blood-brain barrier (BBB) opening is a disruptive therapeutic modality. Unlocking its full potential will require an understanding of how FUS parameters (e.g., peak-negative pressure (PNP)) affect transfected cell populations. Following plasmid (mRuby) delivery across the BBB with 1 MHz FUS, we used single-cell RNA-sequencing to ascertain that distributions of transfected cell types were highly dependent on PNP. Cells of the BBB (i.e., endothelial cells, pericytes, and astrocytes) were enriched at 0.2 MPa PNP, while transfection of cells distal to the BBB (i.e., neurons, oligodendrocytes, and microglia) was augmented at 0.4 MPa PNP. PNP-dependent differential gene expression was observed for multiple cell types. Cell stress genes were upregulated proportional to PNP, independent of cell type. Our results underscore how FUS may be tuned to bias transfection toward specific brain cell types in vivo and predict how those cells will respond to transfection.

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