Decision letter: A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons

AbstractAmong the brainstem raphe nuclei, the dorsal raphe nucleus (DR) contains the greatest number of Pet1-lineage neurons, a predominantly serotonergic group distributed throughout DR subdomains. These neurons collectively regulate diverse physiology and behavior and are often therapeutically targeted to treat affective disorders. Characterizing Pet1 neuron molecular heterogeneity and relating it to anatomy is vital for understanding DR functional organization, with potential to inform therapeutic separability. Here we use high-throughput and DR subdomain-targeted single-cell transcriptomics and intersectional genetic tools to map molecular and anatomical diversity of DR-Pet1 neurons. We describe up to fourteen neuron subtypes, many showing biased cell body distributions across the DR. We further show that P2ry1-Pet1 DR neurons – the most molecularly distinct subtype – possess unique efferent projections and electrophysiological properties. These data complement and extend previous DR characterizations, combining intersectional genetics with multiple transcriptomic modalities to achieve fine-scale molecular and anatomic identification of Pet1 neuron subtypes.

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Author response: A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons

10.7554/elife.55523.sa2 ◽

2020 ◽

Cited By ~ 1

Author(s):

Benjamin W Okaty ◽

Nikita Sturrock ◽

Yasmin Escobedo Lozoya ◽

YoonJeung Chang ◽

Rebecca A Senft ◽

...

Keyword(s):

Single Cell ◽

Dorsal Raphe ◽

Author Response ◽

Dorsal Raphé

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Single-cell analysis of antiviral neuroinflammatory responses in the mouse dorsal raphe nucleus

10.1101/780205 ◽

2019 ◽

Author(s):

Kee Wui Huang ◽

Bernardo L. Sabatini

Keyword(s):

Gene Delivery ◽

Single Cell ◽

Dorsal Raphe Nucleus ◽

Single Cell Analysis ◽

Critical Evaluation ◽

Dorsal Raphe ◽

Raphe Nucleus ◽

Viral Gene ◽

Transcriptional Responses ◽

Dorsal Raphé

ABSTRACTNeuroinflammatory processes have been implicated in neurodegenerative and psychiatric diseases, and limit the utility of viruses for gene delivery. Here we analyzed 60,212 single-cell RNA profiles to assess both global and cell type-specific transcriptional responses in the mouse dorsal raphe nucleus following axonal infection of neurons by rabies viruses. We identified several leukocyte populations, which infiltrate the brain, that are distinct from resident immune cells. Additionally, we uncovered transcriptionally distinct states of microglia along an activation trajectory that may serve different functions, ranging from surveillance to antigen presentation and cytokine secretion. Our study also provides a critical evaluation of the compatibility between rabies-mediated connectivity mapping and single-cell transcriptional profiling. These findings provide additional insights into the distinct contributions of various cell types in the antiviral response, and will serve as a resource for the design of strategies to circumvent immune responses to improve the efficacy of viral gene delivery.

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Molecular and anatomical organization of the dorsal raphe nucleus

eLife ◽

10.7554/elife.46464 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 22

Author(s):

Kee Wui Huang ◽

Nicole E Ochandarena ◽

Adrienne C Philson ◽

Minsuk Hyun ◽

Jaclyn E Birnbaum ◽

...

Keyword(s):

Single Cell ◽

Dorsal Raphe Nucleus ◽

Cell Types ◽

Dorsal Raphe ◽

Raphe Nucleus ◽

Molecular Organization ◽

Serotonergic Neuron ◽

Multiple Cell ◽

Dorsal Raphé

The dorsal raphe nucleus (DRN) is an important source of neuromodulators and has been implicated in a wide variety of behavioral and neurological disorders. The DRN is subdivided into distinct anatomical subregions comprised of multiple cell types, and its complex cellular organization has impeded efforts to investigate the distinct circuit and behavioral functions of its subdomains. Here we used single-cell RNA sequencing, in situ hybridization, anatomical tracing, and spatial correlation analysis to map the transcriptional and spatial profiles of cells from the mouse DRN. Our analysis of 39,411 single-cell transcriptomes revealed at least 18 distinct neuron subtypes and 5 serotonergic neuron subtypes with distinct molecular and anatomical properties, including a serotonergic neuron subtype that preferentially innervates the basal ganglia. Our study lays out the molecular organization of distinct serotonergic and non-serotonergic subsystems, and will facilitate the design of strategies for further dissection of the DRN and its diverse functions.

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Neuron-type specificity of dorsal raphe projections to ventral tegmental area

10.1101/2021.01.06.425641 ◽

2021 ◽

Author(s):

Anna J. Chang ◽

Lihua Wang ◽

Federica Lucantonio ◽

Maya Adams ◽

Andy Lemire ◽

...

Keyword(s):

Single Cell ◽

Ventral Tegmental Area ◽

Cell Types ◽

Dorsal Raphe ◽

Physiological Data ◽

Differential Distribution ◽

Ventral Tegmental ◽

And Behavior ◽

Long Timescales ◽

Dorsal Raphé

The midbrain dorsal raphe (DR) and ventral tegmental area (VTA) contain two of the brain’s main ascending neuromodulatory transmitters: serotonin and dopamine. We studied the pathway from DR to VTA using single-cell RNA sequencing, anatomical tracing, and electrophysiology and behavior in mice. Single-cell sequencing confirmed a differential distribution of dopamine cell types between medial and lateral aspects of the VTA. This molecular diversity included differential expression of a subset of glutamatergic and serotonergic receptors. Anatomical data showed that distinct serotonergic and glutamatergic populations of DR neurons project to distinct medial-lateral locations in VTA. Physiological data showed that serotonergic neurons are positioned to excite putative dopaminergic neurons in lateral VTA on short timescales (within trial), and inhibit them on long timescales (on the next trial). Our results reveal precise anatomical specificity of DR projections to VTA, and suggest a functional role for serotonergic modulation of dopaminergic function across multiple timescales.

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A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons

eLife ◽

10.7554/elife.55523 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 6

Author(s):

Benjamin W Okaty ◽

Nikita Sturrock ◽

Yasmin Escobedo Lozoya ◽

YoonJeung Chang ◽

Rebecca A Senft ◽

...

Keyword(s):

Single Cell ◽

Functional Organization ◽

Dorsal Raphe ◽

Molecular Heterogeneity ◽

Electrophysiological Properties ◽

Efferent Projections ◽

Brainstem Raphe ◽

And Behavior ◽

Distinct Subtype ◽

Dorsal Raphé

Among the brainstem raphe nuclei, the dorsal raphe nucleus (DR) contains the greatest number of Pet1-lineage neurons, a predominantly serotonergic group distributed throughout DR subdomains. These neurons collectively regulate diverse physiology and behavior and are often therapeutically targeted to treat affective disorders. Characterizing Pet1 neuron molecular heterogeneity and relating it to anatomy is vital for understanding DR functional organization, with potential to inform therapeutic separability. Here we use high-throughput and DR subdomain-targeted single-cell transcriptomics and intersectional genetic tools to map molecular and anatomical diversity of DR-Pet1 neurons. We describe up to fourteen neuron subtypes, many showing biased cell body distributions across the DR. We further show that P2ry1-Pet1 DR neurons – the most molecularly distinct subtype – possess unique efferent projections and electrophysiological properties. These data complement and extend previous DR characterizations, combining intersectional genetics with multiple transcriptomic modalities to achieve fine-scale molecular and anatomic identification of Pet1 neuron subtypes.

Download Full-text