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The Journal of Neuroscience : the... Jul 2020Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively...
Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing to profile >32,000 ACs from mice of both sexes and applied computational methods to identify 63 AC types. We identified molecular markers for each type and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types expressed markers for the canonical inhibitory neurotransmitters GABA or glycine, but several expressed neither or both. In addition, many expressed one or more neuropeptides, and two expressed glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were and , expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological, and morphologic analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in the mouse retina. The mouse retina is a leading model for analyzing the development, structure, function, and pathology of neural circuits. A complete molecular atlas of retinal cell types provides an important foundation for these studies. We used high-throughput single-cell RNA sequencing to characterize the most heterogeneous class of retinal interneurons, amacrine cells, identifying 63 distinct types. The atlas includes types identified previously as well as many novel types. We provide evidence for the use of multiple neurotransmitters and neuropeptides, and identify transcription factors expressed by groups of closely related types. Combining these results with those obtained previously, we proposed that the mouse retina contains ∼130 neuronal types and is therefore comparable in complexity to other regions of the brain.
Topics: Amacrine Cells; Animals; Female; Glycine; High-Throughput Nucleotide Sequencing; Homeodomain Proteins; Male; Mice; Mice, Inbred C57BL; Neuropeptides; Neurotransmitter Agents; Receptors, Neurotransmitter; Retina; Transcription Factor 4; Transcription Factors; gamma-Aminobutyric Acid
PubMed: 32457074
DOI: 10.1523/JNEUROSCI.0471-20.2020 -
Nature Communications Aug 2023The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have...
The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing 8 previously unknown displaced amacrine cell subtypes and establishing the connection between the molecular classification of many cell subtypes and their spatial arrangement. Furthermore, we identified spatially dependent differential gene expression between subtypes, suggesting the possibility of functional tuning of neuronal types based on location.
Topics: Animals; Mice; Gene Expression Profiling; In Situ Hybridization, Fluorescence; Retina; Amacrine Cells; Single-Cell Analysis
PubMed: 37582959
DOI: 10.1038/s41467-023-40674-3 -
Visual Neuroscience Jan 2016Amacrine cells are a diverse set of local circuit neurons of the inner retina, and they all release either GABA or glycine, amino acid neurotransmitters that are... (Review)
Review
Amacrine cells are a diverse set of local circuit neurons of the inner retina, and they all release either GABA or glycine, amino acid neurotransmitters that are generally inhibitory. But some types of amacrine cells have another function besides inhibiting other neurons. One glycinergic amacrine cell, the Aii type, excites a subset of bipolar cells via extensive gap junctions while inhibiting others at chemical synapses. Many types of GABAergic amacrine cells also release monoamines, acetylcholine, or neuropeptides. There is now good evidence that another type of amacrine cell releases glycine at some of its synapses and releases the excitatory amino acid glutamate at others. The glutamatergic synapses are made onto a subset of retinal ganglion cells and amacrine cells and have the asymmetric postsynaptic densities characteristic of central excitatory synapses. The glycinergic synapses are made onto other types of ganglion cells and have the symmetric postsynaptic densities characteristic of central inhibitory synapses. These amacrine cells, which contain vesicular glutamate transporter 3, will be the focus of this brief review.
Topics: Amacrine Cells; Animals; GABA Plasma Membrane Transport Proteins; Glucose Transporter Type 3; Glycine Plasma Membrane Transport Proteins; Humans
PubMed: 28359349
DOI: 10.1017/S0952523816000146 -
Development (Cambridge, England) Jan 2022The mammalian retina contains a complex mixture of different types of neurons. We find that microRNA miR-216b is preferentially expressed in postmitotic retinal amacrine...
The mammalian retina contains a complex mixture of different types of neurons. We find that microRNA miR-216b is preferentially expressed in postmitotic retinal amacrine cells in the mouse retina, and expression of miR-216a/b and miR-217 in retina depend in part on Ptf1a, a transcription factor required for amacrine cell differentiation. Surprisingly, ectopic expression of miR-216b directed the formation of additional amacrine cells and reduced bipolar neurons in the developing retina. We identify the Foxn3 mRNA as a retinal target of miR-216b by Argonaute PAR-CLIP and reporter analysis. Inhibition of Foxn3, a transcription factor, in the postnatal developing retina by RNAi increased the formation of amacrine cells and reduced bipolar cell formation. Foxn3 disruption by CRISPR in embryonic retinal explants also increased amacrine cell formation, whereas Foxn3 overexpression inhibited amacrine cell formation prior to Ptf1a expression. Co-expression of Foxn3 partially reversed the effects of ectopic miR-216b on retinal cell formation. Our results identify Foxn3 as a novel regulator of interneuron formation in the developing retina and suggest that miR-216b likely regulates Foxn3 and other genes in amacrine cells.
Topics: Amacrine Cells; Animals; Cell Cycle Proteins; Female; Forkhead Transcription Factors; HEK293 Cells; Humans; Male; Mice; MicroRNAs; Neurogenesis; Transcription Factors
PubMed: 34919141
DOI: 10.1242/dev.199484 -
Visual Neuroscience Jan 2012Amacrine cells represent the most diverse class of retinal neuron, comprising dozens of distinct cell types. Each type exhibits a unique morphology and generates... (Review)
Review
Amacrine cells represent the most diverse class of retinal neuron, comprising dozens of distinct cell types. Each type exhibits a unique morphology and generates specific visual computations through its synapses with a subset of excitatory interneurons (bipolar cells), other amacrine cells, and output neurons (ganglion cells). Here, we review the intrinsic and network properties that underlie the function of the most common amacrine cell in the mammalian retina, the AII amacrine cell. The AII connects rod and cone photoreceptor pathways, forming an essential link in the circuit for rod-mediated (scotopic) vision. As such, the AII has become known as the rod-amacrine cell. We, however, now understand that AII function extends to cone-mediated (photopic) vision, and AII function in scotopic and photopic conditions utilizes the same underlying circuit: AIIs are electrically coupled to each other and to the terminals of some types of ON cone bipolar cells. The direction of signal flow, however, varies with illumination. Under photopic conditions, the AII network constitutes a crossover inhibition pathway that allows ON signals to inhibit OFF ganglion cells and contributes to motion sensitivity in certain ganglion cell types. We discuss how the AII's combination of intrinsic and network properties accounts for its unique role in visual processing.
Topics: Amacrine Cells; Animals; Cell Communication; Computer Simulation; Gap Junctions; Humans; Models, Biological; Nerve Net; Retina; Retinal Bipolar Cells; Retinal Rod Photoreceptor Cells; Visual Pathways
PubMed: 22310372
DOI: 10.1017/S0952523811000368 -
Journal of Anatomy Aug 2023The precise specification of cellular fate is thought to ensure the production of the correct number of neurons within a population. Programmed cell death may be an... (Review)
Review
The precise specification of cellular fate is thought to ensure the production of the correct number of neurons within a population. Programmed cell death may be an additional mechanism controlling cell number, believed to refine the proper ratio of pre- to post-synaptic neurons for a given species. Here, we consider the size of three different neuronal populations in the rod pathway of the mouse retina: rod photoreceptors, rod bipolar cells, and AII amacrine cells. Across a collection of 28 different strains of mice, large variation in the numbers of all three cell types is present. The variation in their numbers is not correlated, so that the ratio of rods to rod bipolar cells, as well as rod bipolar cells to AII amacrine cells, varies as well. Establishing connectivity between such variable pre- and post-synaptic populations relies upon plasticity that modulates process outgrowth and morphological differentiation, which we explore experimentally for both rod bipolar and AII amacrine cells in a mouse retina with elevated numbers of each cell type. While both rod bipolar dendritic and axonal arbors, along with AII lobular arbors, modulate their areal size in relation to local homotypic cell densities, the dendritic appendages of the AII amacrine cells do not. Rather, these processes exhibit a different form of plasticity, regulating the branching density of their overlapping arbors. Each form of plasticity should ensure uniformity in retinal coverage in the presence of the independent specification of afferent and target cell number.
Topics: Mice; Animals; Dendrites; Retina; Amacrine Cells; Axons
PubMed: 35292986
DOI: 10.1111/joa.13653 -
Visual Neuroscience Jan 2012Their unique patterns of size, numbers, and stratification indicate that amacrine cells have diverse functions. These are mostly unknown, as studies using imaging and... (Review)
Review
Their unique patterns of size, numbers, and stratification indicate that amacrine cells have diverse functions. These are mostly unknown, as studies using imaging and electrophysiological methods have only recently begun. However, some of the events that occur within the amacrine cell population--and some important unresolved puzzles--can be stated purely from structural reasoning.
Topics: Amacrine Cells; Animals; Humans; Nerve Net; Retina; Synapses; Visual Fields
PubMed: 22416289
DOI: 10.1017/s0952523811000344 -
The Journal of Physiology Aug 2017Visual processing starts in the retina. Within only two synaptic layers, a large number of parallel information channels emerge, each encoding a highly processed feature... (Review)
Review
Visual processing starts in the retina. Within only two synaptic layers, a large number of parallel information channels emerge, each encoding a highly processed feature like edges or the direction of motion. Much of this functional diversity arises in the inner plexiform layer, where inhibitory amacrine cells modulate the excitatory signal of bipolar and ganglion cells. Studies investigating individual amacrine cell circuits like the starburst or A17 circuit have demonstrated that single types can possess specific morphological and functional adaptations to convey a particular function in one or a small number of inner retinal circuits. However, the interconnected and often stereotypical network formed by different types of amacrine cells across the inner plexiform layer prompts that they should be also involved in more general computations. In line with this notion, different recent studies systematically analysing inner retinal signalling at a population level provide evidence that general functions of the ensemble of amacrine cells across types are critical for establishing universal principles of retinal computation like parallel processing or motion anticipation. Combining recent advances in the development of indicators for imaging inhibition with large-scale morphological and genetic classifications will help to further our understanding of how single amacrine cell circuits act together to help decompose the visual scene into parallel information channels. In this review, we aim to summarise the current state-of-the-art in our understanding of how general features of amacrine cell inhibition lead to general features of computation.
Topics: Amacrine Cells; Animals; Pattern Recognition, Visual
PubMed: 28332227
DOI: 10.1113/JP273648 -
Progress in Retinal and Eye Research Sep 2019In this review, we summarize studies investigating the types and distribution of voltage- and calcium-gated ion channels in the different classes of retinal neurons:... (Review)
Review
In this review, we summarize studies investigating the types and distribution of voltage- and calcium-gated ion channels in the different classes of retinal neurons: rods, cones, horizontal cells, bipolar cells, amacrine cells, interplexiform cells, and ganglion cells. We discuss differences among cell subtypes within these major cell classes, as well as differences among species, and consider how different ion channels shape the responses of different neurons. For example, even though second-order bipolar and horizontal cells do not typically generate fast sodium-dependent action potentials, many of these cells nevertheless possess fast sodium currents that can enhance their kinetic response capabilities. Ca channel activity can also shape response kinetics as well as regulating synaptic release. The L-type Ca channel subtype, Ca1.4, expressed in photoreceptor cells exhibits specific properties matching the particular needs of these cells such as limited inactivation which allows sustained channel activity and maintained synaptic release in darkness. The particular properties of K and Cl channels in different retinal neurons shape resting membrane potentials, response kinetics and spiking behavior. A remaining challenge is to characterize the specific distributions of ion channels in the more than 100 individual cell types that have been identified in the retina and to describe how these particular ion channels sculpt neuronal responses to assist in the processing of visual information by the retina.
Topics: Amacrine Cells; Animals; Humans; Ion Channels; Retinal Cone Photoreceptor Cells; Retinal Ganglion Cells; Retinal Neurons; Retinal Rod Photoreceptor Cells; Synaptic Transmission
PubMed: 31078724
DOI: 10.1016/j.preteyeres.2019.05.001 -
Developmental Biology Nov 2022The axonal projections of retinal ganglion cells (RGCs) of the eye are topographically organized so that spatial information from visual images is preserved. This...
PURPOSE
The axonal projections of retinal ganglion cells (RGCs) of the eye are topographically organized so that spatial information from visual images is preserved. This retinotopic organization is established during development by secreted morphogens that pattern domains of transcription factor expression within naso-temporal and dorso-ventral quadrants of the embryonic eye. Poorly understood are the downstream signaling molecules that generate the topographically organized retinal cells and circuits. The secreted signaling molecule Semaphorin 3fa (Sema3fa) belongs to the Sema family of molecules that provide positional information to developing cells. Here, we test a role for Sema3fa in cell genesis of the temporal zebrafish retina.
METHODS
We compare retinal cell genesis in wild type and sema3fa CRISPR zebrafish mutants by in situ hybridization and immunohistochemistry.
RESULTS
We find that mRNAs for sema3fa and known receptors, neuropilin2b (nrp2b) and plexina1a (plxna1a), are expressed by progenitors of the temporal, but not nasal zebrafish embryonic retina. In the sema3fa embryo, initially the domains of expression for atoh7 and neurod4, transcription factors necessary for the specification of RGCs and amacrine cells, respectively, are disrupted. Yet, post-embryonically only amacrine cells of the temporal retina are reduced in numbers, with both GABAergic and glycinergic subtypes affected.
CONCLUSIONS
These data suggest that Sema3fa acts early on embryonic temporal progenitors to control in a spatially-dependent manner the production of amacrine cells, possibly to allow the establishment of neural circuits with domain-specific functions. We propose that spatially restricted extrinsic signals in the neural retina control cell genesis in a domain-dependent manner.
Topics: Amacrine Cells; Animals; Gene Expression Regulation, Developmental; Retina; Semaphorins; Transcription Factors; Zebrafish
PubMed: 36058267
DOI: 10.1016/j.ydbio.2022.08.008