@article {69251, title = {The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain.}, journal = {Cell Reports}, volume = {43}, year = {2024}, month = {2024 Feb 29}, pages = {113842}, abstract = {

Understanding the cell-type composition and spatial organization of brain regions is crucial for interpreting brain computation and function. In the thalamus, the anterior thalamic nuclei (ATN) are involved in a wide variety of functions, yet the cell-type composition of the ATN remains unmapped at a single-cell and spatial resolution. Combining single-cell RNA sequencing, spatial transcriptomics, and multiplexed fluorescent in situ hybridization, we identify three discrete excitatory cell-type clusters that correspond to the known nuclei of the ATN and uncover marker genes, molecular pathways, and putative functions of these cell types. We further illustrate graded spatial variation along the dorsomedial-ventrolateral axis for all individual nuclei of the ATN and additionally demonstrate that the anteroventral nucleus exhibits spatially covarying protein products and long-range inputs. Collectively, our study reveals discrete and continuous cell-type organizational principles of the ATN, which will help to guide and interpret experiments on ATN computation and function.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2024.113842}, author = {Kapustina, Margarita and Zhang, Angela A and Tsai, Jennifer Y J and Bristow, Brianna N and Kraus, Larissa and Sullivan, Kaitlin E and Erwin, Sarah R and Wang, Lihua and Stach, Tara R and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {67673, title = {Spatially patterned excitatory neuron subtypes and projections of the claustrum.}, journal = {eLife}, volume = {10}, year = {2021}, month = {2021 Aug 16}, abstract = {

The claustrum is a functionally and structurally complex brain region, whose very spatial extent remains debated. Histochemical-based approaches typically treat the claustrum as a relatively narrow anatomical region that primarily projects to the neocortex, whereas circuit-based approaches can suggest a broader claustrum region containing projections to the neocortex and other regions. Here, in the mouse, we took a bottom-up and cell-type-specific approach to complement and possibly unite these seemingly disparate conclusions. Using single-cell RNA-sequencing, we found that the claustrum comprises two excitatory neuron subtypes that are differentiable from the surrounding cortex. Multicolor retrograde tracing in conjunction with 12-channel multiplexed in situ hybridization revealed a core-shell spatial arrangement of these subtypes, as well as differential downstream targets. Thus, the claustrum comprises excitatory neuron subtypes with distinct molecular and projection properties, whose spatial patterns reflect the narrower and broader claustral extents debated in previous research. This subtype-specific heterogeneity likely shapes the functional complexity of the claustrum.

}, issn = {2050-084X}, doi = {10.7554/eLife.68967}, author = {Erwin, Sarah R and Bristow, Brianna N and Sullivan, Kaitlin E and Kendrick, Rennie M and Marriott, Brian and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Jackson, Jesse and Cembrowski, Mark S} } @article {65720, title = {Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Sep 01}, abstract = {

The basolateral amygdala complex (BLA), extensively connected with both local amygdalar nuclei as well as long-range circuits, is involved in a diverse array of functional roles. Understanding the mechanisms of such functional diversity will be greatly informed by understanding the cell-type-specific landscape of the BLA. Here, beginning with single-cell RNA sequencing, we identified both discrete and graded continuous gene-expression differences within the mouse BLA. Via in situ hybridization, we next mapped this discrete transcriptomic heterogeneity onto a sharp spatial border between the basal and lateral amygdala nuclei, and identified continuous spatial gene-expression gradients within each of these regions. These discrete and continuous spatial transformations of transcriptomic cell-type identity were recapitulated by local morphology as well as long-range connectivity. Thus, BLA excitatory neurons are a highly heterogenous collection of neurons that spatially covary in molecular, cellular, and circuit properties. This heterogeneity likely drives pronounced spatial variation in BLA computation and function.

}, issn = {2050-084X}, doi = {10.7554/eLife.59003}, author = {O{\textquoteright}Leary, Timothy P and Sullivan, Kaitlin E and Wang, Lihua and Clements, Jody and Lemire, Andrew L and Cembrowski, Mark S} } @article {65584, title = {A Sparse, Spatially Biased Subtype of Mature Granule Cell Dominates Recruitment in Hippocampal-Associated Behaviors.}, journal = {Cell Reports}, volume = {31}, year = {2020}, month = {2020 Apr 28}, pages = {107551}, abstract = {

Animals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we find that a range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identify a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we map these traits onto a sparse and discrete granule cell subtype that is recruited at a 10-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, in behaviors known to involve hippocampal-dependent memory formation, a rare and spatially localized subtype dominates overall granule cell recruitment.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2020.107551}, author = {Erwin, Sarah R and Sun, Weinan and Copeland, Monique and Lindo, Sarah and Spruston, Nelson and Cembrowski, Mark S} } @article {64824, title = {Heterogeneity within classical cell types is the rule: lessons from hippocampal pyramidal neurons.}, journal = {Nature Reviews. Neuroscience}, volume = {20}, year = {2019}, month = {2019 Feb 18}, pages = {193-204}, abstract = {

The mechanistic operation of brain regions is often interpreted by partitioning constituent neurons into {\textquoteright}cell types{\textquoteright}. Historically, such cell types were broadly defined by their correspondence to gross features of the nervous system (such as cytoarchitecture). Modern-day neuroscientific techniques, enabling a more nuanced examination of neuronal properties, have illustrated a wealth of heterogeneity within these classical cell types. Here, we review the extent of this within-cell-type heterogeneity in one of the simplest cortical regions of the mammalian brain, the rodent hippocampus. We focus on the mounting evidence\ that the classical CA3, CA1 and subiculum pyramidal cell types all exhibit prominent\ and spatially patterned within-cell-type heterogeneity, and suggest these cell\ types\ provide a model system for exploring the organization and function of such heterogeneity. Given that the hippocampus is structurally simple and evolutionarily ancient,\ within-cell-type heterogeneity is likely to be a general and crucial feature of the\ mammalian brain.

}, issn = {1471-0048}, doi = {10.1038/s41583-019-0125-5}, author = {Cembrowski, Mark S and Spruston, Nelson} } @article {49118, title = {Continuous variation within cell types of the nervous system.}, journal = {Trends in Neurosciences}, volume = {41}, year = {2018}, month = {2018 Mar 22}, pages = {337-48}, abstract = {

The brain is an organ of immense complexity. Next-generation RNA sequencing (RNA-seq) is becoming increasingly popular in the deconstruction of this complexity into distinct classes of {\textquoteright}cell types{\textquoteright}. Notably, in addition to revealing the organization of this distinct cell-type landscape, the technology has also begun to illustrate that continuous variation can be found within narrowly defined cell types. Here we summarize the evidence for graded transcriptomic heterogeneity being present, widespread, and functionally relevant in the nervous system. We explain how these graded differences can map onto higher-order organizational features and how they may reframe existing interpretations of higher-order heterogeneity. Ultimately, a multimodal approach incorporating continuously variable cell types will facilitate an accurate reductionist interpretation of the nervous system.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2018.02.010}, author = {Cembrowski, Mark S and Menon, Vilas} } @article {49174, title = {Dissociable structural and functional hippocampal outputs via distinct subiculum cell classes.}, journal = {Cell}, volume = {173}, year = {2018}, month = {2018 Apr 10}, pages = {1280-92}, abstract = {

The mammalian hippocampus, comprised of serially connected subfields, participates in diverse behavioral and cognitive functions. It has been postulated that parallel circuitry embedded within hippocampal subfields may underlie such functional diversity. We sought to identify, delineate, and manipulate this putatively parallel architecture in the dorsal subiculum, the primary output subfield of the dorsal hippocampus. Population and single-cell RNA-seq revealed that the subiculum can be divided into two spatially adjacent subregions associated with prominent differences in pyramidal cell gene expression. Pyramidal cells occupying these two regions differed in their long-range inputs, local wiring, projection targets, and electrophysiological properties. Leveraging gene-expression differences across these regions, we use genetically restricted neuronal silencing to show that\ these regions differentially contribute to spatial working memory. This work provides a coherent molecular-, cellular-, circuit-, and behavioral-level demonstration that the hippocampus embeds structurally and functionally dissociable streams within its serial architecture.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.03.031}, author = {Cembrowski, Mark S and Phillips, Matthew G and DiLisio, Salvatore F and Shields, Brenda C and Winnubst, Johan and Chandrashekar, Jayaram and Bas, Erhan and Spruston, Nelson} } @article {49046, title = {Single excitatory axons form clustered synapses onto CA1 pyramidal cell dendrites.}, journal = {Nature Neuroscience}, volume = {21}, year = {2018}, month = {2018 Mar}, pages = {353-63}, abstract = {

CA1 pyramidal neurons are a major output of the hippocampus and encode features of experience that constitute episodic memories. Feature-selective firing of these neurons results from the dendritic integration of inputs from multiple brain regions. While it is known that synchronous activation of spatially clustered inputs can contribute to firing through the generation of dendritic spikes, there is no established mechanism for spatiotemporal synaptic clustering. Here we show that single presynaptic axons form multiple, spatially clustered inputs onto the distal, but not proximal, dendrites of CA1 pyramidal neurons. These compound connections exhibit ultrastructural features indicative of strong synapses and occur much more commonly in entorhinal than in thalamic afferents. Computational simulations revealed that compound connections depolarize dendrites in a biophysically efficient manner, owing to their inherent spatiotemporal clustering. Our results suggest that distinct afferent projections use different connectivity motifs that differentially contribute to dendritic integration.

}, doi = {10.1038/s41593-018-0084-6}, author = {Bloss, Erik B and Cembrowski, Mark S and Karsh, Bill and Colonell, Jennifer and Fetter, Richard D and Spruston, Nelson} } @article {49492, title = {The subiculum is a patchwork of discrete subregions.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Oct 30}, abstract = {

In the hippocampus, the classical pyramidal cell type of the subiculum acts as a primary output, conveying hippocampal signals to a diverse suite of downstream regions. Accumulating evidence suggests that the subiculum pyramidal cell population may actually be comprised of discrete subclasses. Here, we investigated the extent and organizational principles governing pyramidal cell heterogeneity throughout the mouse subiculum. Using single-cell RNA-seq, we find that the subiculum pyramidal cell population can be deconstructed into eight separable subclasses. These subclasses were mapped onto abutting spatial domains, ultimately producing a complex laminar and columnar organization with heterogeneity across classical dorsal-ventral, proximal-distal, and superficial-deep axes. We further show that these transcriptomically defined subclasses correspond to differential protein products and can be associated with specific projection targets. This work deconstructs the complex landscape of subiculum pyramidal cells into spatially segregated subclasses that may be observed, controlled, and interpreted in future experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.37701}, author = {Cembrowski, Mark S and Wang, Lihua and Lemire, Andrew L and Copeland, Monique and DiLisio, Salvatore F and Clements, Jody and Spruston, Nelson} } @article {48492, title = {Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 May 17}, pages = {747-751.e1}, abstract = {

Elucidating the diversity and spatial organization of cell types in the brain is an essential goal of neuroscience, with many emerging technologies helping to advance this endeavor. Using a new in\ situ hybridization method that can measure the expression of hundreds of genes in a given mouse brain section (amplified seqFISH), Shah et\ al. (2016) describe a spatial organization of hippocampal cell types that differs from previous reports. In seeking to understand this discrepancy, we find that many of the barcoded genes used by seqFISH to characterize this spatial organization, when cross-validated by other sensitive methodologies, exhibit negligible expression in the hippocampus. Additionally, the results of Shah et\ al. (2016) do not recapitulate canonical cellular hierarchies and improperly classify major neuronal cell types. We suggest that, when describing the spatial organization of brain regions, cross-validation using multiple techniques should be used to yield robust and informative cellular classification. This Matters Arising paper is in response to Shah et\ al. (2016), published in Neuron. See also the response by Shah et\ al. (2017), published in this issue.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.04.023}, author = {Cembrowski, Mark S and Spruston, Nelson} } @article {47442, title = {Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.

}, issn = {2050-084X}, doi = {10.7554/eLife.14997}, author = {Cembrowski, Mark S and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {48008, title = {Illuminating the neuronal architecture underlying context in fear memory.}, journal = {Cell}, volume = {167}, year = {2016}, month = {2016 Nov 3}, pages = {888-9}, abstract = {

Context plays a foundational role in determining how to interpret potentially fear-producing stimuli, yet the precise neurobiological substrates of context are poorly understood. In this issue of Cell, Xu et\ al. elegantly show that parallel neuronal circuits are necessary for two distinct roles of context in fear conditioning.

}, author = {Cembrowski, Mark S and Spruston, N} } @article {47278, title = {Spatial gene-expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons.}, journal = {Neuron}, year = {2016}, month = {2016 Jan 13}, abstract = {

Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but it may be further hampered by prominent within-class variability. Here, we considered a well-defined canonical neuronal population-hippocampal CA1 pyramidal cells (CA1 PCs)-and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences within CA1 along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous gene-expression gradients, producing a transcriptional profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.12.013}, author = {Cembrowski, Mark S and Bachman, Julia L and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {47322, title = {Structured dendritic inhibition supports branch-selective integration in CA1 pyramidal cells.}, journal = {Neuron}, year = {2016}, month = {2016 Feb 18}, abstract = {

Neuronal circuit function is governed by precise patterns of connectivity between specialized groups of neurons. The diversity of GABAergic interneurons is a hallmark of cortical circuits, yet little is known about their targeting to individual postsynaptic dendrites. We examined synaptic connectivity between molecularly defined inhibitory interneurons and CA1 pyramidal cell dendrites using correlative light-electron microscopy and large-volume array tomography. We show that interneurons can be highly selective in their connectivity to specific dendritic branch types and, furthermore, exhibit precisely targeted connectivity to the origin or end of individual branches. Computational simulations indicate that the observed subcellular targeting enables control over the nonlinear integration of synaptic input or the initiation and backpropagation of action potentials in a branch-selective manner. Our results demonstrate that connectivity between interneurons and pyramidal cell dendrites is more precise and spatially segregated than previously appreciated, which may be a critical determinant of how inhibition shapes dendritic computation.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.01.029}, author = {Bloss, Erik B and Cembrowski, Mark S and Karsh, Bill and Colonell, Jennifer and Fetter, Richard D and Spruston, Nelson} } @article {47201, title = {Dendritic sodium spikes are required for long-term potentiation at distal synapses on hippocampal pyramidal neurons.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 06}, abstract = {

Dendritic integration of synaptic inputs mediates rapid neural computation as well as longer-lasting plasticity. Several channel types can mediate dendritically initiated spikes (dSpikes), which may impact information processing and storage across multiple timescales; however, the roles of different channels in the rapid vs long-term effects of dSpikes are unknown. We show here that dSpikes mediated by Nav channels (blocked by a low concentration of TTX) are required for long-term potentiation (LTP) in the distal apical dendrites of hippocampal pyramidal neurons. Furthermore, imaging, simulations, and buffering experiments all support a model whereby fast Nav channel-mediated dSpikes (Na-dSpikes) contribute to LTP induction by promoting large, transient, localized increases in intracellular calcium concentration near the calcium-conducting pores of NMDAR and L-type Cav channels. Thus, in addition to contributing to rapid neural processing, Na-dSpikes are likely to contribute to memory formation via their role in long-lasting synaptic plasticity.

}, issn = {2050-084X}, doi = {10.7554/eLife.06414}, author = {Kim, Yujin and Hsu, Ching-Lung and Cembrowski, Mark S and Mensh, Brett D and Spruston, Nelson} } @article {46049, title = {Adaptation to background light enables contrast coding at rod bipolar cell synapses.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 22}, pages = {388-401}, abstract = {

Rod photoreceptors contribute to vision over an \~{} 6-log-unit range of light intensities. The wide dynamic range of rod vision is thought to depend upon light intensity-dependent switching between two parallel pathways linking rods to ganglion cells: a rod {\textrightarrow} rod bipolar (RB) cell pathway that operates at dim backgrounds and a rod {\textrightarrow} cone {\textrightarrow} cone bipolar cell pathway that operates at brighter backgrounds. We evaluated this conventional model of rod vision by recording rod-mediated light responses from ganglion and AII amacrine cells and by recording RB-mediated synaptic currents from AII amacrine cells in mouse retina. Contrary to the conventional model, we found that the RB pathway functioned at backgrounds sufficient to activate the rod {\textrightarrow} cone pathway. As background light intensity increased, the RB{\textquoteright}s role changed from encoding the absorption of single photons to encoding contrast modulations around mean luminance. This transition is explained by the intrinsic dynamics of transmission from RB synapses.

}, keywords = {2-Amino-5-phosphonovalerate, Adaptation, Ocular, Animals, Biophysics, Computer Simulation, Excitatory Amino Acid Antagonists, Glucosamine 6-Phosphate N-Acetyltransferase, Green Fluorescent Proteins, In Vitro Techniques, Light, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Models, Neurological, Patch-Clamp Techniques, Quinoxalines, Retinal Bipolar Cells, Retinal Rod Photoreceptor Cells, Synapses, Visual Pathways}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.054}, author = {Ke, Jiang-Bin and Wang, Yanbin V and Borghuis, Bart G and Cembrowski, Mark S and Riecke, Hermann and Kath, William L and Demb, Jonathan B and Singer, Joshua H} } @article {45459, title = {Intrinsic bursting of aII amacrine cells underlies oscillations in the rd1 mouse retina.}, journal = {Journal of Neurophysiology}, volume = {112}, year = {2014}, month = {2014 Sep 15}, pages = {1491-504}, abstract = {

In many forms of retinal degeneration, photoreceptors die but inner retinal circuits remain intact. In the rd1 mouse, an established model for blinding retinal diseases, spontaneous activity in the coupled network of AII amacrine and ON cone bipolar cells leads to rhythmic bursting of ganglion cells. Since such activity could impair retinal and/or cortical responses to restored photoreceptor function, understanding its nature is important for developing treatments of retinal pathologies. Here we analyzed a compartmental model of the wild-type mouse AII amacrine cell to predict that the cell{\textquoteright}s intrinsic membrane properties, specifically, interacting fast Na and slow, M-type K conductances, would allow its membrane potential to oscillate when light-evoked excitatory synaptic inputs were withdrawn following photoreceptor degeneration. We tested and confirmed this hypothesis experimentally by recording from AIIs in a slice preparation of rd1 retina. Additionally, recordings from ganglion cells in a whole mount preparation of rd1 retina demonstrated that activity in AIIs was propagated unchanged to elicit bursts of action potentials in ganglion cells. We conclude that oscillations are not an emergent property of a degenerated retinal network. Rather, they arise largely from the intrinsic properties of a single retinal interneuron, the AII amacrine cell.

}, issn = {1522-1598}, doi = {10.1152/jn.00437.2014}, author = {Choi, Hannah and Zhang, Lei and Cembrowski, Mark S and Sabottke, Carl F and Markowitz, Alexander L and Butts, Daniel A and Kath, William L and Singer, Joshua H and Riecke, Hermann} } @article {46048, title = {The mechanisms of repetitive spike generation in an axonless retinal interneuron.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {155-66}, abstract = {

Several types of retinal interneurons exhibit spikes but lack axons. One such neuron is the AII amacrine cell, in which spikes recorded at the soma exhibit small amplitudes (\<10 mV) and broad time courses (\>5 ms). Here, we used electrophysiological recordings and computational analysis to examine the mechanisms underlying this atypical spiking. We found that somatic spikes likely represent large, brief action potential-like events initiated in a single, electrotonically distal dendritic compartment. In this same compartment, spiking undergoes slow modulation, likely by an M-type K conductance. The structural correlate of this compartment is a thin neurite that extends from the primary dendritic tree: local application of TTX to this neurite, or excision of it, eliminates spiking. Thus, the physiology of the axonless AII is much more complex than would be anticipated from morphological descriptions and somatic recordings; in particular, the AII possesses a single dendritic structure that controls its firing pattern.

}, keywords = {Action Potentials, Amacrine Cells, Animals, Axons, Female, Interneurons, Ion Channel Gating, Mice, Mice, Inbred C57BL, Models, Neurological, Potassium Channels, Retina, Time Factors}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.006}, author = {Cembrowski, Mark S and Logan, Stephen M and Tian, Miao and Jia, Li and Li, Wei and Kath, William L and Riecke, Hermann and Singer, Joshua H} }