Biology subjects

Callaway, E. M.

Publications and source records attributed to Callaway, E. M..

12 recordsLinked to original sources

bioRxiv2024

A disinhibitory basal forebrain to cortex projection supports sustained attention

Sustained attention, as an essential cognitive faculty governing selective sensory processing, exhibits remarkable temporal fluctuations. However, the underlying neural circuits and computational mechanisms driving moment-to-moment attention fluctuations remain elusive. Here we demonstrate that cortex-projecting basal forebrain parvalbumin-expressing inhibitory neurons (BF-PV) mediate sustained attention in mice performing an attention task. BF-PV activity predicts the fluctuations of attentional performance metrics [-] reaction time and accuracy [-] trial-by-trial, and optogenetic activation of these neurons enhances performance. BF-PV neurons also respond to motivationally salient events, such as predictive cues, rewards, punishments, and surprises, which a computational model explains as representing motivational salience for allocating attention over time. Furthermore, we found that BF-PV neurons produce cortical disinhibition by inhibiting cortical PV+ inhibitory neurons, potentially underpinning the observed attentional gain modulation in the cortex. These findings reveal a disinhibitory BF-to-cortex projection that regulates cortical gain based on motivational salience, thereby promoting sustained attention. HIGHLIGHTSO_LIBF-PV activity predicts attentional performance metrics: reaction time and accuracy C_LIO_LIBF-PV responses reflect the computation of motivational salience-guided attention allocation C_LIO_LIOptogenetic activation of BF-PV neurons improves attentional performance C_LIO_LIBF-PV neurons produce cortical disinhibition through topographic projections and mediate gain modulation C_LI

neuroscience↗

bioRxiv2024

Complementary Organization of Driver and Modulator Cortico-Thalamo-Cortical Circuits

Corticocortical (CC) projections in the visual system facilitate the hierarchical processing of sensory information. In addition to direct CC connections, indirect cortico-thalamo-cortical (CTC) pathways through the pulvinar nucleus of the thalamus can relay sensory signals and mediate interactions between areas according to behavioral demands. While the pulvinar is extensively connected to the entire visual cortex, it is unknown whether transthalamic pathways link all cortical areas or whether they follow systematic organizational rules. Because pulvinar neurons projecting to different cortical areas are spatially intermingled, their input/output relationships have been difficult to characterize using traditional anatomical methods. To determine the organization of CTC circuits, we mapped the higher visual areas (HVAs) of mice with intrinsic signal imaging and targeted five pulvinar[->]HVA pathways for projection-specific rabies tracing. We aligned post- mortem cortical tissue to in vivo maps for precise quantification of the areas and cell types projecting to each pulvinar[->]HVA population. Layer 5 corticothalamic (L5CT) "driver" inputs to the pulvinar originate predominantly from primary visual cortex (V1), consistent with the CC hierarchy. L5CT inputs from lateral HVAs specifically avoid driving reciprocal connections, consistent with the "no-strong-loops" hypothesis. Conversely, layer 6 corticothalamic (L6CT) "modulator" inputs are distributed across areas and are biased toward reciprocal connections. Unlike previous studies in primates, we find that every HVA receives disynaptic input from the superior colliculus. CTC circuits in the pulvinar thus depend on both target HVA and input cell type, such that driving and modulating higher-order pathways follow complementary connection rules similar to those governing first-order CT circuits. Significance StatementUnderstanding the functional role of the visual pulvinar will require knowledge of its anatomical connections. Using state-of-the-art rabies tracing, we establish a comprehensive map of brain-wide and CTC pulvinar connections. While the tectopulvinar pathway in primates selectively targets dorsal visual areas, we find SC input to every projection population in the mouse. This extrageniculate projection can support unconscious visually-guided behavior, suggesting that in mice all visual cortical areas contribute to such functions. Our results also unify several longstanding theories of thalamocortical anatomy. Namely, "driver" CTC inputs are feedforward relays that mirror the CC hierarchy and adhere to the "no-strong-loops" hypothesis. "Modulator" L6CT inputs to pulvinar[->]HVA projections are overrepresented in the target HVA, reflecting the reciprocal connectivity described in previous bulk tracing studies. Together, these findings constitute a definitive and comprehensive map which can inform future physiological experiments and theoretical models of pulvinar function.

neuroscience↗

bioRxiv2023

Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

genomics↗

bioRxiv2022

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Variation in cortical cytoarchitecture is the basis for histology-based definition of cortical areas, such as Brodmann areas. Single cell transcriptomics enables higher-resolution characterization of cell types in human cortex, which we used to revisit the idea of the canonical cortical microcircuit and to understand functional areal specialization. Deeply sampled single nucleus RNA-sequencing of eight cortical areas spanning cortical structural variation showed highly consistent cellular makeup for 24 coarse cell subclasses. However, proportions of excitatory neuron subclasses varied strikingly, reflecting differences in intra- and extracortical connectivity across primary sensorimotor and association cortices. Astrocytes and oligodendrocytes also showed differences in laminar organization across areas. Primary visual cortex showed dramatically different organization, including major differences in the ratios of excitatory to inhibitory neurons, expansion of layer 4 excitatory neuron types and specialized inhibitory neurons. Finally, gene expression variation in conserved neuron subclasses predicts differences in synaptic function across areas. Together these results provide a refined cellular and molecular characterization of human cortical cytoarchitecture that reflects functional connectivity and predicts areal specialization.

neuroscience↗

bioRxiv2021

Distinct 'driving' versus 'modulatory' influences of different visual corticothalamic pathways

Higher-order (HO) thalamic nuclei interact extensively with the cerebral cortex and are innervated by excitatory corticothalamic (CT) populations in layers 5 and 6. While these distinct CT projections have long been thought to have different functional influences on the HO thalamus, this has never been directly tested. By optogenetically inactivating different CT populations in the primary visual cortex (V1) of awake mice, we demonstrate that layer 5, but not layer 6, CT projections drive visual responses in the HO visual pulvinar, even while both pathways provide retinotopic, baseline excitation to their thalamic targets. Inactivating the superior colliculus also suppressed visual responses in the pulvinar, demonstrating that cortical layer 5 and subcortical inputs both contribute to HO visual thalamic activity - even at the level of putative single neurons. Altogether, these results indicate a functional division of driver and modulator CT pathways from V1 to the visual thalamus in vivo.

neuroscience↗

bioRxiv2020

A multimodal cell census and atlas of the mammalian primary motor cortex

We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

neuroscience↗

bioRxiv2020

Functional Organization for Color Appearance Mechanisms in Primary Visual Cortex

Studies of color perception have led to mechanistic models of how cone-opponent signals from retinal ganglion cells are integrated to generate color appearance. But it is unknown how this hypothesized integration occurs in the brain. Here we show that cone-opponent signals transmitted from retina to primary visual cortex (V1) are integrated through highly organized circuits within V1 to implement the color opponent interactions required for color appearance. Combining intrinsic signal optical imaging (ISI) and 2-photon calcium imaging (2PCI) at single cell resolution, we demonstrate cone-opponent functional domains (COFDs) that combine L/M cone-opponent and S/L+M cone-opponent signals following the rules predicted from psychophysical studies of color perception. These give rise to an orderly organization of hue preferences of the neurons within the COFDs and the generation of hue "pinwheels". Thus, spatially organized neural circuits mediate an orderly transition from cone-opponency to color appearance that begins in V1.

neuroscience↗

bioRxiv2020

DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

Mammalian brain cells are remarkably diverse in gene expression, anatomy, and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. We carried out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single nucleus DNA methylation sequencing to profile 110,294 nuclei from 45 regions of the mouse cortex, hippocampus, striatum, pallidum, and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements, and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types, and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, an artificial neural network model was constructed that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data allowed prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse brain.

genomics↗

bioRxiv2020

Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain

Neuronal cell types are classically defined by their molecular properties, anatomy, and functions. While recent advances in single-cell genomics have led to high-resolution molecular characterization of cell type diversity in the brain, neuronal cell types are often studied out of the context of their anatomical properties. To better understand the relationship between molecular and anatomical features defining cortical neurons, we combined retrograde labeling with single-nucleus DNA methylation sequencing to link epigenomic properties of cell types to neuronal projections. We examined 11,827 single neocortical neurons from 63 cortico-cortical (CC) and cortico-subcortical long-distance projections. Our results revealed unique epigenetic signatures of projection neurons that correspond to their laminar and regional location and projection patterns. Based on their epigenomes, intra-telencephalic (IT) cells projecting to different cortical targets could be further distinguished, and some layer 5 neurons projecting to extra-telencephalic targets (L5-ET) formed separate subclusters that aligned with their axonal projections. Such separation varied between cortical areas, suggesting area-specific differences in L5-ET subtypes, which were further validated by anatomical studies. Interestingly, a population of CC projection neurons clustered with L5-ET rather than IT neurons, suggesting a population of L5-ET cortical neurons projecting to both targets (L5-ET+CC). We verified the existence of these neurons by labeling the axon terminals of CC projection neurons and observed clear labeling in ET targets including thalamus, superior colliculus, and pons. These findings highlight the power of single-cell epigenomic approaches to connect the molecular properties of neurons with their anatomical and projection properties.

neuroscience↗

bioRxiv2019

Context-Dependent and Dynamic Functional Influence of Corticothalamic Pathways to First- and Higher-order Visual Thalamus

Layer 6 (L6) is the sole purveyor of corticothalamic (CT) feedback to first-order thalamus and also sends projections to higher-order thalamus, yet how it engages the full corticothalamic circuit to contribute to sensory processing in an awake animal remains unknown. We sought to elucidate the functional impact of L6CT projections from primary visual cortex to visual thalamic nuclei dLGN (first-order) and pulvinar (higher-order) using optogenetics and extracellular electrophysiology in awake mice. While sustained L6CT photostimulation suppresses activity in both visual thalamic nuclei in vivo, moderate-frequency (10Hz) stimulation powerfully facilitates thalamic spiking. We show that each stimulation paradigm differentially influences the balance between monosynaptic excitatory and disynaptic inhibitory corticothalamic pathways to dLGN and pulvinar as well as the prevalence of burst versus tonic firing. Altogether, our results support a model in which L6CTs modulate first- and higher-order thalamus through parallel excitatory and inhibitory pathways that are highly dynamic and context-dependent. SignificanceLayer 6 corticothalamic (L6CT) projections play important modulatory roles in thalamic processing, yet how this modulation is executed is unclear. While some studies suggest fundamentally inhibitory influence of L6CTs over first-order thalamus, potential complex, frequency-dependent effects have not been investigated in vivo. Moreover, how L6CTs affect higher-order nuclei in vivo has not been explored. This study utilizes various optogenetic manipulations of L6CTs with single-unit recordings from multiple thalamic nuclei in awake mice to address these questions. Our results illustrate similar effects of L6CTs on first- and higher-order visual thalamic nuclei, yet very different effects within-nucleus depending on how L6CTs are engaged. These findings suggest that L6CT modulation is not simply inhibitory by nature, but instead is dynamic and context-dependent.

neuroscience↗

bioRxiv2019

Monosynaptic projections to excitatory and inhibitory preBotzinger Complex neurons

The key driver of breathing rhythm is the preBotzinger Complex (preBotC) whose activity is modulated by various categorical inputs, e.g., volitional, physiological, emotional. While the preBotC is highly interconnected with other regions of the breathing central pattern generator (bCPG) in the brainstem, there is no data about the direct projections to either excitatory and inhibitory preBotC subpopulations from other elements of the bCPG or from suprapontine regions. Using modified rabies tracing, we identified neurons throughout the brain that send monosynaptic projections to identified excitatory and inhibitory preBotC neurons. Within the brainstem, neurons from sites in the bCPG, including the contralateral preBotC, Botzinger Complex (BotC), the nucleus of the solitary tract (NTS), parafacial region (pFL/pFV or RTN/pFRG), and parabrachial nuclei, send direct projections to both excitatory and inhibitory preBotC neurons. Suprapontine inputs to the excitatory and inhibitory preBotC neurons include the superior colliculus, red nucleus, amygdala, hypothalamus, and cortex; these projections represent potential direct pathways for volitional, emotional, and physiological control of breathing.

neuroscience↗

bioRxiv2018

Distinct higher-order thalamic circuits channel parallel streams of visual information in mice

Higher-order thalamic nuclei, such as the visual pulvinar, play essential roles in cortical function by connecting functionally-related cortical and subcortical brain regions. Yet a coherent framework describing pulvinar function remains elusive due to its anatomical complexity and involvement in diverse cognitive processes. Here we combined large-scale anatomical circuit mapping with high-density electrophysiological recordings to dissect a homolog of pulvinar in mice, the lateral posterior nucleus (LP). We define three broad LP subregions based on correspondence between input/output connectivity and functional properties. These subregions form corticothalamic loops biased towards ventral or dorsal stream cortical areas and contain separate representations of visual space. To reveal which input sources drive LP activity, we silenced visual cortex or superior colliculus and found they drive visual tuning properties in separate LP subregions. Thus, by specifying the driving input sources, functional properties, and downstream targets of LP circuits, our data provide a roadmap for understanding the mechanisms of higher-order thalamic function in vision.

neuroscience↗