Brain connectomes come of age

Hierarchical organization of the forebrain cholinergic system in rats

The basal forebrain (BF) cholinergic system (BFCS) participates in functions that are global across the brain, such as sleep-wake cycles, but also participates in capacities that are more behaviorally and anatomically specific, including sensory perception. However, how it orchestrates all the diverse local and global functions remains to be understood. To uncover the underlying organization principles, we combined data from rat brains by tracing projections from the BF to cortical areas and analyzed spatial-numerical relations of neurons to their cortical targets. The combined dataset revealed algorithmically identified and hierarchically organized three principal networks: somatosensory-motor, auditory, and visual, as defined by the sensory modality most predominant within them. These clusters of cholinergic neurons could enable the BFCS to coordinate spatially selective signaling, including the parallel modulation of multiple functionally interconnected yet diverse groups of cortical areas. This previously unseen blueprint of the hierarchy of cholinergic clusters is ready for functional testing.

Bifurcation in space: Emergence of functional modularity in the neocortex

How does functional modularity emerge in a cortex composed of repeats of a canonical local circuit? Focusing on distributed working memory, we show that a rigorous description of bifurcation in space describes the emergence of modularity. A connectome-based model of monkey cortex displays bifurcation in space during decision-making and working memory, demonstrating this new concept's generality. In a generative model and multi-regional cortex models of both macaque monkey and mouse, we found an inverted-V-shaped profile of neuronal timescales across the cortical hierarchy during working memory, providing an experimentally testable prediction of modularity. The cortex displays simultaneously many bifurcations in space, so that the corresponding modules could potentially subserve distinct internal mental processes. Therefore, a distributed process subserves the brain's functional specificity. We propose that bifurcation in space, resulting from connectivity and macroscopic gradients of neurobiological properties across the cortex, represents a fundamental principle for understanding the brain's modular organization.

Predicting modular functions and neural coding of behavior from a synaptic wiring diagram

A long-standing goal in neuroscience is to understand how a circuit's form influences its function. Here, we reconstruct and analyze a synaptic wiring diagram of the larval zebrafish brainstem to predict key functional properties and validate them through comparison with physiological data. We identify modules of strongly connected neurons that turn out to be specialized for different behavioral functions, the control of eye and body movements. The eye movement module is further organized into two three-block cycles that support the positive feedback long hypothesized to underlie low-dimensional attractor dynamics in oculomotor control. We construct a neural network model based directly on the reconstructed wiring diagram that makes predictions for the cellular-resolution coding of eye position and neural dynamics. These predictions are verified statistically with calcium imaging-based neural activity recordings. This work demonstrates how connectome-based brain modeling can reveal previously unknown anatomical structure in a neural circuit and provide insights linking network form to function.

Functional architecture of the forebrain cholinergic system in rodents

The basal forebrain cholinergic system (BFCS) participates in functions that are global across the brain, such as sleep-wake cycles, but also participates in capacities that are more behaviorally and anatomically specific, including sensory perception. To better understand the underlying organization principles of the BFCS, more and higher quality anatomical data and analysis is needed. Here, we created a "virtual Basal Forebrain", combining data from numerous rats with cortical retrograde tracer injections into a common 3D reference coordinate space and developed a "spatial density correlation" methodology to analyze patterns in BFCS cortical projection targets, revealing that the BFCS is organized into three principal networks: somatosensory-motor, auditory, and visual. Within each network, clusters of cholinergic cells with increasing complexity innervate cortical targets. These networks represent hierarchically organized building blocks that may enable the BFCS to coordinate spatially selective signaling, including parallel modulation of multiple functionally interconnected yet diverse groups of cortical areas.

The meso-connectomes of mouse, marmoset, and macaque: network organization and the emergence of higher cognition

The recent publications of the inter-areal connectomes for mouse, marmoset, and macaque cortex have allowed deeper comparisons across rodent vs. primate cortical organization. In general, these show that the mouse has very widespread, "all-to-all" inter-areal connectivity (i.e. a "highly dense" connectome in a graph theoretical framework), while primates have a more modular organization. In this review, we highlight the relevance of these differences to function, including the example of primary visual cortex (V1) which, in the mouse, is interconnected with all other areas, therefore including other primary sensory and frontal areas. We argue that this dense inter-areal connectivity benefits multimodal associations, at the cost of reduced functional segregation. Conversely, primates have expanded cortices with a modular connectivity structure, where V1 is almost exclusively interconnected with other visual cortices, themselves organized in relatively segregated streams, and hierarchically higher cortical areas such as prefrontal cortex provide top-down regulation for specifying precise information for working memory storage and manipulation. Increased complexity in cytoarchitecture, connectivity, dendritic spine density, and receptor expression additionally reveal a sharper hierarchical organization in primate cortex. Together, we argue that these primate specializations permit separable deconstruction and selective reconstruction of representations, which is essential to higher cognition.

Theory of the Multiregional Neocortex: Large-Scale Neural Dynamics and Distributed Cognition

The neocortex is a complex neurobiological system with many interacting regions. How these regions work together to subserve flexible behavior and cognition has become increasingly amenable to rigorous research. Here, I review recent experimental and theoretical work on the modus operandi of a multiregional cortex. These studies revealed several general principles for the neocortical interareal connectivity, low-dimensional macroscopic gradients of biological properties across cortical areas, and a hierarchy of timescales for information processing. Theoretical work suggests testable predictions regarding differential excitation and inhibition along feedforward and feedback pathways in the cortical hierarchy. Furthermore, modeling of distributed working memory and simple decision-making has given rise to a novel mathematical concept, dubbed bifurcation in space, that potentially explains how different cortical areas, with a canonical circuit organization but gradients of biological heterogeneities, are able to subserve their respective (e.g., sensory coding versus executive control) functions in a modularly organized brain.

Dendritic Domain-Specific Sampling of Long-Range Axons Shapes Feedforward and Feedback Connectivity of L5 Neurons

Feedforward and feedback pathways interact in specific dendritic domains to enable cognitive functions such as predictive processing and learning. Based on axonal projections, hierarchically lower areas are thought to form synapses primarily on dendrites in middle cortical layers, whereas higher-order areas are thought to target dendrites in layer 1 and in deep layers. However, the extent to which functional synapses form in regions of axodendritic overlap has not been extensively studied. Here, we use viral tracing in the secondary visual cortex of male mice to map brain-wide inputs to thick-tufted layer 5 pyramidal neurons. Furthermore, we provide a comprehensive map of input locations through subcellular optogenetic circuit mapping. We show that input pathways target distinct dendritic domains with far greater specificity than appears from their axonal branching, often deviating substantially from the canonical patterns. Common assumptions regarding the dendrite-level interaction of feedforward and feedback inputs may thus need revisiting.SIGNIFICANCE STATEMENT Perception and learning depend on the ability of the brain to shape neuronal representations across all processing stages. Long-range connections across different hierarchical levels enable diverse sources of contextual information, such as predictions or motivational state, to modify feedforward signals. Assumptions regarding the organization of this hierarchical connectivity have not been extensively verified. Here, we assess the synaptic connectivity of brain-wide projections onto pyramidal neurons in the visual cortex of mice. Using trans-synaptic viral tracing and subcellular optogenetic circuit mapping, we show that functional synapses do not follow the consistent connectivity rule predicted by their axonal branching patterns. These findings highlight the diversity of computational strategies operating throughout cortical networks and may aid in building better artificial networks.

The nonhuman primate neuroimaging and neuroanatomy project

Multi-modal neuroimaging projects such as the Human Connectome Project (HCP) and UK Biobank are advancing our understanding of human brain architecture, function, connectivity, and their variability across individuals using high-quality non-invasive data from many subjects. Such efforts depend upon the accuracy of non-invasive brain imaging measures. However, 'ground truth' validation of connectivity using invasive tracers is not feasible in humans. Studies using nonhuman primates (NHPs) enable comparisons between invasive and non-invasive measures, including exploration of how "functional connectivity" from fMRI and "tractographic connectivity" from diffusion MRI compare with long-distance connections measured using tract tracing. Our NonHuman Primate Neuroimaging & Neuroanatomy Project (NHP_NNP) is an international effort (6 laboratories in 5 countries) to: (i) acquire and analyze high-quality multi-modal brain imaging data of macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii) map the distributions of different brain cell types with immunocytochemical stains to better define brain areal boundaries. We are acquiring high-resolution structural, functional, and diffusion MRI data together with behavioral measures from over 100 individual macaques and marmosets in order to generate non-invasive measures of brain architecture such as myelin and cortical thickness maps, as well as functional and diffusion tractography-based connectomes. We are using classical and next-generation anatomical tracers to generate quantitative connectivity maps based on brain-wide counting of labeled cortical and subcortical neurons, providing ground truth measures of connectivity. Advanced statistical modeling techniques address the consistency of both kinds of data across individuals, allowing comparison of tracer-based and non-invasive MRI-based connectivity measures. We aim to develop improved cortical and subcortical areal atlases by combining histological and imaging methods. Finally, we are collecting genetic and sociality-associated behavioral data in all animals in an effort to understand how genetic variation shapes the connectome and behavior.

Comparative 2D and 3D Ultrastructural Analyses of Dendritic Spines from CA1 Pyramidal Neurons in the Mouse Hippocampus

Three-dimensional (3D) reconstruction from electron microscopy (EM) datasets is a widely used tool that has improved our knowledge of synapse ultrastructure and organization in the brain. Rearrangements of synapse structure following maturation and in synaptic plasticity have been broadly described and, in many cases, the defective architecture of the synapse has been associated to functional impairments. It is therefore important, when studying brain connectivity, to map these rearrangements with the highest accuracy possible, considering the affordability of the different EM approaches to provide solid and reliable data about the structure of such a small complex. The aim of this work is to compare quantitative data from two dimensional (2D) and 3D EM of mouse hippocampal CA1 (apical dendrites), to define whether the results from the two approaches are consistent. We examined asymmetric excitatory synapses focusing on post synaptic density and dendritic spine area and volume as well as spine density, and we compared the results obtained with the two methods. The consistency between the 2D and 3D results questions the need—for many applications—of using volumetric datasets (costly and time consuming in terms of both acquisition and analysis), with respect to the more accessible measurements from 2D EM projections.