Lineage Is a Poor Predictor of Interneuron Positioning within the Forebrain

Clonally related, Notch-differentiated spinal neurons integrate into distinct circuits

Shared lineage has diverse effects on patterns of neuronal connectivity. In mammalian cortex, excitatory sister neurons assemble into shared microcircuits. In Drosophila, in contrast, sister neurons with different levels of Notch expression (NotchON/NotchOFF) develop distinct identities and diverge into separate circuits. Notch-differentiated sister neurons have been observed in vertebrate spinal cord and cerebellum, but whether they integrate into shared or distinct circuits remains unknown. Here, we evaluate how sister V2a (NotchOFF)/V2b (NotchON) neurons in the zebrafish integrate into spinal circuits. Using an in vivo labeling approach, we identified pairs of sister V2a/b neurons born from individual Vsx1+ progenitors and observed that they have somata in close proximity to each other and similar axonal trajectories. However, paired whole-cell electrophysiology and optogenetics revealed that sister V2a/b neurons receive input from distinct presynaptic sources, do not communicate with each other, and connect to largely distinct targets. These results resemble the divergent connectivity in Drosophila and represent the first evidence of Notch-differentiated circuit integration in a vertebrate system.

Coordinating cerebral cortical construction and connectivity: Unifying influence of radial progenitors

Radial progenitor development and function lay the foundation for the construction of the cerebral cortex. Radial glial scaffold, through its functions as a source of neurogenic progenitors and neuronal migration guide, is thought to provide a template for the formation of the cerebral cortex. Emerging evidence is challenging this limited view. Intriguingly, radial glial scaffold may also play a role in axonal growth, guidance, and neuronal connectivity. Radial glial cells not only facilitate the generation, placement, and allocation of neurons in the cortex but also regulate how they wire up. The organization and function of radial glial cells may thus be a unifying feature of the developing cortex that helps to precisely coordinate the right patterns of neurogenesis, neuronal placement, and connectivity necessary for the emergence of a functional cerebral cortex. This perspective critically explores this emerging view and its impact in the context of human brain development and disorders.

Characterization and Stage-Dependent Lineage Analysis of Intermediate Progenitors of Cortical GABAergic Interneurons

Intermediate progenitors of both excitatory and inhibitory neurons, which can replenish neurons in the adult brain, were recently identified. However, the generation of intermediate progenitors of GABAergic inhibitory neurons (IPGNs) has not been studied in detail. Here, we characterized the spatiotemporal distribution of IPGNs in mouse cerebral cortex. IPGNs generated neurons during both embryonic and postnatal stages, but the embryonic IPGNs were more proliferative. Our lineage tracing analyses showed that the embryonically proliferating IPGNs tended to localize to the superficial layers rather than the deep cortical layers at 3 weeks after birth. We also found that embryonic IPGNs derived from the medial and caudal ganglionic eminence (CGE) but more than half of the embryonic IPGNs were derived from the CGE and broadly distributed in the cerebral cortex. Taken together, our data indicate that the broadly located IPGNs during embryonic and postnatal stages exhibit a different proliferative property and layer distribution.

The Emergence of Network Activity Patterns in the Somatosensory Cortex - An Early Window to Autism Spectrum Disorders

Across mammalian species, patterned activity in neural populations is a prominent feature of developing sensory cortices. Numerous studies have long appreciated the diversity of these patterns, characterizing their differences in spatial and temporal dynamics. In the murine somatosensory cortex, neuronal co-activation is thought to guide the formation of sensory maps and prepare the cortex for sensory processing after birth. While pioneering studies deftly utilized slice electrophysiology and unit recordings to characterize correlated activity, a detailed understanding of the underlying circuits remains poorly understood. More recently, advances in in vivo calcium imaging in awake mouse pups and increasing genetic tractability of neuronal types have allowed unprecedented manipulation of circuit components at select developmental timepoints. These novel approaches have proven fundamental in uncovering the identity of neurons engaged in correlated activity during development. In particular, recent studies have highlighted interneurons as key in refining the spatial extent and temporal progression of patterned activity. Here, we discuss how emergent synchronous activity across the first postnatal weeks is shaped by underlying gamma aminobutyric acid (GABA)ergic contributors in the somatosensory cortex. Further, the importance of participation in specific activity patterns per se for neuronal maturation and perdurance will be of particular highlight in this survey of recent literature. Finally, we underscore how aberrant neuronal synchrony and disrupted inhibitory interneuron activity underlie sensory perturbations in neurodevelopmental disorders, particularly Autism Spectrum Disorders (ASDs), emphasizing the importance of future investigative approaches that incorporate the spatiotemporal features of patterned activity alongside the cellular components to probe disordered circuit assembly.

The role of cell lineage in the development of neuronal circuitry and function

Complex nervous systems have a modular architecture, whereby reiterative groups of neurons ("modules") that share certain structural and functional properties are integrated into large neural circuits. Neurons develop from proliferating progenitor cells that, based on their location and time of appearance, are defined by certain genetic programs. Given that genes expressed by a given progenitor play a fundamental role in determining the properties of its lineage (i.e., the neurons descended from that progenitor), one efficient developmental strategy would be to have lineages give rise to the structural modules of the mature nervous system. It is clear that this strategy plays an important role in neural development of many invertebrate animals, notably insects, where the availability of genetic techniques has made it possible to analyze the precise relationship between neuronal origin and differentiation since several decades. Similar techniques, developed more recently in the vertebrate field, reveal that functional modules of the mammalian cerebral cortex are also likely products of developmentally defined lineages. We will review studies that relate cell lineage to circuitry and function from a comparative developmental perspective, aiming at enhancing our understanding of neural progenitors and their lineages, and translating findings acquired in different model systems into a common conceptual framework.

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq

Striatal locally projecting neurons, or interneurons, act on nearby circuits and shape functional output to the rest of the basal ganglia. We performed single-cell RNA sequencing of striatal cells enriching for interneurons. We find seven discrete interneuron types, six of which are GABAergic. In addition to providing specific markers for the populations previously described, including those expressing Sst/Npy, Th, Npy without Sst, and Chat, we identify two small populations of cells expressing Cck with or without Vip. Surprisingly, the Pvalb-expressing cells do not constitute a discrete cluster but rather are part of a larger group of cells expressing Pthlh with a spatial gradient of Pvalb expression. Using PatchSeq, we show that Pthlh cells exhibit a continuum of electrophysiological properties correlated with expression of Pvalb. Furthermore, we find significant molecular differences that correlate with differences in electrophysiological properties between Pvalb-expressing cells of the striatum and those of the cortex.

Development and Arealization of the Cerebral Cortex

Adult cortical areas consist of specialized cell types and circuits that support unique higher-order cognitive functions. How this regional diversity develops from an initially uniform neuroepithelium has been the subject of decades of seminal research, and emerging technologies, including single-cell transcriptomics, provide a new perspective on area-specific molecular diversity. Here, we review the early developmental processes that underlie cortical arealization, including both cortex intrinsic and extrinsic mechanisms as embodied by the protomap and protocortex hypotheses, respectively. We propose an integrated model of serial homology whereby intrinsic genetic programs and local factors establish early transcriptomic differences between excitatory neurons destined to give rise to broad "proto-regions," and activity-dependent mechanisms lead to progressive refinement and formation of sharp boundaries between functional areas. Finally, we explore the potential of these basic developmental processes to inform our understanding of the emergence of functional neural networks and circuit abnormalities in neurodevelopmental disorders.

Illumination of neural development by in vivo clonal analysis

Single embryonic and adult neural stem cells (NSCs) are characterized by their self-renewal and differentiation potential. Lineage tracing via clonal analysis allows for specific labeling of a single NSC and tracking of its progeny throughout development. Over the past five decades, a plethora of clonal analysis methods have been developed in tandem with integration of chemical, genetic, imaging and sequencing techniques. Applications of these approaches have gained diverse insights into the heterogeneous behavior of NSCs, lineage relationships between cells, molecular regulation of fate specification and ontogeny of complex neural tissues. In this review, we summarize the history and methods of clonal analysis as well as highlight key findings revealed by single-cell lineage tracking of stem cells in developing and adult brains across different animal models.

Shaping Diversity Into the Brain's Form and Function

The brain contains a large diversity of unique cell types that use specific genetic programs to control development and instruct the intricate wiring of sensory, motor, and cognitive brain regions. In addition to their cellular diversity and specialized connectivity maps, each region's dedicated function is also expressed in their characteristic gross external morphologies. The folds on the surface of the cerebral cortex and cerebellum are classic examples. But, to what extent does structure relate to function and at what spatial scale? We discuss the mechanisms that sculpt functional brain maps and external morphologies. We also contrast the cryptic structural defects in conditions such as autism spectrum disorders to the overt microcephaly after Zika infections, taking into consideration that both diseases disrupt proper cognitive development. The data indicate that dynamic processes shape all brain areas to fit into jigsaw-like patterns. The patterns in each region reflect circuit connectivity, which ultimately supports local signal processing and accomplishes multi-areal integration of information processing to optimize brain functions.

Linking neuronal lineage and wiring specificity

Brain function requires precise neural circuit assembly during development. Establishing a functional circuit involves multiple coordinated steps ranging from neural cell fate specification to proper matching between pre- and post-synaptic partners. How neuronal lineage and birth timing influence wiring specificity remains an open question. Recent findings suggest that the relationships between lineage, birth timing, and wiring specificity vary in different neuronal circuits. In this review, we summarize our current understanding of the cellular, molecular, and developmental mechanisms linking neuronal lineage and birth timing to wiring specificity in a few specific systems in Drosophila and mice, and review different methods employed to explore these mechanisms.

Homeostatic and regenerative neurogenesis in salamanders

Large-scale regeneration in the adult central nervous system is a unique capacity of salamanders among tetrapods. Salamanders can replace neuronal populations, repair damaged nerve fibers and restore tissue architecture in retina, brain and spinal cord, leading to functional recovery. The underlying mechanisms have long been difficult to study due to the paucity of available genomic tools. Recent technological progress, such as genome sequencing, transgenesis and genome editing provide new momentum for systematic interrogation of regenerative processes in the salamander central nervous system. Understanding central nervous system regeneration also entails designing the appropriate molecular, cellular, and behavioral assays. Here we outline the organization of salamander brain structures. With special focus on ependymoglial cells, we integrate cellular and molecular processes of neurogenesis during developmental and adult homeostasis as well as in various injury models. Wherever possible, we correlate developmental and regenerative neurogenesis to the acquisition and recovery of behaviors. Throughout the review we place the findings into an evolutionary context for inter-species comparisons.

Lineage Relationships Do Not Drive MGE/PoA-Derived Interneuron Clustering in the Brain

Neocortical excitatory and inhibitory neurons derive from distinct progenitor domains during embryonic development and migrate to their final positions, where they assemble into functional circuits. This process appears to be influenced by lineage relationships among locally born excitatory neurons, raising the intriguing possibility that this might be true for cortical interneurons. Two recent articles by the Fishell laboratory and our own used retrovirus-encoded DNA barcodes as unambiguous lineage-tracing tools to address this question, finding that clonally related inhibitory interneurons dispersed widely across the forebrain (Harwell et al., 2015; Mayer et al., 2015). This Matters Arising Response addresses the Sultan et al. (2016) Matters Arising paper, published concurrently in Neuron, where the authors reanalyze the datasets from both studies and propose a new interpretation, whereby clonally related interneurons would be considered clustered according to specific spatial constraints. After studying the report from Sultan et al. (2016) and carefully revisiting previously published studies, we find no evidence of lineage-dependent MGE/PoA-derived interneuron clustering in the forebrain.

Hippocampal GABAergic Inhibitory Interneurons

In the hippocampus GABAergic local circuit inhibitory interneurons represent only ~10-15% of the total neuronal population; however, their remarkable anatomical and physiological diversity allows them to regulate virtually all aspects of cellular and circuit function. Here we provide an overview of the current state of the field of interneuron research, focusing largely on the hippocampus. We discuss recent advances related to the various cell types, including their development and maturation, expression of subtype-specific voltage- and ligand-gated channels, and their roles in network oscillations. We also discuss recent technological advances and approaches that have permitted high-resolution, subtype-specific examination of their roles in numerous neural circuit disorders and the emerging therapeutic strategies to ameliorate such pathophysiological conditions. The ultimate goal of this review is not only to provide a touchstone for the current state of the field, but to help pave the way for future research by highlighting where gaps in our knowledge exist and how a complete appreciation of their roles will aid in future therapeutic strategies.

Clonally Related GABAergic Interneurons Do Not Randomly Disperse but Frequently Form Local Clusters in the Forebrain

Progenitor cells in the medial ganglionic eminence (MGE) and preoptic area (PoA) give rise to GABAergic inhibitory interneurons that are distributed in the forebrain, largely in the cortex, hippocampus, and striatum. Two previous studies suggest that clonally related interneurons originating from individual MGE/PoA progenitors frequently form local clusters in the cortex. However, Mayer et al. and Harwell et al. recently argued that MGE/PoA-derived interneuron clones disperse widely and populate different forebrain structures. Here, we report further analysis of the spatial distribution of clonally related interneurons and demonstrate that interneuron clones do not non-specifically disperse in the forebrain. Around 70% of clones are restricted to one brain structure, predominantly the cortex. Moreover, the regional distribution of clonally related interneurons exhibits a clear clustering feature, which cannot occur by chance from a random diffusion. These results confirm that lineage relationship influences the spatial distribution of inhibitory interneurons in the forebrain. This Matters Arising paper is in response to Harwell et al. (2015) and Mayer et al. (2015), published in Neuron. See also the response by Turrero García et al. (2016) and Mayer et al. (2016), published in this issue.

Programming and reprogramming the brain: a meeting of minds in neural fate

In early April 2017, over 130 delegates met in Munich, Germany, to discuss the latest research in the development and reprogramming of cells of the nervous system. The conference, which was organised by Abcam and entitled 'Programming and Reprogramming the Brain', was a great success, and provided an excellent snapshot of the current state of the field, and what the challenges are for the future. This Meeting Review provides a summary of the talks presented and the major themes that emerged from the conference.

Radial glia in the ventral telencephalon

The ventral telencephalon is the developmental origin of the basal ganglia and the source of neuronal and glial cells that integrate into developing circuits in other areas of the brain. Radial glia in the embryonic subpallium give rise to an enormous diversity of mature cell types, either directly or through other transit-amplifying progenitors. Here, we review current knowledge about these subpallial neural stem cells and their progeny, focusing on the period of neurogenesis. We describe their cell biological features and the extrinsic and intrinsic molecular codes that guide their fate specification in defined temporal and spatial sequences. We also discuss the role of clonal lineage in the organization and specification of mature neurons.

GABAergic Interneuron Differentiation in the Basal Forebrain Is Mediated through Direct Regulation of Glutamic Acid Decarboxylase Isoforms by Dlx Homeobox Transcription Factors

GABA is the key inhibitory neurotransmitter in the cortex but regulation of its synthesis during forebrain development is poorly understood. In the telencephalon, members of the distal-less (Dlx) homeobox gene family are expressed in, and regulate the development of, the basal ganglia primodia from which many GABAergic neurons originate and migrate to other forebrain regions. The Dlx1/Dlx2 double knock-out mice die at birth with abnormal cortical development, including loss of tangential migration of GABAergic inhibitory interneurons to the neocortex (Anderson et al., 1997a). We have discovered that specific promoter regulatory elements of glutamic acid decarboxylase isoforms (Gad1 and Gad2), which regulate GABA synthesis from the excitatory neurotransmitter glutamate, are direct transcriptional targets of both DLX1 and DLX2 homeoproteins in vivo Further gain- and loss-of-function studies in vitro and in vivo demonstrated that both DLX1 and DLX2 are necessary and sufficient for Gad gene expression. DLX1 and/or DLX2 activated the transcription of both Gad genes, and defects in Dlx function disrupted the differentiation of GABAergic interneurons with global reduction in GABA levels in the forebrains of the Dlx1/Dlx2 double knock-out mouse in vivo Identification of Gad genes as direct Dlx transcriptional targets is significant; it extends our understanding of Dlx gene function in the developing forebrain beyond the regulation of tangential interneuron migration to the differentiation of GABAergic interneurons arising from the basal telencephalon, and may help to unravel the pathogenesis of several developmental brain disorders.SIGNIFICANCE STATEMENT GABA is the major inhibitory neurotransmitter in the brain. We show that Dlx1/Dlx2 homeobox genes regulate GABA synthesis during forebrain development through direct activation of glutamic acid decarboxylase enzyme isoforms that convert glutamate to GABA. This discovery helps explain how Dlx mutations result in abnormal forebrain development, due to defective differentiation, in addition to the loss of tangential migration of GABAergic inhibitory interneurons to the neocortex. Reduced numbers or function of cortical GABAergic neurons may lead to hyperactivity states such as seizures (Cobos et al., 2005) or contribute to the pathogenesis of some autism spectrum disorders. GABAergic dysfunction in the basal ganglia could disrupt the learning and development of complex motor and cognitive behaviors (Rubenstein and Merzenich, 2003).

Precise inhibitory microcircuit assembly of developmentally related neocortical interneurons in clusters

GABA-ergic interneurons provide diverse inhibitions that are essential for the operation of neuronal circuits in the neocortex. However, the mechanisms that control the functional organization of neocortical interneurons remain largely unknown. Here we show that developmental origins influence fine-scale synapse formation and microcircuit assembly of neocortical interneurons. Spatially clustered neocortical interneurons originating from low-titre retrovirus-infected radial glial progenitors in the embryonic medial ganglionic eminence and preoptic area preferentially develop electrical, but not chemical, synapses with each other. This lineage-related electrical coupling forms predominantly between the same interneuron subtype over an extended postnatal period and across a range of distances, and promotes action potential generation and synchronous firing. Interestingly, this selective electrical coupling relates to a coordinated inhibitory chemical synapse formation between sparsely labelled interneurons in clusters and the same nearby excitatory neurons. These results suggest a link between the lineage relationship of neocortical interneurons and their precise functional organization.

Developmental neuroscientists have long asked if clonally-related neurons retain functional relationships after maturation. The authors show that sparsely labelled neocortical interneurons in clusters with high possibility of clonal relation preferentially form electrical, but not chemical, synapses.

Temporal Cohorts of Lineage-Related Neurons Perform Analogous Functions in Distinct Sensorimotor Circuits

Neuronal stem cell lineages are the fundamental developmental units of the brain, and neuronal circuits are the fundamental functional units of the brain. Determining lineage-circuitry relationships is essential for deciphering the developmental logic of circuit assembly. While the spatial distribution of lineage-related neurons has been investigated in a few brain regions [1-9], an important, but unaddressed question is whether temporal information that diversifies neuronal progeny within a single lineage also impacts circuit assembly. Circuits in the sensorimotor system (e.g., spinal cord) are thought to be assembled sequentially [10-14], making this an ideal brain region for investigating the circuit-level impact of temporal patterning within a lineage. Here, we use intersectional genetics, optogenetics, high-throughput behavioral analysis, single-neuron labeling, connectomics, and calcium imaging to determine how a set of bona fide lineage-related interneurons contribute to sensorimotor circuitry in the Drosophila larva. We show that Even-skipped lateral interneurons (ELs) are sensory processing interneurons. Late-born ELs contribute to a proprioceptive body posture circuit, whereas early-born ELs contribute to a mechanosensitive escape circuit. These data support a model in which a single neuronal stem cell can produce a large number of interneurons with similar functional capacity that are distributed into different circuits based on birth timing. In summary, these data establish a link between temporal specification of neuronal identity and circuit assembly at the single-cell level.

Cortical interneuron specification: the juncture of genes, time and geometry

A fundamental question in developmental neuroscience is how hundreds of diverse cell types are generated to form specialized brain regions. The ganglionic eminences (GEs) are embryonic brain structures located in the ventral telencephalon that produce many inhibitory GABA (γ-Aminobutyric acid)-ergic cell types, including long-range projection neurons and local interneurons (INs), which disperse widely throughout the brain. While much has been discovered about the origin and wiring of these cells, a major question remains: how do neurons originating in the GEs become specified during development as one differentiated subtype versus another? This review will cover recent work that has advanced our knowledge of the mechanisms governing cortical interneuron subtype specification, particularly progenitors' spatial origin, birthdates, lineage, and mode of division.