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Single-cell delineation of lineage and genetic identity in the mouse brain

Bandler, Rachel C; Vitali, Ilaria; Delgado, Ryan N; Ho, May C; Dvoretskova, Elena; Ibarra Molinas, Josue S; Frazel, Paul W; Mohammadkhani, Maesoumeh; Machold, Robert; Maedler, Sophia; Liddelow, Shane A; Nowakowski, Tomasz J; Fishell, Gord; Mayer, Christian
During neurogenesis, mitotic progenitor cells lining the ventricles of the embryonic mouse brain undergo their final rounds of cell division, giving rise to a wide spectrum of postmitotic neurons and glia1,2. The link between developmental lineage and cell-type diversity remains an open question. Here we used massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during mouse forebrain development. We quantified clonal divergence and convergence across all major cell classes postnatally, and found diverse types of GABAergic neuron that share a common lineage. Divergence of GABAergic clones occurred during embryogenesis upon cell-cycle exit, suggesting that differentiation into subtypes is initiated as a lineage-dependent process at the progenitor cell level.
PMID: 34912118
ISSN: 1476-4687
CID: 5106272

Bottom-up inputs are required for establishment of top-down connectivity onto cortical layer 1 neurogliaform cells

Ibrahim, Leena Ali; Huang, Shuhan; Fernandez-Otero, Marian; Sherer, Mia; Qiu, Yanjie; Vemuri, Spurti; Xu, Qing; Machold, Robert; Pouchelon, Gabrielle; Rudy, Bernardo; Fishell, Gord
Higher-order projections to sensory cortical areas converge on layer 1 (L1), the primary site for integration of top-down information via the apical dendrites of pyramidal neurons and L1 GABAergic interneurons. Here we investigated the contribution of early thalamic inputs onto L1 interneurons for establishment of top-down connectivity in the primary visual cortex. We find that bottom-up thalamic inputs predominate during L1 development and preferentially target neurogliaform cells. We show that these projections are critical for the subsequent strengthening of top-down inputs from the anterior cingulate cortex onto L1 neurogliaform cells. Sensory deprivation or selective removal of thalamic afferents blocked this phenomenon. Although early activation of the anterior cingulate cortex resulted in premature strengthening of these top-down afferents, this was dependent on thalamic inputs. Our results demonstrate that proper establishment of top-down connectivity in the visual cortex depends critically on bottom-up inputs from the thalamus during postnatal development.
PMID: 34478630
ISSN: 1097-4199
CID: 5079122

Neocortical Layer 1: An Elegant Solution to Top-Down and Bottom-Up Integration

Schuman, Benjamin; Dellal, Shlomo; Prönneke, Alvar; Machold, Robert; Rudy, Bernardo
Many of our daily activities, such as riding a bike to work or reading a book in a noisy cafe, and highly skilled activities, such as a professional playing a tennis match or a violin concerto, depend upon the ability of the brain to quickly make moment-to-moment adjustments to our behavior in response to the results of our actions. Particularly, they depend upon the ability of the neocortex to integrate the information provided by the sensory organs (bottom-up information) with internally generated signals such as expectations or attentional signals (top-down information). This integration occurs in pyramidal cells (PCs) and their long apical dendrite, which branches extensively into a dendritic tuft in layer 1 (L1). The outermost layer of the neocortex, L1 is highly conserved across cortical areas and species. Importantly, L1 is the predominant input layer for top-down information, relayed by a rich, dense mesh of long-range projections that provide signals to the tuft branches of the PCs. Here, we discuss recent progress in our understanding of the composition of L1 and review evidence that L1 processing contributes to functions such as sensory perception, cross-modal integration, controlling states of consciousness, attention, and learning. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see for revised estimates.
PMID: 33730511
ISSN: 1545-4126
CID: 4851042

FoxG1 regulates the formation of cortical GABAergic circuit during an early postnatal critical period resulting in autism spectrum disorder-like phenotypes

Miyoshi, Goichi; Ueta, Yoshifumi; Natsubori, Akiyo; Hiraga, Kou; Osaki, Hironobu; Yagasaki, Yuki; Kishi, Yusuke; Yanagawa, Yuchio; Fishell, Gord; Machold, Robert P; Miyata, Mariko
Abnormalities in GABAergic inhibitory circuits have been implicated in the aetiology of autism spectrum disorder (ASD). ASD is caused by genetic and environmental factors. Several genes have been associated with syndromic forms of ASD, including FOXG1. However, when and how dysregulation of FOXG1 can result in defects in inhibitory circuit development and ASD-like social impairments is unclear. Here, we show that increased or decreased FoxG1 expression in both excitatory and inhibitory neurons results in ASD-related circuit and social behavior deficits in our mouse models. We observe that the second postnatal week is the critical period when regulation of FoxG1 expression is required to prevent subsequent ASD-like social impairments. Transplantation of GABAergic precursor cells prior to this critical period and reduction in GABAergic tone via Gad2 mutation ameliorates and exacerbates circuit functionality and social behavioral defects, respectively. Our results provide mechanistic insight into the developmental timing of inhibitory circuit formation underlying ASD-like phenotypes in mouse models.
PMID: 34145239
ISSN: 2041-1723
CID: 4916462

Sleep down state-active ID2/Nkx2.1 interneurons in the neocortex

Valero, Manuel; Viney, Tim J; Machold, Robert; Mederos, Sara; Zutshi, Ipshita; Schuman, Benjamin; Senzai, Yuta; Rudy, Bernardo; Buzsáki, György
Pyramidal cells and GABAergic interneurons fire together in balanced cortical networks. In contrast to this general rule, we describe a distinct neuron type in mice and rats whose spiking activity is anti-correlated with all principal cells and interneurons in all brain states but, most prevalently, during the down state of non-REM (NREM) sleep. We identify these down state-active (DSA) neurons as deep-layer neocortical neurogliaform cells that express ID2 and Nkx2.1 and are weakly immunoreactive to neuronal nitric oxide synthase. DSA neurons are weakly excited by deep-layer pyramidal cells and strongly inhibited by several other GABAergic cell types. Spiking of DSA neurons modified the sequential firing order of other neurons at down-up transitions. Optogenetic activation of ID2+Nkx2.1+ interneurons in the posterior parietal cortex during NREM sleep, but not during waking, interfered with consolidation of cue discrimination memory. Despite their sparsity, DSA neurons perform critical physiological functions.
PMID: 33619404
ISSN: 1546-1726
CID: 4794392

Cellular birthdate predicts laminar and regional cholinergic projection topography in the forebrain

Allaway, Kathryn C; Muñoz, William; Tremblay, Robin; Sherer, Mia; Herron, Jacob; Rudy, Bernardo; Machold, Robert; Fishell, Gordon
The basal forebrain cholinergic system projects broadly throughout the cortex and constitutes a critical source of neuromodulation for arousal and attention. Traditionally, this system was thought to function diffusely. However, recent studies have revealed a high degree of spatiotemporal specificity in cholinergic signaling. How the organization of cholinergic afferents confers this level of precision remains unknown. Here, using intersectional genetic fate mapping, we demonstrate that cholinergic fibers within the mouse cortex exhibit remarkable laminar and regional specificity and that this is organized in accordance with cellular birthdate. Strikingly, birthdated cholinergic projections within the cortex follow an inside-out pattern of innervation. While early born cholinergic populations target deep layers, late born ones innervate superficial laminae. We also find that birthdate predicts cholinergic innervation patterns within the amygdala, hippocampus, and prefrontal cortex. Our work reveals previously unappreciated specificity within the cholinergic system and the developmental logic by which these circuits are assembled.
PMID: 33355093
ISSN: 2050-084x
CID: 4731082

Author Correction: Innovations present in the primate interneuron repertoire

Krienen, Fenna M; Goldman, Melissa; Zhang, Qiangge; Del Rosario, Ricardo C H; Florio, Marta; Machold, Robert; Saunders, Arpiar; Levandowski, Kirsten; Zaniewski, Heather; Schuman, Benjamin; Wu, Carolyn; Lutservitz, Alyssa; Mullally, Christopher D; Reed, Nora; Bien, Elizabeth; Bortolin, Laura; Fernandez-Otero, Marian; Lin, Jessica D; Wysoker, Alec; Nemesh, James; Kulp, David; Burns, Monika; Tkachev, Victor; Smith, Richard; Walsh, Christopher A; Dimidschstein, Jordane; Rudy, Bernardo; Kean, Leslie S; Berretta, Sabina; Fishell, Gord; Feng, Guoping; McCarroll, Steven A
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
PMID: 33230336
ISSN: 1476-4687
CID: 4684702

Innovations present in the primate interneuron repertoire

Krienen, Fenna M; Goldman, Melissa; Zhang, Qiangge; C H Del Rosario, Ricardo; Florio, Marta; Machold, Robert; Saunders, Arpiar; Levandowski, Kirsten; Zaniewski, Heather; Schuman, Benjamin; Wu, Carolyn; Lutservitz, Alyssa; Mullally, Christopher D; Reed, Nora; Bien, Elizabeth; Bortolin, Laura; Fernandez-Otero, Marian; Lin, Jessica D; Wysoker, Alec; Nemesh, James; Kulp, David; Burns, Monika; Tkachev, Victor; Smith, Richard; Walsh, Christopher A; Dimidschstein, Jordane; Rudy, Bernardo; S Kean, Leslie; Berretta, Sabina; Fishell, Gord; Feng, Guoping; McCarroll, Steven A
Primates and rodents, which descended from a common ancestor around 90 million years ago1, exhibit profound differences in behaviour and cognitive capacity; the cellular basis for these differences is unknown. Here we use single-nucleus RNA sequencing to profile RNA expression in 188,776 individual interneurons across homologous brain regions from three primates (human, macaque and marmoset), a rodent (mouse) and a weasel (ferret). Homologous interneuron types-which were readily identified by their RNA-expression patterns-varied in abundance and RNA expression among ferrets, mice and primates, but varied less among primates. Only a modest fraction of the genes identified as 'markers' of specific interneuron subtypes in any one species had this property in another species. In the primate neocortex, dozens of genes showed spatial expression gradients among interneurons of the same type, which suggests that regional variation in cortical contexts shapes the RNA expression patterns of adult neocortical interneurons. We found that an interneuron type that was previously associated with the mouse hippocampus-the 'ivy cell', which has neurogliaform characteristics-has become abundant across the neocortex of humans, macaques and marmosets but not mice or ferrets. We also found a notable subcortical innovation: an abundant striatal interneuron type in primates that had no molecularly homologous counterpart in mice or ferrets. These interneurons expressed a unique combination of genes that encode transcription factors, receptors and neuropeptides and constituted around 30% of striatal interneurons in marmosets and humans.
PMID: 32999462
ISSN: 1476-4687
CID: 4636632

Four Unique Interneuron Populations Reside in Neocortical Layer 1

Schuman, Benjamin; Machold, Robert P; Hashikawa, Yoshiko; Fuzik, János; Fishell, Gord J; Rudy, Bernardo
Sensory perception depends on neocortical computations that contextually adjust sensory signals in different internal and environmental contexts. Neocortical layer 1 (L1) is the main target of cortical and subcortical inputs that provide "top-down" information for context-dependent sensory processing. Although L1 is devoid of excitatory cells, it contains the distal "tuft" dendrites of pyramidal cells (PCs) located in deeper layers. L1 also contains a poorly characterized population of GABAergic interneurons (INs), which regulate the impact that different top-down inputs have on PCs. A poor comprehension of L1 IN subtypes and how they affect PC activity has hampered our understanding of the mechanisms that underlie contextual modulation of sensory processing. We used novel genetic strategies in male and female mice combined with electrophysiological and morphological methods to help resolve differences that were unclear when using only electrophysiological and/or morphological approaches. We discovered that L1 contains four distinct populations of INs, each with a unique molecular profile, morphology, and electrophysiology, including a previously overlooked IN population (named here "canopy cells") representing 40% of L1 INs. In contrast to what is observed in other layers, most L1 neurons appear to be unique to the layer, highlighting the specialized character of the signal processing that takes place in L1. This new understanding of INs in L1, as well as the application of genetic methods based on the markers described here, will enable investigation of the cellular and circuit mechanisms of top-down processing in L1 with unprecedented detail.SIGNIFICANCE STATEMENT Neocortical layer 1 (L1) is the main target of corticocortical and subcortical projections that mediate top-down or context-dependent sensory perception. However, this unique layer is often referred to as "enigmatic" because its neuronal composition has been difficult to determine. Using a combination of genetic, electrophysiological, and morphological approaches that helped to resolve differences that were unclear when using a single approach, we were able to decipher the neuronal composition of L1. We identified markers that distinguish L1 neurons and found that the layer contains four populations of GABAergic interneurons, each with unique molecular profiles, morphologies, and electrophysiological properties. These findings provide a new framework for studying the circuit mechanisms underlying the processing of top-down inputs in neocortical L1.
PMID: 30413647
ISSN: 1529-2401
CID: 3562702

Developmental diversification of cortical inhibitory interneurons

Mayer, Christian; Hafemeister, Christoph; Bandler, Rachel C; Machold, Robert; Brito, Renata Batista; Jaglin, Xavier; Allaway, Kathryn; Butler, Andrew; Fishell, Gord; Satija, Rahul
Diverse subsets of cortical interneurons have vital roles in higher-order brain functions. To investigate how this diversity is generated, here we used single-cell RNA sequencing to profile the transcriptomes of mouse cells collected along a developmental time course. Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity. Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state. By integrating datasets across developmental time points, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, and uncovered the embryonic emergence of cardinal interneuron subtypes. Our analysis revealed that the transcription factor Mef2c, which is linked to various neuropsychiatric and neurodevelopmental disorders, delineates early precursors of parvalbumin-expressing neurons, and is essential for their development. These findings shed new light on the molecular diversification of early inhibitory precursors, and identify gene modules that may influence the specification of human interneuron subtypes.
PMID: 29513653
ISSN: 1476-4687
CID: 2975202