scholarly journals Single-cell genomics identifies cell type–specific molecular changes in autism

Science ◽  
2019 ◽  
Vol 364 (6441) ◽  
pp. 685-689 ◽  
Author(s):  
Dmitry Velmeshev ◽  
Lucas Schirmer ◽  
Diane Jung ◽  
Maximilian Haeussler ◽  
Yonatan Perez ◽  
...  
Keyword(s):  
Cell Types ◽  
Molecular State ◽  
Clinical Severity ◽  
Projection Neurons ◽  
Specific Cell ◽  
Cortical Projection ◽  
Molecular Changes ◽  
Single Nucleus ◽  
Gene Expression Studies ◽  
Transcriptomic Changes

Despite the clinical and genetic heterogeneity of autism, bulk gene expression studies show that changes in the neocortex of autism patients converge on common genes and pathways. However, direct assessment of specific cell types in the brain affected by autism has not been feasible until recently. We used single-nucleus RNA sequencing of cortical tissue from patients with autism to identify autism-associated transcriptomic changes in specific cell types. We found that synaptic signaling of upper-layer excitatory neurons and the molecular state of microglia are preferentially affected in autism. Moreover, our results show that dysregulation of specific groups of genes in cortico-cortical projection neurons correlates with clinical severity of autism. These findings suggest that molecular changes in upper-layer cortical circuits are linked to behavioral manifestations of autism.

scholarly journals Mapping Mesoscale Axonal Projections in the Mouse Brain Using A 3D Convolutional Network

2019 ◽  
Author(s):  
Drew Friedmann ◽  
Albert Pun ◽  
Eliza L Adams ◽  
Jan H Lui ◽  
Justus M Kebschull ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Neural Circuit ◽  
Cell Types ◽  
Ease Of Use ◽  
Projection Neurons ◽  
Specific Cell ◽  
Cortical Projection ◽  
Convolutional Network ◽  
Light Sheet Microscopy ◽  
Axonal Projections

AbstractThe projection targets of a neuronal population are a key feature of its anatomical characterization. Historically, tissue sectioning, confocal microscopy, and manual scoring of specific regions of interest have been used to generate coarse summaries of mesoscale projectomes. We present here TrailMap, a 3D convolutional network for extracting axonal projections from intact cleared mouse brains imaged by light-sheet microscopy. TrailMap allows region-based quantification of total axon content in large and complex 3D structures after registration to a standard reference atlas. The identification of axonal structures as thin as one voxel benefits from data augmentation but also requires a loss function that tolerates errors in annotation. A network trained with volumes of serotonergic axons in all major brain regions can be generalized to map and quantify axons from thalamocortical, deep cerebellar, and cortical projection neurons, validating transfer learning as a tool to adapt the model to novel categories of axonal morphology. Speed of training, ease of use, and accuracy improve over existing tools without a need for specialized computing hardware. Given the recent emphasis on genetically and functionally defining cell types in neural circuit analysis, TrailMap will facilitate automated extraction and quantification of axons from these specific cell types at the scale of the entire mouse brain, an essential component of deciphering their connectivity.

scholarly journals Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network

2020 ◽  
Vol 117 (20) ◽  
pp. 11068-11075 ◽  
Author(s):  
Drew Friedmann ◽  
Albert Pun ◽  
Eliza L. Adams ◽  
Jan H. Lui ◽  
Justus M. Kebschull ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Neural Circuit ◽  
Cell Types ◽  
Ease Of Use ◽  
Projection Neurons ◽  
Specific Cell ◽  
Cortical Projection ◽  
Convolutional Network ◽  
Light Sheet Microscopy ◽  
Axonal Projections

The projection targets of a neuronal population are a key feature of its anatomical characteristics. Historically, tissue sectioning, confocal microscopy, and manual scoring of specific regions of interest have been used to generate coarse summaries of mesoscale projectomes. We present here TrailMap, a three-dimensional (3D) convolutional network for extracting axonal projections from intact cleared mouse brains imaged by light-sheet microscopy. TrailMap allows region-based quantification of total axon content in large and complex 3D structures after registration to a standard reference atlas. The identification of axonal structures as thin as one voxel benefits from data augmentation but also requires a loss function that tolerates errors in annotation. A network trained with volumes of serotonergic axons in all major brain regions can be generalized to map and quantify axons from thalamocortical, deep cerebellar, and cortical projection neurons, validating transfer learning as a tool to adapt the model to novel categories of axonal morphology. Speed of training, ease of use, and accuracy improve over existing tools without a need for specialized computing hardware. Given the recent emphasis on genetically and functionally defining cell types in neural circuit analysis, TrailMap will facilitate automated extraction and quantification of axons from these specific cell types at the scale of the entire mouse brain, an essential component of deciphering their connectivity.

Vertebrate retinal ganglion cells are selected from competent progenitors by the action of Notch

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3637-3650 ◽  
Author(s):  
C.P. Austin ◽  
D.E. Feldman ◽  
J.A. Ida ◽  
C.L. Cepko
Keyword(s):  
Cell Fate ◽  
Ganglion Cells ◽  
Notch Pathway ◽  
Cell Types ◽  
Projection Neurons ◽  
Specific Cell ◽  
Vitro Assay ◽  
Notch Activity

The first cells generated during development of the vertebrate retina are the ganglion cells, the projection neurons of the retina. Although they are one of the most intensively studied cell types within the central nervous system, little is known of the mechanisms that determine ganglion cell fate. We demonstrate that ganglion cells are selected from a large group of competent progenitors that comprise the majority of the early embryonic retina and that differentiation within this group is regulated by Notch. Notch activity in vivo was diminished using antisense oligonucleotides or augmented using a retrovirally transduced constitutively active allele of Notch. The number of ganglion cells produced was inversely related to the level of Notch activity. In addition, the Notch ligand Delta inhibited retinal progenitors from differentiating as ganglion cells to the same degree as did activated Notch in an in vitro assay. These results suggest a conserved strategy for neurogenesis in the retina and describe a versatile in vitro and in vivo system with which to examine the action of the Notch pathway in a specific cell fate decision in a vertebrate.

scholarly journals Single-nucleus RNA sequencing shows convergent evidence from different cell types for altered synaptic plasticity in major depressive disorder

2018 ◽  
Author(s):  
Corina Nagy ◽  
Malosree Maitra ◽  
Arnaud Tanti ◽  
Matthew Suderman ◽  
Jean-Francois Théroux ◽  
...  
Keyword(s):  
Gene Expression ◽  
Major Depressive Disorder ◽  
Synaptic Plasticity ◽  
Depressive Disorder ◽  
Cell Types ◽  
Specific Cell ◽  
Major Depressive ◽  
Differential Correlation ◽  
Dorsolateral Prefrontal ◽  
Single Nucleus

AbstractMajor depressive disorder (MDD) is a complex illness that involves the interaction of different brain systems, pathways, and cell types. Past molecular studies of MDD relied on cellular homogenates of post-mortem brain tissue, making it impossible to determine gene expression changes within individual cells. Using single-cell transcriptomics, we examined almost 80,000 nuclei from the dorsolateral prefrontal cortex of individuals with MDD and healthy controls. Our analyses identified 26 distinct cellular clusters, and over 60% of these showed transcriptional differences between groups. Specifically, 96 genes were differentially expressed, the majority of which were downregulated. Convergent evidence from our analyses, including gene expression, differential correlation, and gene ontology implicated dysregulation of synaptic plasticity in the etiopathogenesis of MDD. Our results show that this high-resolution approach can reveal previously undetectable changes in specific cell types in the context of complex phenotypes and heterogeneous tissues.

scholarly journals Altered cell and RNA isoform diversity in aging Down syndrome brains

2021 ◽  
Vol 118 (47) ◽  
pp. e2114326118
Author(s):  
Carter R. Palmer ◽  
Christine S. Liu ◽  
William J. Romanow ◽  
Ming-Hsiang Lee ◽  
Jerold Chun
Keyword(s):  
Down Syndrome ◽  
Large Scale ◽  
Cell Types ◽  
Chromosome 21 ◽  
Specific Cell ◽  
Sequencing Technologies ◽  
Isoform Diversity ◽  
Long Read ◽  
Single Nucleus ◽  
Altered Cell

Down syndrome (DS), trisomy of human chromosome 21 (HSA21), is characterized by lifelong cognitive impairments and the development of the neuropathological hallmarks of Alzheimer’s disease (AD). The cellular and molecular modifications responsible for these effects are not understood. Here we performed single-nucleus RNA sequencing (snRNA-seq) employing both short- (Illumina) and long-read (Pacific Biosciences) sequencing technologies on a total of 29 DS and non-DS control prefrontal cortex samples. In DS, the ratio of inhibitory-to-excitatory neurons was significantly increased, which was not observed in previous reports examining sporadic AD. DS microglial transcriptomes displayed AD-related aging and activation signatures in advance of AD neuropathology, with increased microglial expression of C1q complement genes (associated with dendritic pruning) and the HSA21 transcription factor gene RUNX1. Long-read sequencing detected vast RNA isoform diversity within and among specific cell types, including numerous sequences that differed between DS and control brains. Notably, over 8,000 genes produced RNAs containing intra-exonic junctions, including amyloid precursor protein (APP) that had previously been associated with somatic gene recombination. These and related results illuminate large-scale cellular and transcriptomic alterations as features of the aging DS brain.

The Subventricular Zone: A Key Player in Human Neocortical Development

2017 ◽  
Vol 24 (2) ◽  
pp. 156-170 ◽  
Author(s):  
J. Alberto Ortega ◽  
Fani Memi ◽  
Nevena Radonjic ◽  
Radmila Filipovic ◽  
Inseyah Bagasrawala ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
Subventricular Zone ◽  
Ventricular Zone ◽  
Cell Types ◽  
Projection Neurons ◽  
Cortical Projection ◽  
Intrauterine Development ◽  
Vitro Model ◽  
Primate Cerebral Cortex

One of the main characteristics of the developing brain is that all neurons and the majority of macroglia originate first in the ventricular zone (VZ), next to the lumen of the cerebral ventricles, and later on in a secondary germinal area above the VZ, the subventricular zone (SVZ). The SVZ is a transient compartment mitotically active in humans for several gestational months. It serves as a major source of cortical projection neurons as well as an additional source of glial cells and potentially some interneuron subpopulations. The SVZ is subdivided into the smaller inner (iSVZ) and the expanded outer SVZ (oSVZ). The enlargement of the SVZ and, in particular, the emergence of the oSVZ are evolutionary adaptations that were critical to the expansion and unique cellular composition of the primate cerebral cortex. In this review, we discuss the cell types and organization of the human SVZ during the first half of the 40 weeks of gestation that comprise intrauterine development. We focus on this period as it is when the bulk of neurogenesis in the human cerebral cortex takes place. We consider how the survival and fate of SVZ cells depend on environmental influences, by analyzing the results from in vitro experiments with human cortical progenitor cells. This in vitro model is a powerful tool to better understand human neocortex formation and the etiology of neurodevelopmental disorders, which in turn will facilitate the design of targeted preventive and/or therapeutic strategies.

scholarly journals Hippocampal and thalamic afferents form distinct synaptic microcircuits in the mouse frontal cortex

2021 ◽  
Author(s):  
Kourtney Graham ◽  
Nelson Spruston ◽  
Erik B. Bloss
Keyword(s):  
Information Processing ◽  
Frontal Cortex ◽  
Cortical Neurons ◽  
Basolateral Amygdala ◽  
Cell Types ◽  
Brain Regions ◽  
Projection Neurons ◽  
Specific Cell ◽  
Nucleus Reuniens ◽  
Level Information

AbstractNeural circuits within the frontal cortex support the flexible selection of goal-directed behaviors by integrating input from brain regions associated with sensory, emotional, episodic, and semantic memory functions. From a connectomics perspective, determining how these disparate afferent inputs target their synapses to specific cell types in the frontal cortex may prove crucial in understanding circuit-level information processing. Here, we used monosynaptic retrograde rabies mapping to examine the distribution of afferent neurons targeting four distinct classes of local inhibitory interneurons and four distinct classes of excitatory projection neurons in mouse infralimbic cortex. Interneurons expressing parvalbumin, somatostatin, or vasoactive intestinal peptide received a large proportion of inputs from hippocampal regions, while interneurons expressing neuron-derived neurotrophic factor received a large proportion of inputs from thalamic regions. A more moderate hippocampal-thalamic dichotomy was found among the inputs targeting excitatory neurons that project to the basolateral amygdala, lateral entorhinal cortex, nucleus reuniens of the thalamus, and the periaqueductal gray. Together, these results show a prominent bias among hippocampal and thalamic afferent systems in their targeting to genetically or anatomically defined sets of frontal cortical neurons. Moreover, they suggest the presence of two distinct local microcircuits that control how different inputs govern frontal cortical information processing.

scholarly journals FIN-Seq: Transcriptional profiling of specific cell types in frozen archived tissue from the human central nervous system

2019 ◽  
Author(s):  
Ryoji Amamoto ◽  
Emanuela Zuccaro ◽  
Nathan C. Curry ◽  
Sonia Khurana ◽  
Hsu-Hsin Chen ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Single Cell ◽  
Human Tissue ◽  
Cell Types ◽  
Transcriptional Analysis ◽  
Specific Cell ◽  
Cell Type Specificity ◽  
Human Central Nervous System ◽  
Single Nucleus

ABSTRACTThousands of frozen, archived tissues from postmortem human central nervous system (CNS) are currently available in brain banks. As single cell and single nucleus technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that transcriptional analysis of the human CNS requires cell type specificity. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples. Here, we developed FIN-Seq (FrozenImmunolabeledNucleiSequencing), a method that accomplishes these goals. FIN-Seq uses immunohisto-chemical isolation of nuclei of specific cell types from frozen human tissue, followed by RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.

scholarly journals Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic axis and transcriptional resilience

2020 ◽  
Author(s):  
W. Brad Ruzicka ◽  
Shahin Mohammadi ◽  
Jose Davila-Velderrain ◽  
Sivan Subburaju ◽  
Daniel Reed Tso ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Synaptic Function ◽  
Inhibitory Neurons ◽  
Projection Neurons ◽  
Cell Type ◽  
Cortical Projection ◽  
Human Neurons ◽  
Small Effect Size ◽  
Therapeutic Development

AbstractSchizophrenia is a devastating mental disorder with a high societal burden, complex pathophysiology, and diverse genetic and environmental risk factors. Its complexity, polygenicity, and small-effect-size and cell-type-specific contributors have hindered mechanistic elucidation and the search for new therapeutics. Here, we present the first single-cell dissection of schizophrenia, across 500,000+ cells from 48 postmortem human prefrontal cortex samples, including 24 schizophrenia cases and 24 controls. We annotate 20 cell types/states, providing a high-resolution atlas of schizophrenia-altered genes and pathways in each. We find neurons are the most affected cell type, with deep-layer cortico-cortical projection neurons and parvalbumin-expressing inhibitory neurons showing significant transcriptional changes converging on genetically-implicated regions. We discover a novel excitatory-neuron cell-state indicative of transcriptional resilience and enriched in schizophrenia subjects with less-perturbed transcriptional signatures. We identify key trans-acting factors as candidate drivers of observed transcriptional perturbations, including MEF2C, TCF4, SOX5, and SATB2, and map their binding patterns in postmortem human neurons. These factors regulate distinct gene sets underlying fetal neurodevelopment and adult synaptic function, bridging two leading models of schizophrenia pathogenesis. Our results provide the most detailed map to date for mechanistic understanding and therapeutic development in neuropsychiatric disorders.

scholarly journals Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Trygve E Bakken ◽  
Cindy TJ van Velthoven ◽  
Vilas Menon ◽  
Rebecca D Hodge ◽  
Zizhen Yao ◽  
...  
Keyword(s):  
Visual Information ◽  
Cell Types ◽  
Dorsal Lateral Geniculate Nucleus ◽  
Rna Seq ◽  
Cortical Projection ◽  
Significant Differential Expression ◽  
Neuronal Populations ◽  
Dominant Feature ◽  
Single Nucleus ◽  
Dorsal Lateral Geniculate

Abundant evidence supports the presence of at least three distinct types of thalamocortical (TC) neurons in the primate dorsal lateral geniculate nucleus (dLGN) of the thalamus, the brain region that conveys visual information from the retina to the primary visual cortex (V1). Different types of TC neurons in mice, humans, and macaques have distinct morphologies, distinct connectivity patterns, and convey different aspects of visual information to the cortex. To investigate the molecular underpinnings of these cell types, and how these relate to differences in dLGN between human, macaque, and mice, we profiled gene expression in single nuclei and cells using RNA-sequencing. These efforts identified four distinct types of TC neurons in the primate dLGN: magnocellular (M) neurons, parvocellular (P) neurons, and two types of koniocellular (K) neurons. Despite extensively documented morphological and physiological differences between M and P neurons, we identified few genes with significant differential expression between transcriptomic cell types corresponding to these two neuronal populations. Likewise, the dominant feature of TC neurons of the adult mouse dLGN is high transcriptomic similarity, with an axis of heterogeneity that aligns with core vs. shell portions of mouse dLGN. Together, these data show that transcriptomic differences between principal cell types in the mature mammalian dLGN are subtle relative to the observed differences in morphology and cortical projection targets. Finally, alignment of transcriptome profiles across species highlights expanded diversity of GABAergic neurons in primate versus mouse dLGN and homologous types of TC neurons in primates that are distinct from TC neurons in mouse.

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