Biology subjects

Huang, Z. J.

Publications and source records attributed to Huang, Z. J..

5 recordsLinked to original sources

bioRxiv2018

Radial glial lineage progression and differential intermediate progenitor amplification underlie striatal compartments and circuit organization

The circuitry of the striatum is characterized by two organizational plans: the division into striosome and matrix compartments, thought to mediate evaluation and action, and the direct and indirect pathways, thought to promote or suppress behavior. The developmental origins of and relationships between these organizations are unknown, leaving a conceptual gap in understanding the cortico-basal ganglia system. Through genetic fate mapping, we demonstrate that striosome-matrix compartmentalization arises from a lineage program embedded in lateral ganglionic eminence radial glial progenitors mediating neurogenesis through two distinct types of intermediate progenitors (IPs). The early phase of this program produces striosomal spiny projection neurons (SPNs) through fate-restricted apical IPs (aIPSs) with limited capacity; the late phase produces matrix SPNs through fate-restricted basal IPs (bIPMs) with expanded capacity. Remarkably, direct and indirect pathway SPNs arise within both aIPS and bIPM pools, suggesting that striosome-matrix architecture is the fundamental organizational plan of basal ganglia circuitry organization.

neuroscience↗

bioRxiv2017

Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes

Parsing diverse nerve cells into biological types is necessary for understanding neural circuit organization. Morphology is an intuitive criterion for neuronal classification and a proxy of connectivity, but morphological diversity and variability often preclude resolving the granularity of discrete cell groups from population continuum. Combining genetic labeling with high-resolution, large volume light microscopy, we established a platform of genetic single neuron anatomy that resolves, registers and quantifies complete neuron morphologies in the mouse brain. We discovered that cortical axo-axonic cells (AACs), a cardinal GABAergic interneuron type that controls pyramidal neuron (PyN) spiking at axon initial segment, consist of multiple subtypes distinguished by laminar position, dendritic and axonal arborization patterns. Whereas the laminar arrangements of AAC dendrites reflect differential recruitment by input streams, the laminar distribution and local geometry of AAC axons enable differential innervation of PyN ensembles. Therefore, interneuron types likely consist of fine-grained subtypes with distinct input-output connectivity patterns.

neuroscience↗

bioRxiv2017

Transcriptional Architecture of Synaptic Communication Delineates Cortical GABAergic Neuron Identity

Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuron type diversity and identity, but there is no consensus on defining a neuron type. We analyzed single cell transcriptomes of anatomically and physiologically characterized cortical ground truth populations and conducted a computational genomic screen for transcription profiles that distinguish them. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns. This architecture comprises 6 categories of ~40 gene families including cell adhesion molecules, transmitter-modulator receptors, ion channels, signaling proteins, neuropeptides and vesicular release components, and transcription factors. Combinatorial expression of select members across families shapes a multi-layered molecular scaffold along cell membrane that may customize synaptic connectivity patterns and input-output signaling properties. This molecular genetic framework of neuronal identity integrates cell phenotypes along multiple axes and provides a foundation for discovering and classifying neuron types.

neuroscience↗

bioRxiv2017

Addressing the looming identity crisis in single cell RNA-seq

Single cell RNA-sequencing technology (scRNA-seq) provides a new avenue to discover and characterize cell types, but the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine the replicability of these studies. Meta-analysis of rapidly accumulating data is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that allows researchers to quantify the degree to which cell types replicate across datasets, and to rapidly identify clusters with high similarity for further testing. We first measure the replicability of neuronal identity by comparing more than 13 thousand individual scRNA-seq transcriptomes, then assess cross-dataset evidence for novel pyramidal neuron and cortical interneuron subtypes identified by scRNA-seq. We find that 24/45 cortical interneuron subtypes and 10/48 pyramidal neuron subtypes have evidence of replication in at least one other study. Identifying these putative replicates allows us to re-analyze the data for differential expression and provide lists of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types and subtypes with high accuracy, indicating many of the transcriptional changes characterizing cell identity are pervasive and easily detected.

bioinformatics↗

bioRxiv2017

Selective Inhibitory Control Of Pyramidal Neuron Ensembles And Cortical Subnetworks By Chandelier Cells

The neocortex comprises multiple information processing streams mediated by subsets of glutamatergic pyramidal cells (PCs) that receive diverse inputs and project to distinct targets. How GABAergic interneurons regulate the segregation and communication among intermingled PC subsets that contribute to separate brain networks remains unclear. Here we demonstrate that a subset of GABAergic chandelier cells (ChCs) in the prelimbic cortex (PL), which innervate PCs at spike initiation site, selectively control PCs projecting to the basolateral amygdala (BLAPC) compared to those projecting to contralateral cortex (ccPC). These ChCs in turn receive preferential input from local and contralateral CCPCs as opposed to BLAPCs and BLA neurons (the PL-BLA network). Accordingly, optogenetic activation of ChCs rapidly suppresses BLAPCs and BLA activity in freely behaving mice. Thus, the exquisite connectivity of ChCs not only mediates directional inhibition between local PC ensembles but may also shape communication hierarchies between global networks.

neuroscience↗