INTRODUCTION Neurons are by far the most diverse of all cell types in animals, to the extent that “cell types” in mammalian brains are still mostly heterogeneous groups, and there is no consensus definition of the term. The Drosophila optic lobes, with approximately 200 well-defined cell types, provides a tractable system with which to address the genetic basis of neuronal type diversity. We previously characterized the distinct developmental gene expression program of each of these types using single-cell RNA sequencing (scRNA-seq), with one-to-one correspondence to the known morphological types. RATIONALE The identity of fly neurons is determined by temporal and spatial patterning mechanisms in stem cell progenitors, but it remained unclear how these cell fate decisions are implemented and maintained in postmitotic neurons. It was proposed in Caenorhabditis elegans that unique combinations of terminal selector transcription factors (TFs) that are continuously expressed in each neuron control nearly all of its type-specific gene expression. This model implies that it should be possible to engineer predictable and complete switches of identity between different neurons just by modifying these sustained TFs. We aimed to test this prediction in the Drosophila visual system. RESULTS Here, we used our developmental scRNA-seq atlases to identify the potential terminal selector genes in all optic lobe neurons. We found unique combinations of, on average, 10 differentially expressed and stably maintained (across all stages of development) TFs in each neuron. Through genetic gain- and loss-of-function experiments in postmitotic neurons, we showed that modifications of these selector codes are sufficient to induce predictable switches of identity between various cell types. Combinations of terminal selectors jointly control both developmental (e.g., morphology) and functional (e.g., neurotransmitters and their receptors) features of neurons. The closely related Transmedullary 1 (Tm1), Tm2, Tm4, and Tm6 neurons (see the figure) share a similar code of terminal selectors, but can be distinguished from each other by three TFs that are continuously and specifically expressed in one of these cell types: Drgx in Tm1, Pdm3 in Tm2, and SoxN in Tm6. We showed that the removal of each of these selectors in these cell types reprograms them to the default Tm4 fate. We validated these conversions using both morphological features and molecular markers. In addition, we performed scRNA-seq to show that ectopic expression of pdm3 in Tm4 and Tm6 neurons converts them to neurons with transcriptomes that are nearly indistinguishable from that of wild-type Tm2 neurons. We also show that Drgx expression in Tm1 neurons is regulated by Klumpfuss, a TF expressed in stem cells that instructs this fate in progenitors, establishing a link between the regulatory programs that specify neuronal fates and those that implement them. We identified an intronic enhancer in the Drgx locus whose chromatin is specifically accessible in Tm1 neurons and in which Klu motifs are enriched. Genomic deletion of this region knocked down Drgx expression specifically in Tm1 neurons, leaving it intact in the other cell types that normally express it. We further validated this concept by demonstrating that ectopic expression of Vsx (visual system homeobox) genes in Mi15 neurons not only converts them morphologically to Dm2 neurons, but also leads to the loss of their aminergic identity. Our results suggest that selector combinations can be further sculpted by receptor tyrosine kinase signaling after neurogenesis, providing a potential mechanism for postmitotic plasticity of neuronal fates. Finally, we combined our transcriptomic datasets with previously generated chromatin accessibility datasets to understand the mechanisms that control brain wiring downstream of terminal selectors. We built predictive computational models of gene regulatory networks using the Inferelator framework. Experimental validations of these networks revealed how selectors interact with ecdysone-responsive TFs to activate a large and specific repertoire of cell surface proteins and other effectors in each neuron at the onset of synapse formation. We showed that these network models can be used to identify downstream effectors that mediate specific cellular decisions during circuit formation. For instance, reduced levels of cut expression in Tm2 neurons, because of its negative regulation by pdm3 , controls the synaptic layer targeting of their axons. Knockdown of cut in Tm1 neurons is sufficient to redirect their axons to the Tm2 layer in the lobula neuropil without affecting other morphological features. CONCLUSION Our results support a model in which neuronal type identity is primarily determined by a relatively simple code of continuously expressed terminal selector TFs in each cell type throughout development. Our results provide a unified framework of how specific fates are initiated and maintained in postmitotic neurons and open new avenues to understanding synaptic specificity through gene regulatory networks. The conservation of this regulatory logic in both C. elegans and Drosophila makes it likely that the terminal selector concept will also be useful in understanding and manipulating the neuronal diversity of mammalian brains. Terminal selectors enable predictive cell fate reprogramming. Tm1, Tm2, Tm4, and Tm6 neurons of the Drosophila visual system share a core set of TFs continuously expressed by each cell type (simplified). The default Tm4 fate is overridden by the expression of a single additional terminal selector to generate Tm1 ( Drgx ), Tm2 ( pdm3 ), or Tm6 ( SoxN ) fates.
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A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing
Abstract During development, neural progenitors are temporally patterned to sequentially generate a variety of neural types. In Drosophila neural progenitors called neuroblasts, temporal patterning is regulated by cascades of Temporal Transcription Factors (TTFs). However, known TTFs were mostly identified through candidate approaches and may not be complete. In addition, many fundamental questions remain concerning the TTF cascade initiation, progression, and termination. In this work, we use single-cell RNA sequencing of Drosophila medulla neuroblasts of all ages to identify a list of previously unknown TTFs, and experimentally characterize their roles in temporal patterning and neuronal specification. Our study reveals a comprehensive temporal gene network that patterns medulla neuroblasts from start to end. Furthermore, the speed of the cascade progression is regulated by Lola transcription factors expressed in all medulla neuroblasts. Our comprehensive study of the medulla neuroblast temporal cascade illustrates mechanisms that may be conserved in the temporal patterning of neural progenitors.
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- Award ID(s):
- 1764421
- NSF-PAR ID:
- 10336430
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 13
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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INTRODUCTION Balance between excitatory and inhibitory neuron (interneuron) populations in the cortex promotes normal brain function. Interneurons are primarily generated in the medial, caudal, and lateral ganglionic eminences (MGE, CGE, and LGE) of the ventral embryonic forebrain; these subregions give rise to distinct interneuron subpopulations. In rodents, the MGE generates cortical interneurons, the parvalbumin + (PV + ) and somatostatin + (SST + ) subtypes that connect with excitatory neurons to regulate their activity. Defects in interneuron production have been implicated in neurodevelopmental and psychiatric disorders including autism, epilepsy, and schizophrenia. RATIONALE How does the human MGE (hMGE) produce the number of interneurons required to populate the forebrain? The hMGE contains progenitor clusters distinct from what has been observed in the rodent MGE and other germinal zones of the human brain. This cytoarchitecture could be the key to understanding interneuron neurogenesis. We investigated the cellular and molecular properties of different compartments within the developing hMGE, from 14 gestational weeks (GW) to 39 GW (term), to study their contribution to the production of inhibitory interneurons. We developed a xenotransplantation assay to follow the migration and maturation of the human interneurons derived from this germinal region. RESULTS Within the hMGE, densely packed aggregates (nests) of doublecortin + (DCX + ) and LHX6 + cells were surrounded by nestin + progenitor cells and their processes. These DCX + cell–enriched nests (DENs) were observed in the hMGE but not in the adjacent LGE. We found that cells within DENs expressed molecular markers associated with young neurons, such as DCX, and polysialylated neural cell adhesion molecule (PSA-NCAM). A subpopulation also expressed Ki-67, a marker of proliferation; therefore, we refer to these cells as neuroblasts. A fraction of DCX + cells inside DENs expressed SOX2 and E2F1, transcription factors associated with progenitor and proliferative properties. More than 20% of DCX + cells in the hMGE were dividing, specifically within DENs. Proliferating neuroblasts in DENs persisted in the hMGE throughout prenatal human brain development. The division of DCX + cells was confirmed by transmission electron microscopy and time-lapse microscopy. Electron microscopy revealed adhesion contacts between cells within DENs, providing multiple sites to anchor DEN cells together. Neuroblasts within DENs express PCDH19, and nestin + progenitors surrounding DENs express PCDH10; these findings suggest a role for differential cell adhesion in DEN formation and maintenance. When transplanted into the neonatal mouse brain, dissociated hMGE cells reformed DENs containing proliferative DCX + cells, similar to DENs observed in the prenatal human brain. This suggests that DENs are generated by cell-autonomous mechanisms. In addition to forming DENs, transplanted hMGE-derived neuroblasts generated young neurons that migrated extensively into cortical and subcortical regions in the host mouse brain. One year after transplantation, these neuroblasts had differentiated into distinct γ-aminobutyric acid–expressing (GABAergic) interneuron subtypes, including SST + and PV + cells, that showed morphological and functional maturation. CONCLUSION The hMGE harbors DENs, where cells expressing early neuronal markers continue to divide and produce GABAergic interneurons. This MGE-specific arrangement of neuroblasts in the human brain is present until birth, supporting expanded neurogenesis for inhibitory neurons. Given the robust neurogenic output from this region, knowledge of the mechanisms underlying cortical interneuron production in the hMGE will provide insights into the cell types and developmental periods that are most vulnerable to genetic or environmental insults. Nests of DCX + cells in the ventral prenatal brain. Schematic of a coronal view of the embryonic human forebrain showing the medial ganglionic eminence (MGE, green), with nests of DCX + cells (DENs, green). Nestin + progenitor cells (blue) are present within the VZ and iSVZ and are intercalated in the oSVZ (where DENs reside). The initial segment of the oSVZ contains palisades of nestin + progenitors referred to as type I clusters (light blue cells) around DENs. In the outer part of the oSVZ, DENs transition to chains of migrating DCX + cells; surrounding nestin + progenitors are arranged into groups of cells referred to as type II clusters (white cells). In addition to proliferation of nestin + progenitors, cell division is present among DCX + cells within DENs, suggesting multiple progenitor states for the generation of MGE-derived interneurons in the human forebrain. ILLUSTRATION: NOEL SIRIVANSANTImore » « less
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null (Ed.)The mechanisms specifying neuronal diversity are well characterized, yet it remains unclear how or if these mechanisms regulate neural circuit assembly. To address this, we mapped the developmental origin of 160 interneurons from seven bilateral neural progenitors (neuroblasts) and identify them in a synapse-scale TEM reconstruction of the Drosophila larval central nervous system. We find that lineages concurrently build the sensory and motor neuropils by generating sensory and motor hemilineages in a Notch-dependent manner. Neurons in a hemilineage share common synaptic targeting within the neuropil, which is further refined based on neuronal temporal identity. Connectome analysis shows that hemilineage-temporal cohorts share common connectivity. Finally, we show that proximity alone cannot explain the observed connectivity structure, suggesting hemilineage/temporal identity confers an added layer of specificity. Thus, we demonstrate that the mechanisms specifying neuronal diversity also govern circuit formation and function, and that these principles are broadly applicable throughout the nervous system.more » « less
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Abstract Nervous system development has been intensely studied in insects (especially
Drosophila melanogaster ), providing detailed insights into the genetic regulatory network governing the formation and maintenance of the neural stem cells (neuroblasts) and the differentiation of their progeny. Despite notable advances over the last two decades, neurogenesis in other arthropod groups remains by comparison less well understood, hampering finer resolution of evolutionary cell type transformations and changes in the genetic regulatory network in some branches of the arthropod tree of life. Although the neurogenic cellular machinery in malacostracan crustaceans is well described morphologically, its genetic molecular characterization is pending. To address this, we established an in situ hybridization protocol for the crayfishProcambarus virginalis and studied embryonic expression patterns of a suite of key genes, encompassing threeSoxB group transcription factors, twoachaete –scute homologs, aSnail family member, the differentiation determinantsProspero andBrain tumor , and the neuron markerElav . We document cell type expression patterns with notable similarities to insects and branchiopod crustaceans, lending further support to the homology of hexapod–crustacean neuroblasts and their cell lineages. Remarkably, in the crayfish head region, cell emigration from the neuroectoderm coupled with gene expression data points to a neuroblast‐independent initial phase of brain neurogenesis. Further,SoxB group expression patterns suggest an involvement ofDichaete in segmentation, in concordance with insects. Our target gene set is a promising starting point for further embryonic studies, as well as for the molecular genetic characterization of subregions and cell types in the neurogenic systems in the adult crayfish brain. -
Neurogenesis is the generation of neurons from stem cells, a process that is regulated by SoxB transcription factors (TFs) in many animals. Although the roles of these TFs are well understood in bilaterians, how their neural function evolved is unclear. Here, we use Hydractinia symbiolongicarpus , a member of the early-branching phylum Cnidaria, to provide insight into this question. Using a combination of mRNA in situ hybridization, transgenesis, gene knockdown, transcriptomics, and in vivo imaging, we provide a comprehensive molecular and cellular analysis of neurogenesis during embryogenesis, homeostasis, and regeneration in this animal. We show that SoxB genes act sequentially at least in some cases. Stem cells expressing Piwi1 and Soxb1 , which have broad developmental potential, become neural progenitors that express Soxb2 before differentiating into mature neural cells. Knockdown of SoxB genes resulted in complex defects in embryonic neurogenesis. Hydractinia neural cells differentiate while migrating from the aboral to the oral end of the animal, but it is unclear whether migration per se or exposure to different microenvironments is the main driver of their fate determination. Our data constitute a rich resource for studies aiming at addressing this question, which is at the heart of understanding the origin and development of animal nervous systems.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41467-022-28915-3
