Transient expression of the basic helix-loop-helix protein NSCL-2 in the mouse cerebellum during postnatal development

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

BACKGROUND

Cerebellar neurogenesis involves the generation of large numbers of cerebellar granule neurons (GNs) throughout development of the cerebellum, a process that involves tight regulation of proliferation and differentiation of granule neuron progenitors (GNPs). A number of transcriptional regulators, including Math1, and the signaling molecules Wnt and Shh have been shown to have important roles in GNP proliferation and differentiation, and deregulation of granule cell development has been reported to be associated with the pathogenesis of medulloblastoma. While the progenitor/differentiation states of cerebellar granule cells have been broadly investigated, a more detailed association between developmental differentiation programs and spatial gene expression patterns, and how these lead to differential generation of distinct types of medulloblastoma remains poorly understood. Here, we provide a comparative single-cell spatial transcriptomics analysis to better understand the similarities and differences between developing granule and medulloblastoma cells.

RESULTS

To acquire an enhanced understanding of the precise cellular states of developing cerebellar granule cells, we performed single-cell RNA sequencing of 24,919 murine cerebellar cells from granule neuron-specific reporter mice (Math1-GFP; Dcx-DsRed mice). Our single-cell analysis revealed that there are four major states of developing cerebellar granule cells, including two subsets of granule progenitors and two subsets of differentiating/differentiated granule neurons. Further spatial transcriptomics technology enabled visualization of their spatial locations in cerebellum. In addition, we performed single-cell RNA sequencing of 18,372 cells from Patched+/- mutant mice and found that the transformed granule cells in medulloblastoma closely resembled developing granule neurons of varying differentiation states. However, transformed granule neuron progenitors in medulloblastoma exhibit noticeably less tendency to differentiate compared with cells in normal development.

CONCLUSION

In sum, our study revealed the cellular and spatial organization of the detailed states of cerebellar granule cells and provided direct evidence for the similarities and discrepancies between normal cerebellar development and tumorigenesis.

NeuroD1 is an upstream regulator of NSCL1

Cell fate determination and differentiation during neurogenesis and myogenesis involve the sequential expression of several basic helix-loop-helix (bHLH) transcription factors. The expression of NeuroD1/2 and the expression of NSCL(Nhlh)1/2 are closely related in many developing peripheral and central neuronal cells, suggesting an epistatic relationship between these two bHLH transcription factor families during neurogenesis. To investigate this relationship, a murine neuroblastoma cell culture system and single/double knock-out (KO) mice of NeuroD1 and NeuroD2 were utilized for the gain-of-function and loss-of-function approaches, respectively. Both NeuroD1 and NeuroD2 were able to induce the transcription of NSCL1 in vitro; however, they were not able to activate NSCL2 transcription. The DNA-binding ability of NeuroD1 was essential for NSCL1 induction. To examine the epistatic relationship in vivo, we examined the expression of NSCL1 and NSCL2 in NeuroD1 and NeuroD2 KO mice and NeuroD1/2 compound KO mice by in situ hybridization, RT-PCR and Northern blotting. The expression of NSCL1 was lower in the NeuroD1 KO mice and was not further decreased in the double KO mice. However, the expression of NSCL2 did not change in either the single KO or double KO mice. These results demonstrate that NeuroD1 is an upstream regulator of the NSCL1 gene but not the NSCL2 gene in mice. In addition, NeuroD2 is not involved in this regulatory pathway in vivo.

Functional redundancy of NSCL-1 and NeuroD during development of the petrosal and vestibulocochlear ganglia

To study the role of different members of the bHLH gene family for sensory organ development we have generated NSCL-1 and NeuroD compound-mutant mice. Double homozygous animals were characterized by a more severe reduction of the petrosal and vestibulocochlear ganglia than NeuroD-knockout mice. The more severe reduction of the petrosal and vestibulocochlear ganglia in double-knockout mice indicates overlapping functions of the two genes during neuronal development. Interestingly, we also found that the two genes are jointly regulated by thyroid hormone during sensory hair cell development. We further present a detailed expression analysis of NSCL-1 and NSCL-2 during sensory neuron development. NSCL-1 expression was detected in all developing cranial ganglia including the petrosal and vestibulocochlear ganglion, in inner and outer hair cells of the organ of Corti and in hair cells of the vestibular system. Expression domains in other sensory structures include the retina, Merkel cells of the developing skin and sensory cells of the tongue. The expression of NSCL-2 was restricted to developing cranial ganglia, the retina and the vestibular nerve. Both NSCL-1 and NSCL-2 genes are active only in postmitotic neurons, indicating a role for neuronal cell migration and/or differentiation within the sensory system.

Screening for mammalian neural genes via fluorescence-activated cell sorter purification of neural precursors from Sox1-gfp knock-in mice

The transcription factor Sox1 is the earliest and most specific known marker for mammalian neural progenitors. During fetal development, Sox1 is expressed by proliferating progenitor cells throughout the central nervous system and in no tissue but the lens. We generated a reporter mouse line in which egfp is inserted into the Sox1 locus. Sox1GFP animals faithfully recapitulate the expression of the endogenous gene. We have used the GFP reporter to purify neuroepithelial cells by fluorescence-activated cell sorting from embryonic day 10.5 embryos. RNAs prepared from Sox1GFP+ and Sox1GFP- embryo cells were then used to perform a pilot screen of subtracted cDNAs prepared from differentiating embryonic stem cells and arrayed on a glass chip. Fifteen unique differentially expressed genes were identified, all previously associated with fetal or adult neural tissue. Whole mount in situ hybridization against two genes of previously unknown embryonic expression, Lrrn1 and Musashi2, confirmed the selectivity of this screen for early neuroectodermal markers.

The neuronal basic helix-loop-helix transcription factor NSCL-1 is dispensable for normal neuronal development

The neuronal stem cell leukemia (NSCL) basic helix-loop-helix factors are neural cell-specific transcription factors. We have disrupted the NSCL-1 gene by homologous recombination and replaced the coding region with a beta-galactosidase reporter cassette to study the role of NSCL-1 in neuronal development and to follow the fate of NSCL-1 mutant cells. NSCL-1 mutant mice are viable and fertile on various genetic backgrounds and do not show any obvious signs of neurological malfunction. No differences in the distribution of NSCL-1 mutant or heterozygous neuronal cells were observed in the diencephalon, hippocampus, neocortex, and cerebellum at different stages of development. Likewise, no defects were found in the laminar organization of the cortex, and the distinct neuronal subpopulation appeared normal during development of the neocortex. Analysis of sensory neurons which strongly express NSCL-1 revealed that the spatiotemporal expression of neuronal differentiation factors, such as NeuroD and SCG-10, was not altered in developing distal and proximal cranial ganglia of mutant mice. In the cerebellum expression of NSCL-1 was confined to the proliferative and premigratory zone of the external granular layer and the internal granular layer. Interestingly, unlike cerebella of Math1(-/-) or NeuroD2(-/-) mice, NSCL-1-deficient mice have no obvious developmental defect, and neurons of the cerebellum appeared fully differentiated. Despite similar expression patterns of NSCL-1 and NSCL-2 in various areas of the diencephalon, including the arcuate nucleus and paraventricular nucleus, NSCL-1(-/-) mice are fertile and show no adult onset of obesity like NSCL-2 mutant mice. Double-mutant NSCL-1(-/-)-NSCL-2(-/-) mice do not show any additional obvious malformations of the central nervous system, although both genes are expressed in a largely overlapping pattern. Our results argue against a simple functional redundancy within the NSCL gene family.

NeuroD2 is necessary for development and survival of central nervous system neurons

NeuroD2 is sufficient to induce cell cycle arrest and neurogenic differentiation in nonneuronal cells. To determine whether this bHLH transcription factor was necessary for normal brain development, we used homologous recombination to replace the neuroD2 coding region with a beta-galactosidase reporter gene. The neuroD2 gene expressed the reporter in a subset of neurons in the central nervous system, including in neurons of the neocortex and hippocampus and cerebellum. NeuroD2(-/-) mice showed normal development until about day P14, when they began exhibiting ataxia and failure to thrive. Brain areas that expressed neuroD2 were smaller than normal and showed higher rates of apoptosis. Cerebella of neuroD2-null mice expressed reduced levels of genes encoding proteins that support cerebellar granule cell survival, including brain-derived neurotrophic factor (BDNF). Decreased levels of BDNF and higher rates of apoptosis in cerebellar granule cells of neuroD2(-/-) mice indicate that neuroD2 is necessary for the survival of specific populations of central nervous system neurons in addition to its known effects on cell cycle regulation and neuronal differentiation.

Sequence and expression analysis of Nhlh1: a basic helix-loop-helix gene implicated in neurogenesis

Nhlh1 is a basic helix-loop-helix (bHLH) gene that has been implicated in mouse neurogenesis. Previous studies have shown it to be expressed in regions in which there are differentiating neurons during late embryonic and fetal development, but detailed studies of the role of Nhlh1 earlier in embryonic development have not been performed. In this paper, we examine the expression of Nhlh1 transcripts at early embryonic stages (E8.5-E10.5), at the onset of neurogenesis, and compare the pattern of expression with that of Islet-1, a marker of postmitotic neurons. We show that Nhlh1 is expressed in early postmitotic neurons but is down-regulated as these cells migrate from the ventricular zone. We have also determined the genomic structure of mouse Nhlh1 and have characterised the promoter sequence, as a first step towards identifying factors that may control Nhlh1 expression. Nhlh1 has been implicated previously as a candidate for the neural tube defect mutant loop-tail (Lp); here, we present sequence and expression data indicating that Nhlh1 is unlikely to be responsible for the Lp mutation.

Expression of the basic Helix-Loop-Helix ME1 E-protein during development and aging of the murine cerebellum

Genesis of cerebellar granule cells is controlled by key transcription factors, such as the lineage-specific basic Helix-Loop-Helix (bHLH) transcription factor MATH-1, whose activity is dependent upon dimerization with bHLH E-proteins. In an effort to understand the molecular mechanisms of bHLH proteins orchestrating cerebellar development, we explored the spatio-temporal expression of the ME1 E-protein. Our results reveal that ME1 expression is first detected in the cerebellar primordium and then in the rhombic lip cells at E12.5. Its expression persists in the emerging external germinal layer during embryonic expansion. In adult cerebellum, prominent ME1 expression is detected in mature granule cells located in the internal granular layer. However, ME1 expression is not sustained in aged cerebellum. A similar declined pattern of expression is also observed in the aging hippocampus.

The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors

The SCL/TAL-1 gene encodes a basic helix-loop-helix (bHLH) transcription factor essential for the development of all hemopoietic lineages and also acts as a T-cell oncogene. Four related genes have been described in mammals (LYL-1, TAL-2, NSCL1, and NSCL2), all of which exhibit a high degree of sequence similarity to SCL/TAL-1 in the bHLH domain and two of which (LYL-1 and TAL-2) have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia. In this study we describe the identification and characterization of a pufferfish gene termed SLP-1, which represents a new member of this gene family. The genomic structure and sequence of SLP-1 suggests that it forms a subfamily with SCL/TAL-1 and LYL-1 and is most closely related to SCL/TAL-1. However, unlike SCL/TAL-1, SLP-1 is widely expressed. Sequence analysis of a whole cosmid containing SLP-1 shows that SLP-1 is flanked upstream by a zinc finger gene and a fork-head-domain gene and downstream by a heme-oxygenase and a RING finger gene.