Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation during Neurogenesis

ABSTRACT: Neurogenesis in the adult hippocampus contributes to information processing critical for cognition, adaptation, learning and memory, and is implicated in numerous neurological disorders. New neurons are continuously produced from neural stem cells via a well-controlled developmental process. The immature neuron stage defined by doublecortin (DCX) expression is the most sensitive to regulation by extrinsic factors. However, little is known about the dynamic biology within this critical interval that drives maturation and confers susceptibility to regulating signals. This study aims to test the hypothesis that DCX-expressing immature neurons in adult mouse hippocampus progress through developmental stages via activity of specific transcriptional networks. Using single-cell RNA-seq combined with a novel integrative bioinformatics approach, we discovered that individual immature neuron can be classified into distinct developmental subgroups based on characteristic gene expression profiles and subgroup-specific markers. Comparisons between immature and more mature subgroups revealed novel pathways involved in neuronal maturation. Genes enriched in more immature cells shared significant overlap with genes implicated in neurodegenerative diseases, while genes positively associated with neuronal maturation were enriched for autism-related gene sets. Our study thus discovers molecular signatures of individual adult-born immature neurons and unveils potential novel targets for therapeutic approaches to treat neurodevelopmental and neurological diseases. mRNA sequencing and expression estimation in 64 individual DCX-dsRed+ cells isolated from transgenic DCX-dsRed mice by FACS sorting

ORGANISM(S): Mus musculus

SUBMITTER: Brian Eisinger

PROVIDER: E-GEOD-75901 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Human cone photoreceptors represent a rare cell population of the human retina and are largely outnumbered by other retinal cell types. Despite their rarity, cone photoreceptors are critical for optimal daylight vision and their loss has the greatest impact on sight during the progression of retinal dystrophies. This is most applicable to the L/M-opsin cone populations which form the largest proportion of cones in the human retina and are the only cone types present within the fovea, which is responsible for fine detailed vision. Better understanding of the early genesis of these cells within the human developing retina, particularly in relation to the expression of genes that could be involved in regulating early events such as cell fate decision, is required. These molecular determinants could be exploited in vitro to generate more cone photoreceptors within human stem cell-derived retinal differentiation culture systems, suitable for use in cell transpantation therapies or disease modelling purposes. Additionally, the nature of this cell population in terms of their gene expression heterogeneity remains to be defined. State of the art technology has now advanced so that mRNA sequencing can be performed on individual cells, which means the transcriptome of rare cell populations such as cone photoreceptor cells can be interrogated without the need for ample material. Using the AAV2/9 pR2.1:GFP reporter, containing a synthetic promoter region previously characterised to drive expression in cone photoreceptors, we label and isolate human foetal L/M-opsin cone photoreceptors within the 15pcw human retinal retina. Isolated GFP+ cells were separated into individual cells using the Fluidigm C1 microfludics system, before RNA extraction and cDNA library preparation was performed. In total, 74 single cells were captured and processed for RNA sequencing; quality control of the data led to the inclusion of 65 individual cells for the downstream analysis. Principal component analysis revealed a very subtle heterogeneity across the cells, with the highest variability observed according to the first principal component (PC1). Differential gene expression analysis correlated to PC1 led to the identification of 503 significantly differentially expressed genes. Notably, some genes increase in expression across the cells when ordered according to PC1 which have previous associations with photoreceptor maturation, whereas other genes associated with developmental processes became downregulated across the cells. This led to the hypothesis that at this single timepoint in the human foetal retina, developing L/M-opsin cone photoreceptors exist at different stages of maturation. Overlapping genes were identified from comparing RNA seq data from 15pcw single cells and population samples at early and late timepoints of pR2.1:GFP+ cells, which showed the same gene expression trend between experiments. This suggests differences in cell maturation at a single timepoint of development could be representative of their true developmental trajectory. This overlapping gene dataset is also highly useful to define new gene that could be involved in cone photoreceptor development.

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Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation during Neurogenesis

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