Single-cell Transcriptomic Analysis of Cell Type Plasticity in Barrel Cortex of Normal and Autism Model Mice

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PROJECT SUMMARY During postnatal developmental stages known as critical periods (CPs), sensory experience acts upon a genetically-hardwired connectivity map to sculpt the neocortical circuitry that enables mammalian functioning. Neurodevelopmental disorders such as autism disrupt this experience-dependent plasticity and compromise the development of social, cognitive, and physical function. Since autism spectrum disorder (ASD) patients suffer from tactile hyper- or hypo-sensitivity that may reflect abnormal development of sensory circuits, ASD is commonly studied in primary somatosensory cortex (S1). In addition, the mouse whisker S1 is a somatotopic map of the mouse whisker pad, so manipulation of specific whiskers induces observable functional changes in the corresponding barrels of S1. Morphological and physiological studies of experience-dependent plasticity in S1 have revealed several CPs and elucidated the influence of ASD on their emergence in mouse models of autism. However, the gene expression programs underlying experience-dependent plasticity and the influence of ASD on it remain unknown at the resolution of S1’s 100+ transcriptomically distinct cell types. Since these cell types form the circuits that carry out sensory function, it is important to study the influence of experience and ASD on their maturation. This project combines single-nucleus mRNA sequencing (snRNA-seq) and computational biology approaches rooted in machine learning with temporally resolved whisker manipulations and a mouse model of ASD to test two hypotheses. To test the hypothesis that whisker experience is required for cell type development in S1, snRNA-seq will be performed at several time points spanning two established CPs in whisker-deprived and control mice. Unsupervised and supervised machine learning approaches such as dimensionality reduction, clustering, graph embedding, and classification will be used to identify transcriptomic cell types at each time point and assess the influence of whisker experience on their maturation. Hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) will enable the validation of cell type-specific development patterns. To test the hypothesis that ASD disrupts experience-dependent cell type maturation, snRNA-seq will be performed on Fmr1 KO mice under whisker deprivation and control conditions. Fmr1 KO models Fragile X syndrome, the most frequent monogenic cause of intellectual disability and ASD in humans. While Fmr1 deletion has been shown to delay the maturation of circuits in S1 during a CP, its influence on experience-dependent maturation of S1 cell types remains unknown. Comparing gene expression profiles and cell types between KO and wild-type mice with and without whisker-deprivation will reveal transcriptomic signatures of ASD and pinpoint the cell types in which its effects are localized. Knowledge generated from this study about the manifestation of ASD in transcriptomic cell types will improve understanding of ASD pathology and reveal candidate cell types for targeted treatment.