Molecular Connectomics: Spatially Resolved Single-Cell Gene Expression and Neuronal Connectivity Profiling
1 Karolinska Institutet / Department of Cell and Molecular Biology
The mammalian brain contains many different neuron types forming neural circuits with remarkable precision. Recently, single-cell transcriptomics enabled systematic high-throughput measurements of genome-wide RNA-expression in brain cells, and the generated datasets hold promise for a unified transcriptome-based taxonomy of neuronal subtypes. While understanding the brain’s cellular diversity and its origin is necessary, its organization into neural circuits is crucial for explaining diverse behaviors, from reflexes to consciousness. However, most neural circuits remain uncharacterized, and the molecular logic governing circuit assembly and maintenance remain obscure, because we currently lack tools for neural circuit studies at the single-cell level with molecular detail. In this project we will use viral barcoding and sequencing technologies to develop single-cell “molecular connectomics”, a novel method that for the first time allows simultaneous single-cell profiling of gene expression and neuronal connectivity in a tissue context. We will employ this novel approach to study neural circuitry in the normal and diseased prefrontal cortex (PFC) of different genetic backgrounds. PFC is a critical brain region that enables sophisticated cognitive abilities and that is frequently affected in neurodevelopmental disorders such as autism spectrum disorder (ASD). Many genes have been linked to ASD in genetic studies. However, how these mutations affect key features of neurons including gene expression programs, tissue location and neuronal subtype identity and how this leads to changes in synaptic input and output connectivity remains largely unknown. Identifying the molecular, cellular and network alterations in ASD is critical for targeting the correct neural circuit elements for precision medicine.