Our overarching goal is to understand how the relationships between genes contribute to functional properties in neurons and how those functions combine to define types of neurons. This is a central question of basic neuroscience, and one which is newly assessable using single cell RNA sequencing (scRNA-seq). These data provide high-throughput snapshots of gene activities across thousands of cells and thus shed new light on the relationships between genes within and across cells. We propose to exploit this data in conjunction with previously known details about gene function and neuronal identity to learn new features of both. Our research approach is meta-analytic, using data from many different laboratories to obtain a more robust aggregate signal. In addition to developing meta-analytic methods to pursue our direct research interests, the methods are of broad practical relevance to neuroscience laboratories studying many different questions, including diseases of the nervous system. Disseminating our software deliverables in a convenient-to-use form is a central component of each of our research objectives. The three complementary objectives in this project are to: 1. Learn patterns of gene expression which characterize known cell identity. Building on our previous research showing conserved expression patterns across cell-types, we will define shared gene expression patterns, called co-expression, specific to neuronal sub-populations. These shared expression patterns will be used as an assay into cellular identity. 2.Identify novel cell subtypes through changes in the expression relationships between genes. Variation in co-expression is a form of transcriptional rewiring which often indicates a change in function. To find novel neuronal sub-types we will assess the data for changes in co-expression reflecting a change in functions linked to neuronal identity. We will identify novel transcriptional signatures which replicate across laboratories. 3. Determine consensus methods for customized cell-type learning. Defining wholly unknown expression profiles is likely to benefit from a variety of approaches. In order to find agreement between those approaches, we will develop an algorithm to efficiently search through gene sets likely to find those with complementary value. These gene sets will then be assessed across many pre-existing methods, with customized combinations and aggregate output reported and made available through a public web-server.

Public Health Relevance

Recent advances in genetics have it made possible to assess gene activity at a cellular level. The primary goal of this project is to develop and validate methods and data resources which combine data from many laboratories to identify how genes interact to produce different functional effects in different types of neurons. Because most gene functions are accomplished in concert with other genes, knowing how genes change their interactions provides key information into how their function might be disrupted in disease.

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
Research Project (R01)
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Molecular Neurogenetics Study Section (MNG)
Program Officer
Beer, Rebecca Lynn
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Cold Spring Harbor Laboratory
Cold Spring Harbor
United States
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Crow, Megan; Paul, Anirban; Ballouz, Sara et al. (2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun 9:884
Crow, Megan; Gillis, Jesse (2018) Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? Trends Genet 34:823-831
Kalish, Brian T; Cheadle, Lucas; Hrvatin, Sinisa et al. (2018) Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. Proc Natl Acad Sci U S A 115:E1051-E1060
Paul, Anirban; Crow, Megan; Raudales, Ricardo et al. (2017) Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity. Cell 171:522-539.e20