Rapid Molecular Profiling of Defined Cell Types Using Viral TRAP
Alexander R. Nectow,
Maria V. Moya,
Mats I. Ekstrand,
Awni Mousa,
Kelly L. McGuire,
Caroline E. Sferrazza,
Bianca C. Field,
Gabrielle S. Rabinowitz,
Kirsty Sawicka,
Yupu Liang,
Jeffrey M. Friedman,
Nathaniel Heintz,
Eric F. Schmidt
Affiliations
Alexander R. Nectow
Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Princeton Neuroscience Institute, Princeton University, Lot 20 Washington Road, Princeton, NJ 08544, USA; Corresponding author
Maria V. Moya
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Mats I. Ekstrand
Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Awni Mousa
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Kelly L. McGuire
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Caroline E. Sferrazza
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Bianca C. Field
Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Gabrielle S. Rabinowitz
Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Kirsty Sawicka
Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Yupu Liang
Hospital Informatics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Jeffrey M. Friedman
Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Nathaniel Heintz
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Corresponding author
Eric F. Schmidt
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Corresponding author
Summary: Translational profiling methodologies enable the systematic characterization of cell types in complex tissues, such as the mammalian brain, where neuronal isolation is exceptionally difficult. Here, we report a versatile strategy for profiling CNS cell types in a spatiotemporally restricted fashion by engineering a Cre-dependent adeno-associated virus expressing an EGFP-tagged ribosomal protein (AAV-FLEX-EGFPL10a) to access translating mRNAs by translating ribosome affinity purification (TRAP). We demonstrate the utility of this AAV to target a variety of genetically and anatomically defined neural populations expressing Cre recombinase and illustrate the ability of this viral TRAP (vTRAP) approach to recapitulate the molecular profiles obtained by bacTRAP in corticothalamic neurons across multiple serotypes. Furthermore, spatially restricting adeno-associated virus (AAV) injections enabled the elucidation of regional differences in gene expression within this cell type. Altogether, these results establish the broad applicability of the vTRAP strategy for the molecular dissection of any CNS or peripheral cell type that can be engineered to express Cre. : Nectow et al. describe vTRAP, a technology to purify translating mRNAs from genetically defined cell types in a spatiotemporally restricted fashion. Multiplexing vTRAP with other technologies offers a comprehensive strategy to interrogate the precise role of individual, cell-type-specific genes in neural circuit function. Keywords: AAV, molecular profiling, TRAP, MCH, corticothalamic, Ntsr1, RNA-seq
