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Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
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Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
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Paper
Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
2023
Overview
Optical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture, due to limitations associated with in situ sequencing (ISS) of perturbation barcodes. Here, we developed PerturbView, an OPS technology that leverages in vitro transcription (IVT) to amplify barcodes prior to ISS, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in iPSC-derived neurons, primary immune cells, and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NFΚB signaling. Furthermore, we combined PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in vivo screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.Competing Interest StatementAuthors have submitted a provisional patent application that is based on the technology described in this manuscript. All authors are or were employed by Genentech Inc., South San Francisco, CA, USA, at the time of their contribution to this work. A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas and, until 31 July 2020, was a scientific advisory board member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. T.K. is a shareholder of Genomelink, Inc. E.L. is an equity holder in insitro inc. A.M., R.M., Y.C., P.W., J.G., X.H., O.K., R.J., C.F., B.H., H.C.B., J.P.T., R.W., A.R., V.C., C.C., N.K., J.J., N.K., F.S.M., L.M., B.L., A.S., L.G., O.R., A.R. and E.L. are equity holders in Roche.
Publisher
Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
Subject
