Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView Article Swipe
Takamasa Kudo
,
Ana M. Meireles
,
Reuben Moncada
,
Yushu Chen
,
Ping Wu
,
Joshua Gould
,
Xiao‐Yu Hu
,
Opher S. Kornfeld
,
Rajiv Jesudason
,
Conrad Foo
,
Burkhard Höckendorf
,
Héctor Corrada Bravo
,
Jason P. Town
,
Runmin Wei
,
Antonio Ríos
,
Vineethkrishna Chandrasekar
,
Melanie Heinlein
,
Shuangyi Cai
,
Cherry Sakura Lu
,
Cemre Celen
,
Noelyn M. Kljavin
,
Jian Jiang
,
José Sergio Hleap
,
Nobuhiko Kayagaki
,
Felipe de Sousa e Melo
,
Lisa McGinnis
,
Bo Li
,
Avtar Singh
,
Levi A. Garraway
,
Orit Rozenblatt–Rosen
,
Aviv Regev
,
Eric Lubeck
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.12.26.573143
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.12.26.573143
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.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.12.26.573143
- https://www.biorxiv.org/content/biorxiv/early/2023/12/26/2023.12.26.573143.full.pdf
- OA Status
- green
- Cited By
- 11
- References
- 75
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4390245430
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4390245430Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2023.12.26.573143Digital Object Identifier
- Title
-
Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbViewWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-12-26Full publication date if available
- Authors
-
Takamasa Kudo, Ana M. Meireles, Reuben Moncada, Yushu Chen, Ping Wu, Joshua Gould, Xiao‐Yu Hu, Opher S. Kornfeld, Rajiv Jesudason, Conrad Foo, Burkhard Höckendorf, Héctor Corrada Bravo, Jason P. Town, Runmin Wei, Antonio Ríos, Vineethkrishna Chandrasekar, Melanie Heinlein, Shuangyi Cai, Cherry Sakura Lu, Cemre Celen, Noelyn M. Kljavin, Jian Jiang, José Sergio Hleap, Nobuhiko Kayagaki, Felipe de Sousa e Melo, Lisa McGinnis, Bo Li, Avtar Singh, Levi A. Garraway, Orit Rozenblatt–Rosen, Aviv Regev, Eric LubeckList of authors in order
- Landing page
-
https://doi.org/10.1101/2023.12.26.573143Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/12/26/2023.12.26.573143.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2023/12/26/2023.12.26.573143.full.pdfDirect OA link when available
- Concepts
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Transcriptome, Phenotype, Biology, Primary cell, Computational biology, Immune system, Cell biology, Cell culture, Gene, Gene expression, Immunology, GeneticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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11Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 10Per-year citation counts (last 5 years)
- References (count)
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75Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| citation_normalized_percentile.value | 0.87326618 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |