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Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.

Takamasa Kudo1, Ana M Meireles1, Reuben Moncada1

  • 1Genentech Research and Early Development, Genentech, Inc., South San Francisco, CA, USA.

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Summary

PerturbView enhances optical pooled screening (OPS) by enabling highly multiplexed phenotypic readouts in diverse cell types and tissues. This new technology links cellular perturbations to complex phenotypes for broader biological discovery.

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Area of Science:

  • Cell biology
  • Genomics
  • Biotechnology

Background:

  • Optical pooled screening (OPS) links image-based phenotypes to cellular perturbations.
  • Current OPS methods are limited to low-plex readouts in cancer cell lines due to in situ sequencing challenges.

Purpose of the Study:

  • Develop an enhanced OPS technology (PerturbView) for highly multiplexed phenotypic readouts.
  • Expand OPS applications to diverse biological systems, including primary cells and tissues.
  • Enable in situ screens combining optical and transcriptomic phenotypes.

Main Methods:

  • PerturbView utilizes in vitro transcription to amplify barcodes before in situ sequencing.
  • Demonstrated PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells, and animal tumor tissue sections.
  • Combined PerturbView with spatial transcriptomics in mouse xenograft models.

Main Results:

  • PerturbView enables highly multiplexed phenotypic readouts across diverse systems.
  • Screens in primary macrophages identified novel regulators of NF-κB signaling.
  • Integration with spatial transcriptomics allows for rich optical and transcriptomic phenotypes in situ.

Conclusions:

  • PerturbView significantly advances OPS capabilities for complex biological systems.
  • The technology broadens the scope of OPS for various research models and applications.
  • PerturbView facilitates in situ screens with combined optical and transcriptomic data.