Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap

Nat Biotechnol. 2024 Oct 7. doi: 10.1038/s41587-024-02386-x.

Jiacheng Gu ¹, Abhishek Iyer ¹, Ben Wesley ¹, Angelo Taglialatela ², Giuseppe Leuzzi ² ³ ⁴, Sho Hangai ³, Aubrianna Decker ¹, Ruoyu Gu ¹, Naomi Klickstein ¹, Yuanlong Shuai ¹, Kristina Jankovic ³, Lucy Parker-Burns ³, Yinuo Jin ⁵, Jia Yi Zhang ⁵, Justin Hong ⁶, Xiang Niu ⁷ ⁸, Jonathon A Costa ⁹, Mikael G Pezet ¹⁰, Jacqueline Chou ¹ ⁸, Hans-Willem Snoeck ¹⁰ ¹¹ ¹², Dan A Landau ¹³ ⁸, Elham Azizi ⁵ ⁶ ¹⁴, Edmond M Chan ³ ¹³ ¹⁵, Alberto Ciccia ² ³ ⁴, Jellert T Gaublomme ¹⁶ ¹⁷ ¹⁸ ¹⁹

Affiliations

1 Department of Biological Sciences, Columbia University, New York, NY, USA.
2 Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
3 Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
4 Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.
5 Department of Biomedical Engineering, Columbia University, New York, NY, USA.
6 Department of Computer Science, Columbia University, New York, NY, USA.
7 Genentech Research and Early Development, New York, NY, USA.
8 Weill Cornell Medicine, New York, NY, USA.
9 Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
10 Department of Medicine, Columbia Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
11 Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
12 Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
13 New York Genome Center, New York, NY, USA.
14 Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
15 Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
16 Department of Biological Sciences, Columbia University, New York, NY, USA. jg4106@columbia.edu.
17 Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA. jg4106@columbia.edu.
18 New York Genome Center, New York, NY, USA. jg4106@columbia.edu.
19 Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA. jg4106@columbia.edu.

PMID: 39375448 DOI: 10.1038/s41587-024-02386-x

Abstract

Unlike sequencing-based methods, which require Cell Lysis, optical pooled genetic screens enable investigation of spatial phenotypes, including cell morphology, protein subcellular localization, cell-cell interactions and tissue organization, in response to targeted CRISPR perturbations. Here we report a multimodal optical pooled CRISPR screening method, which we call CRISPRmap. CRISPRmap combines in situ CRISPR guide-identifying barcode readout with multiplexed immunofluorescence and RNA detection. Barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency. CRISPRmap enables in situ barcode readout in cell types and contexts that were elusive to conventional optical pooled screening, including cultured primary cells, embryonic stem cells, induced pluripotent stem cells, derived neurons and in vivo cells in a tissue context. We conducted a screen in a breast Cancer cell line of the effects of DNA damage repair gene variants on cellular responses to commonly used Cancer therapies, and we show that optical phenotyping pinpoints likely pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance.

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