Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits.
| العنوان: | Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. |
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| المؤلفون: | Binan L; Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Danquah S; Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Valakh V; Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Simonton B; Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)., Bezney J; Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)., Nehme R; Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA., Cleary B; Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA., Farhi SL; Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. |
| المصدر: | BioRxiv : the preprint server for biology [bioRxiv] 2023 Dec 01. Date of Electronic Publication: 2023 Dec 01. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution. Competing Interests: Conflicts of interest LB, BC, SLF are inventors on a patent application relating to work described in the manuscript which has been filed by the Broad Institute. The authors declare no other conflict of interest. |
| معلومات مُعتمدة: | R01 MH128366 United States MH NIMH NIH HHS; RF1 MH121289 United States MH NIMH NIH HHS |
| تواريخ الأحداث: | Date Created: 20231211 Latest Revision: 20231218 |
| رمز التحديث: | 20231218 |
| مُعرف محوري في PubMed: | PMC10705493 |
| DOI: | 10.1101/2023.11.30.569494 |
| PMID: | 38076932 |
| قاعدة البيانات: | MEDLINE |
| DOI: | 10.1101/2023.11.30.569494 |
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