Transcript-specific enrichment enables profiling rare cell states via scRNA-seq.

Autor:	Abay T; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Pathology, Stanford University, Stanford CA, USA.; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA., Stickels RR; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Pathology, Stanford University, Stanford CA, USA., Takizawa MT; Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Nalbant BN; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Hsieh YH; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Charité Universitätsmedizin Berlin, Germany.; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany., Hwang S; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Pathology, Stanford University, Stanford CA, USA., Snopkowski C; Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Yu KKH; Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Abou-Mrad Z; Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Tabar V; Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Ludwig LS; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany., Chaligné R; Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Satpathy AT; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.; Department of Pathology, Stanford University, Stanford CA, USA.; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA., Lareau CA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Mar 27. Date of Electronic Publication: 2024 Mar 27.
DOI:	10.1101/2024.03.27.587039
Abstrakt:	Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing (scRNA-seq) identifies many rare populations of interest that express specific marker transcript combinations, traditional flow sorting limits our ability to enrich these populations for further profiling, including requiring cell surface markers with high-fidelity antibodies. Additionally, many single-cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. To address these limitations, we describe Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay that enables scRNA-seq profiling of subpopulations from complex cellular mixtures defined by the presence or absence of specific RNA transcripts. Across immune populations ( n = 141,227 cells) and fresh-frozen and formalin-fixed paraffin-embedded brain tissue ( n = 29,522 nuclei), we demonstrate the sorting logic that can be used to enrich for cell populations via RNA-based cytometry followed by high-throughput scRNA-seq. Our approach provides a rational, programmable method for studying rare populations identified by one or more marker transcripts. Competing Interests: Competing interests A.T.S. is a founder of Immunai, Cartography Biosciences, and Prox Biosciences, an advisor to Zafrens, Pallando Therapeutics, and Wing Venture Capital, and receives research funding from Merck Research Laboratories. R.R.S., L.S.L., and C.A.L. are consultants to Cartography Biosciences. R.C. is a consultant for Sanavia Oncology, S2 Genomics, and LevitasBio.
Databáze:	MEDLINE
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