Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq.

Autor: Mylka V; VIB Tech Watch, VIB Headquarters, Ghent, Belgium.; Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium., Matetovici I; VIB Tech Watch, VIB Headquarters, Ghent, Belgium.; VIB Center for Brain & Disease Research, Leuven, Belgium., Poovathingal S; VIB Center for Brain & Disease Research, Leuven, Belgium., Aerts J; VIB Tech Watch, VIB Headquarters, Ghent, Belgium.; VIB Center for Brain & Disease Research, Leuven, Belgium., Vandamme N; Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium., Seurinck R; Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium., Verstaen K; Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium., Hulselmans G; VIB Center for Brain & Disease Research, Leuven, Belgium.; Department of Human Genetics, KU Leuven, Leuven, Belgium., Van den Hoecke S; VIB Tech Watch, VIB Headquarters, Ghent, Belgium., Scheyltjens I; Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium., Movahedi K; Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.; Laboratory for Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium., Wils H; Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium., Reumers J; Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium., Van Houdt J; Discovery Sciences, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium., Aerts S; VIB Center for Brain & Disease Research, Leuven, Belgium. stein.aerts@kuleuven.vib.be.; Department of Human Genetics, KU Leuven, Leuven, Belgium. stein.aerts@kuleuven.vib.be., Saeys Y; Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium. yvan.saeys@ugent.be.; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium. yvan.saeys@ugent.be.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2022 Feb 16; Vol. 23 (1), pp. 55. Date of Electronic Publication: 2022 Feb 16.
DOI: 10.1186/s13059-022-02628-8
Abstrakt: Background: Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-specific batch effects. Recently published multiplexing techniques using oligo-conjugated antibodies or -lipids allow barcoding sample-specific cells, a process called "hashing."
Results: Here, we compare the hashing performance of TotalSeq-A and -C antibodies, custom synthesized lipids and MULTI-seq lipid hashes in four cell lines, both for single-cell RNA-seq and single-nucleus RNA-seq. We also compare TotalSeq-B antibodies with CellPlex reagents (10x Genomics) on human PBMCs and TotalSeq-B with different lipids on primary mouse tissues. Hashing efficiency was evaluated using the intrinsic genetic variation of the cell lines and mouse strains. Antibody hashing was further evaluated on clinical samples using PBMCs from healthy and SARS-CoV-2 infected patients, where we demonstrate a more affordable approach for large single-cell sequencing clinical studies, while simultaneously reducing batch effects.
Conclusions: Benchmarking of different hashing strategies and computational pipelines indicates that correct demultiplexing can be achieved with both lipid- and antibody-hashed human cells and nuclei, with MULTISeqDemux as the preferred demultiplexing function and antibody-based hashing as the most efficient protocol on cells. On nuclei datasets, lipid hashing delivers the best results. Lipid hashing also outperforms antibodies on cells isolated from mouse brain. However, antibodies demonstrate better results on tissues like spleen or lung.
(© 2022. The Author(s).)
Databáze: MEDLINE
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