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mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans

1
Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
2
Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
3
Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA
4
Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
*
Author to whom correspondence should be addressed.
Academic Editor: François Meurens
Vaccines 2022, 10(1), 30; https://doi.org/10.3390/vaccines10010030
Received: 29 October 2021 / Revised: 18 December 2021 / Accepted: 22 December 2021 / Published: 27 December 2021
Advances in high-throughput single-cell RNA sequencing (scRNA-seq) have been limited by technical challenges such as tough cell walls and low RNA quantity that prevent transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is demonstrated on two yeast species, Saccharomyces cerevisiae, a popular model organism, and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat shock S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant species of yeast with a thicker cell wall compared to S. cerevisiae. Single-cell transcriptomes in 39,705 C. albicans cells were characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity when treated with fluconazole. We demonstrate mDrop-seq to be an affordable and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to a better understanding of genetic variation in pathogens in response to stimuli and find immediate applications in investigating drug resistance, infection outcome and developing new drugs and treatment strategies. View Full-Text
Keywords: mDrop-seq; scRNA-seq; high-throughput; fluconazole; Candida albicans; Saccharomyces cerevisiae; stress response; cell-cycle mDrop-seq; scRNA-seq; high-throughput; fluconazole; Candida albicans; Saccharomyces cerevisiae; stress response; cell-cycle
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MDPI and ACS Style

Dohn, R.; Xie, B.; Back, R.; Selewa, A.; Eckart, H.; Rao, R.P.; Basu, A. mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans. Vaccines 2022, 10, 30. https://doi.org/10.3390/vaccines10010030

AMA Style

Dohn R, Xie B, Back R, Selewa A, Eckart H, Rao RP, Basu A. mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans. Vaccines. 2022; 10(1):30. https://doi.org/10.3390/vaccines10010030

Chicago/Turabian Style

Dohn, Ryan, Bingqing Xie, Rebecca Back, Alan Selewa, Heather Eckart, Reeta P. Rao, and Anindita Basu. 2022. "mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans" Vaccines 10, no. 1: 30. https://doi.org/10.3390/vaccines10010030

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