mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq

Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochon...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 120; no. 39; p. e2307722120
Main Authors Lin, Xinrui, Chen, Yingwen, Lin, Li, Yin, Kun, Cheng, Rui, Lin, Xin, Wang, Xiaoyu, Guo, Ye, Wu, Zhaorun, Zhang, Yingkun, Li, Jin, Yang, Chaoyong, Song, Jia
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 26.09.2023
Subjects
Algorithms
Biological Sciences
Carcinoma, Non-Small-Cell Lung
Chemical degradation
Cost analysis
Degradation
Demultiplexing
Genomes
Genotypes
Humans
Lethality
Lung cancer
Lung Neoplasms
Medical research
Mitochondria
Mitochondria - genetics
Non-small cell lung carcinoma
Ribonucleic acid
RNA
RNA, Mitochondrial
Single-Cell Gene Expression Analysis
Small cell lung carcinoma
Tumor cell lines
mitochondrial genome variants
multiplexing
scRNA-seq
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Summary:Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochondrial genomes are small but diverse, providing concise genotype information. We developed "mitoSplitter," an algorithm that demultiplexes samples using mitochondrial RNA (mtRNA) variants, and demonstrated that mtRNA variants can be used to demultiplex large-scale scRNA-seq data. Using affordable computational resources, mitoSplitter can accurately analyze 10 samples and 60,000 cells in 6 h. To avoid the batch effects from separated experiments, we applied mitoSplitter to analyze the responses of five non-small cell lung cancer cell lines to BET (Bromodomain and extraterminal) chemical degradation in a multiplexed fashion. We found the synthetic lethality of inhibition and BET chemical degradation in BET inhibitor-resistant cells. The result indicates that mitoSplitter can accelerate the application of scRNA-seq assays in biomedical research.
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1Xinrui Lin, Y.C., and L.L. contributed equally to this work.
Edited by David Weitz, Harvard University, Cambridge, MA; received May 9, 2023; accepted August 13, 2023
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.2307722120