Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anticancer drug response
Year: 2021
Type: article
Abstract: ABSTRACT The transcriptional plasticity of cancer cells promotes intercellular heterogeneity in response to anti-cancer drugs and facilitates the generation of subpopulation surviving cells. Characterizing single-cell transcriptional heterogeneity after drug treatments can provide mechanistic insights into drug efficacy. Here we used single-cell RNA-seq to examine transcriptomic profiles of cancer cells treated with paclitaxel, celecoxib, and the combination of the two drugs. By normalizing the expression of endogenous genes to spike-in molecules, we found that celluar mRNA abundance shows dynamic regulation after drug treatment. Using a random forest model, we identified gene signatures classifying single cells into three states: transcriptional repression, amplification, and control-like. Treatment with paclitaxel or celecoxib alone generally repressed gene transcription across single cells. Interestingly, the drug combination resulted in transcriptional amplification and hyperactivation of mitochondrial oxidative phosphorylation pathway linking to enhanced cell killing efficiency. Finally, we identified a regulatory module enriched with metabolism and inflammation-related genes activated in a subpopulation of paclitaxel-treated cells, the expression of which predicted paclitaxel efficacy across cancer cell lines and in vivo patient samples. Our study highlights the dynamic global transcriptional activity driving single-cell heterogeneity during drug response and emphasizes the importance of adding spike-in molecules to study gene expression regulation using single-cell RNA-seq.
Source: NAR Genomics and Bioinformatics
Authors: Xin Wang, Jane Frederick, Hongbin Wang, Sheng Hui, Vadim Backman, Zhe Ji
Institutions: Northwestern University, Harvard University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,400
Awards: Reducing Cancer Transcriptional Heterogeneity through Regulation of Chromatin Structure, Area B: Minimally Intrusive Colorectal Cancer Risk Stratification with Nanocytology:Targeting Underscreened Populations, Dissect regulation of RNA translation in human cancers, EFRI CEE: Macrogenomic engineering via modulation of chromatin nanoenvironment, Characterizing functional translation in putative 'noncoding' regions of a genome, Translating buccal nanocytology for lung cancer screening into clinical practice
OpenAlex ID: W3173769416