Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res, 28 (9). pp. 1353-1363. ISSN 1088-9051

DOI: 10.1101/gr.234062.117


Single-cell RNA-seq's (scRNA-seq) unprecedented cellular resolution at a genome wide scale enables us to address questions about cellular heterogeneity that are inaccessible using methods that average over bulk tissue extracts. However, scRNA-seq datasets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present SAKE (Single-cell RNA-seq Analysis and Klustering Evaluation): a robust method for scRNA-seq analysis that provides quantitative statistical metrics at each step of the scRNA-seq analysis pipeline. Comparing SAKE to multiple single-cell analysis methods shows that most methods perform similarly across a wide range cellular contexts, with SAKE outperforming these methods in the case of large complex populations. We next applied the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-seq data from both the Fluidigm C1 and 10x Genomics platforms were analyzed with SAKE to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance. These experimentally validated markers of BRAFi resistance share overlap with previous analysis in different melanoma cell lines, demonstrating the generality of these findings and highlighting the utility of single-cell analysis to elucidate mechanisms of BRAFi resistance.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > genes: types > BRAF
diseases & disorders > cancer > cancer types > melanomas
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > Hammell M. lab
School of Biological Sciences > Publications
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL labs > Hicks lab
Depositing User: Matthew Dunn
Date: 30 July 2018
Date Deposited: 14 Aug 2018 14:45
Last Modified: 05 Nov 2020 19:13
PMCID: PMC6120620
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