Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing.

Summary Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving transcriptional heterogeneity. However, its application to studying cancerous tissues is currently hampered by the lack of coverage across key mutation hotspots in the vast majority of cells; this lack of coverage prevents the correlation of genetic and transcriptional readouts from the same single cell. To overcome this, we developed TARGET-seq, a method for the high-sensitivity detection of multiple mutations within single cells from both genomic and coding DNA, in parallel with unbiased whole-transcriptome analysis. Applying TARGET-seq to 4,559 single cells, we demonstrate how this technique uniquely resolves transcriptional and genetic tumor heterogeneity in myeloproliferative neoplasms (MPN) stem and progenitor cells, providing insights into deregulated pathways of mutant and non-mutant cells. TARGET-seq is a powerful tool for resolving the molecular signatures of genetically distinct subclones of cancer cells. Graphical Abstract Highlights • Conventional scRNA-seq protocols do not allow reliable mutational analysis • TARGET-seq combines high-sensitivity genomic DNA and cDNA genotyping with scRNA-seq • TARGET-seq resolves the distinct transcriptional signatures of tumor genetic subclones • Non-mutant cells from patients show aberrant, inflammation-associated gene expression Rodriguez-Meira et al. developed TARGET-seq, a method for high-sensitivity mutational analysis and parallel RNA sequencing from the same single cell. Applied to 4,559 single cells, TARGET-seq unraveled transcriptional and genetic tumor heterogeneity in myeloproliferative neoplasm (MPN) stem and progenitor cells. TARGET-seq is a powerful tool for resolving the molecular signatures of genetically distinct tumor subclones. [ABSTRACT FROM AUTHOR]