High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

High-throughput single-cell RNA-Sequencing is a powerful technique for gene expression profiling of complex and heterogeneous cellular populations such as the immune system. However, these methods only provide short-read sequences from one end of a cDNA template, making them poorly suited to the investigation of gene-regulatory events such as alternative RNA splicing, adaptive immune responses or somatic genome evolution. To address this challenge, we have developed a method that combines targeted long-read sequencing with short-read based transcriptome profiling of barcoded single cell libraries generated by droplet-based partitioning. We use Repertoire and Gene Expression by Sequencing (RAGE-Seq) on 7,138 lymphocytes sampled from the primary tumor and draining lymph node of a breast cancer patient to accurately characterize full-length T-cell (TCR) and B-cell (BCR) receptor sequences and transcriptional profiles. With this method we show that somatic hypermutation, alternate splicing and clonal evolution of T and B lymphocytes can be tracked across these tissue compartments. Our results demonstrate that RAGE-Seq is an accessible and cost-effective method for high-throughput deep single cell profiling, applicable to a wide range of biological challenges.