Abstract A20: Single-cell immune TCR repertoire profiling in the context of immunotherapy by using three 10x Genomics libraries

Abstract

Abstract 10x Genomics single-cell sequencing provides a comprehensive and scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. For performance comparison of single-cell immune TCR repertoire profiling, we tested three libraries: (1) 5-prime gene expression, (2) direct enrichment for TCR, and (3) post-cDNA-amplification enrichment for TCR, on two invariant natural killer T (iNKT) cells, on B240 and B241, with iNKT purity at 90% and 45%, respectively. We also performed correlation analysis between gene expression data and clonotype data by library 3. About 1,100 cells of B240 and 580 cells of B241 were sequenced. The numbers of productive clonotypes of B240 were identified as 165, 284, and 332 for the three libraries, respectively, while 47 clonotypes overlapped among the libraries. The numbers of productive clonotypes of B241 were 88, 152, and 148, respectively, while 35 clonotypes overlapped. Each sample is a mixture of iNK T cells and non-invariant NK T cells. We were able to identify the clusters of iNKT cells using the 5’ gene expression data by library 1 in tSNE plots for both B240 and B241. More importantly, the clusters correlated strongly with the TCR clonotypes identifying iNKT cells by library 3. Based upon our data, we noticed that the number of clonotypes identified is proportional to the number of cells sequenced regardless of libraries. Library 1 has low sensitivity in terms of clonotype detection, due to un-enrichment of TCR genes, and mainly detected single chain in each cell (beta chain most of the time). The other two libraries are able to identify high and similar number of clonotypes. However, library 3 is able to associate gene expression pattern with TCR clonotype usage, which is a big advantage over the other two libraries for 10x Genomics single-cell immune TCR repertoire profiling. Note: This abstract was not presented at the conference. Citation Format: Yuan Qi, Jin Seon Im, Xiaoping Su. Single-cell immune TCR repertoire profiling in the context of immunotherapy by using three 10x Genomics libraries [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A20.