scRepertoire: An R-based toolkit for single-cell immune receptor analysis

Abstract

Single-cell sequencing is an emerging technology in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. A number of workflows and software packages have been created to process and analyze single-cell transcriptomic data. These packages allow users to take the vast dimensionality of the data generated in single-cell-based experiments and distill the data into novel insights. Unlike the transcriptomic field, there is a lack of options for software that allow for single-cell immune receptor profiling. Enabling users to easily combine mRNA and immune profiling, scRepertoire was built to process data derived from 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat R package. The scRepertoire R package and processed data are open source and available on GitHub and provides in-depth tutorials on the capability of the package.

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics

“…With the extensive literature demonstrating the role of TCR expansion in antitumor immunity and immunotherapy 11 , we first wanted to investigate the dynamics of CD4 + and CD8 + T-cell clonal species in ccRCC. Using our previously described scRepertoire software 32 , we assigned productive TCR sequences for TCRA and TCRB and defined clonotypes by the combination of both the genes and nucleotide sequences. For the identified T cells in ccRCC patients, recovering of at least one TCR chain, ranged from 74.8 to 87.6% after filtering and clonotype reconstruction.…”

“…Enrichment for anti-PD-1 therapy response was derived from Sade-Feldman et al to develop gene signatures for the CD8_B (nonresponsive) and CD8_G (responsive) single-cell populations 22 . TCR analysis utilized our previously described scRepertoire R package (v0.99.3) 32 with clonotype being defined as the combination of the gene components of the VDJ and the nucleotide sequence for both TCRA and TCRB chains and assigned on the integrated Seurat object. Cell trajectory analysis used the slingshot (v1.6.0) R package 36 with default settings for the slingshot function and using the embedding from the subclustering for each cell type.…”

The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD

“…The integrated RNA sequencing object included 12,568 cells with V3: 4,584, V5: 3,523, and V6: 4,461 cells. The filtered contig annotation output of Cell Ranger vdj were loaded into R and processed using the scRepertoire (v1.1.3) R package (Borcherding et al, 2020). Clonotypes were assigned using igraph (v1.2.6) network analysis of components generated from CDR3 sequences greater than or equal to 0.85 normalized Levenshtein distance.…”

A transcriptomic map of murine and human alopecia areata

“…Clonotype analysis was performed using the scRepertoire (version 1.0.0) R package (42) with clonotypes defined as the combination of the genes of the TCR A and B chains and nucleotide sequences. Individual gene sets were derived from the Gene Ontology Consortium (43), the Kyoto Encyclopedia of Genes and Genomes (44), and previously reported pathways (45).…”