T cell fate and clonality inference from single-cell transcriptomes

Abstract

The enormous sequence diversity within T cell receptor (TCR) repertoires allows specific TCR sequences to be used as lineage markers for T cells that derive from a common progenitor. We have developed a computational method, called TraCeR, to reconstruct full-length, paired TCR sequences from T lymphocyte single-cell RNA-seq by combining existing assembly and alignment programs with “combinatorial recombinome” sequences comprising all possible TCR combinations. We validate this method to quantify its accuracy and sensitivity. Inferred TCR sequences reveal clonal relationships between T cells whilst the cells’ complete transcriptional landscapes can be quantified from the remaining RNA-seq data. This provides a powerful tool to link T cell specificity with functional response and we demonstrate this by determining the distribution of members of expanded T cell clonotypes in a mouse Salmonella infection model. Members of the same clonotype span early activated CD4+ T cells, as well as mature effector and memory cells.

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

“…To further support the hypothesis that most cells in Cluster 1 are bona fide T cells, we adapted a recent method for detection of V(D)J recombination events of the TCR locus (see Methods) (Stubbington et al 2016). With a median of only 0.64 million gene-mapped reads per cell, we were able to unambiguously detect V(D)J recombination events in 27 cells ( Fig.…”

“…However, only the beta chain locus was fully annotated (Meeker et al 2010). To explore TCR recombination in our immune cell populations, we adapted the recent method of Stubbington et al (2016). Synthetic beta chain sequences containing all possible combinations of the 52 V and 33 J germline segments were generated, with the addition of 20 N ambiguity bases in the 5 ′ end, seven N's between the V and J segments, and 50 N's at the 3 ′ end to account for unknown leader, possible D, and constant sequences, respectively.…”

Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes

“…After intraislet T cells were isolated and expanded with anti-CD3/CD28 beads (ExpAct, Miltenyi Biotech), cells were FACS purified into CD4 + and CD8 + populations. Individual cells were then sequestered using the Fluidigm C1 platform, mRNA sequences were amplified, and TCR α/β-pair sequences were identified using the TraCeR protocol, as previously described in published methods (64)(65)(66).…”

Computational genomics tools for dissecting tumour–immune cell interactions

“…This has led to novel single-cell sequencing technologies [15][16][17][18] , which will have a growing role in the future, in particular for the phenotyping of immune cells 19 . For example, using these technologies, it is now possible to reconstruct pairs of TCR αβ-chains as well as transcriptional profiles from single-cell RNA-seq data 20 . Although these technologies are opening new frontiers by dissecting the contribution of individual immune cells or cancer cells, technological challenges 21 , sequencing costs and practical restrictions are limiting their use.…”