T cell fate and clonality inference from single cell transcriptomes

By Michael J. T. Stubbington, T. Lönnberg, V. Proserpio, S. Clare, A. Speak, Gordon Dougan, Sarah A. Teichmann. Nature Methods, 2016

414 citations recorded by the source corpus.

We developed TraCeR, a computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. We found that T cell clonotypes in a mouse Salmonella infection model span early activated CD4+ T cells as well as mature effector and memory cells.

Subfields: Immunology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9ba567a51a91071a58cf749f668426624d533cdc

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Immunology

1. John C. Marioni
2. Rahul Satija
3. Martin Hemberg
4. Sarah A. Teichmann
5. Nir Yosef
6. J. Lee
7. Duhee Bang
8. Byungjin Hwang

In Molecular Biology

1. Rahul Satija
2. Sarah A. Teichmann
3. John C. Marioni
4. Nir Yosef
5. J. Lee
6. Duhee Bang
7. Byungjin Hwang
8. Martin Hemberg

Citations in the corpus

• Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. (2017, neutral): “…Kiselev et al., 2017 https://github.com/hemberg-lab/SC3 Monocle 2.0 Trapnell et al., 2014 http://monocle-bio.sourceforge.net/ ScLVM Buettner et al., 2015 https://github.com/PMBio/scLVM TraCeR Stubbington et al., 2016 https://github.com/teichlab/tracer Cell 169, 1342–1356.e1–e5, June 15, 2017 e1”
• The Human Cell Atlas (2017, background): “In humans, immune cells naturally contain lineage barcodes through VDJ recombination in T and B cells and somatic hypermutation in B cells (Stubbington et al., 2016).”
• A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications (2017, background): “scRNA-seq is also ideal for examination of single cells where each one is essentially unique, such as individual T lymphocytes expressing highly diverse T-cell receptors [20], neurons within the brain [15] or cells within an early-stage embryo [21].”
• Single-cell RNA sequencing technologies and bioinformatics pipelines (2018, methodology): “In addition, scRNA-seq is increasingly being utilized to delineate cell lineage relationships in early development 15 , myoblast differentiation 16 , and lymphocyte fate determination 17 .”
• HLA variation and disease (2018, background): “gies, particularly at the single­cell level 98 , are enabling the detailed characterization of TCR sequence hetero geneity, and this has spurred a concomitant effort to ascribe a meaningful order to this variation.”