T cell fate and clonality inference from single-cell transcriptomes

被引：0

作者：

Stubbington, Michael J. T. ^{[1
]}

Lonnberg, Tapio ^{[1
]}

Proserpio, Valentina ^{[1
]}

Clare, Simon ^{[2
]}

Speak, Anneliese ^{[2
]}

Dougan, Gordon ^{[2
]}

Teichmann, Sarah A. ^{[1
,2
]}

机构：

[1] EBI, EMBL, Cambridge, England

[2] Wellcome Trust Sanger Inst, Cambridge, England

来源：

NATURE METHODS | 2016年 / 13卷 / 04期

基金：

欧洲研究理事会;

关键词：

EFFECTOR FUNCTIONS; RNA-SEQ; HETEROGENEITY; REGULATORS; SEQUENCE; LEVEL;

D O I：

10.1038/NMETH.3800

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：329 / 332

页数：4

共 25 条

[1] Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines
Becattini, Simone
Latorre, Daniela
Mele, Federico
Foglierini, Mathilde
De Gregorio, Corinne
Cassotta, Antonino
Fernandez, Blanca
Kelderman, Sander
Schumacher, Ton N.
Corti, Davide
Lanzavecchia, Antonio
Sallusto, Federica
[J]. SCIENCE, 2015, 347 (6220) : 400 - 406
[2] MiXCR: software for comprehensive adaptive immunity profiling
Bolotin, Dmitriy A.
Poslavsky, Stanislav
Mitrophanov, Igor
Shugay, Mikhail
Mamedov, Ilgar Z.
Putintseva, Ekaterina V.
Chudakov, Dmitriy M.
[J]. NATURE METHODS, 2015, 12 (05) : 380 - 381
[3] Antigen Receptor Allelic Exclusion: An Update and Reappraisal
Brady, Brenna L.
Steinel, Natalie C.
Bassing, Craig H.
[J]. JOURNAL OF IMMUNOLOGY, 2010, 185 (07) : 3801 - 3808
[4] Invariant natural killer T cells: an innate activation scheme linked to diverse effector functions
Brennan, Patrick J.
Brigl, Manfred
Brenner, Michael B.
[J]. NATURE REVIEWS IMMUNOLOGY, 2013, 13 (02) : 101 - 117
[5] Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Buettner, Florian
Natarajan, Kedar N.
Casale, F. Paolo
Proserpio, Valentina
Scialdone, Antonio
Theis, Fabian J.
Teichmann, Sarah A.
Marioni, John C.
Stegie, Oliver
[J]. NATURE BIOTECHNOLOGY, 2015, 33 (02) : 155 - 160
[6] Paired analysis of TCRα and TCRβ chains at the single-cell level in mice
Dash, Pradyot
McClaren, Jennifer L.
Oguin, Thomas H., III
Rothwell, William
Todd, Brandon
Morris, Melissa Y.
Becksfort, Jared
Reynolds, Cory
Brown, Scott A.
Doherty, Peter C.
Thomas, Paul G.
[J]. JOURNAL OF CLINICAL INVESTIGATION, 2011, 121 (01) : 288 - 295
[7] Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
Gaublomme, Jellert T.
Yosef, Nir
Lee, Youjin
Gertner, Rona S.
Yang, Li V.
Wu, Chuan
Pandolfi, Pier Paolo
Mak, Tak
Satija, Rahul
Shalek, Alex K.
Kuchroo, Vijay K.
Park, Hongkun
Regev, Aviv
[J]. CELL, 2015, 163 (06) : 1400 - 1412
[8] Linking T-cell receptor sequence to functional phenotype at the single-cell level
Han, Arnold
Glanville, Jacob
Hansmann, Leo
Davis, Mark M.
[J]. NATURE BIOTECHNOLOGY, 2014, 32 (07) : 684 - +
[9] Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types
Jaitin, Diego Adhemar
Kenigsberg, Ephraim
Keren-Shaul, Hadas
Elefant, Naama
Paul, Franziska
Zaretsky, Irina
Mildner, Alexander
Cohen, Nadav
Jung, Steffen
Tanay, Amos
Amit, Ido
[J]. SCIENCE, 2014, 343 (6172) : 776 - 779
[10] Distinct regulation of effector and memory T-cell differentiation
Kallies, Axel
[J]. IMMUNOLOGY AND CELL BIOLOGY, 2008, 86 (04) : 325 - 332

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