Single-cell technologies to study the immune system

Immunology

Volumn 147, Issue 2, 2016, Pages 133-140

  Proserpio, Valentina ^a   Mahata, Bidesh ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

CD4+ T helper cells; Immune cells; Single cell RNA sequencing; Single cell technology

Indexed keywords

MESSENGER RNA; SMALL CYTOPLASMIC RNA; RNA; TRANSCRIPTOME;

ARTICLE; CD4+ T LYMPHOCYTE; CELL HETEROGENEITY; CELL POPULATION; CELLS BY BODY ANATOMY; EXON; GENE EXPRESSION; GENE REGULATORY NETWORK; HELPER CELL; HUMAN; IMMUNE SYSTEM; IMMUNOCOMPETENT CELL; IMMUNOREGULATION; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA SPLICING; SINGLE CELL ANALYSIS; ANIMAL; CELL DIFFERENTIATION; CELL LINEAGE; CYTOLOGY; FORECASTING; GENE EXPRESSION PROFILING; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; IMMUNOLOGICAL TECHNIQUE; IMMUNOLOGY; IMMUNOPHENOTYPING; MASS COMMUNICATION; METABOLISM; PHENOTYPE; SEQUENCE ANALYSIS; TRENDS;

ANIMALS; CD4-POSITIVE T-LYMPHOCYTES; CELL DIFFERENTIATION; CELL LINEAGE; DIFFUSION OF INNOVATION; FORECASTING; GENE EXPRESSION PROFILING; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNE SYSTEM; IMMUNOLOGIC TECHNIQUES; IMMUNOPHENOTYPING; PHENOTYPE; RNA; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS; TRANSCRIPTOME;

EID: 84956681316     PISSN: 00192805     EISSN: 13652567     Source Type: Journal    
DOI: 10.1111/imm.12553     Document Type: Article

References (65)

1. Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol 2014; 32:1053-8.
2. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 2014; 344:1396-401.
3. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 2014; 343:776-9.
4. Hajdu SI. A note from history: the discovery of blood cells. Ann Clin Lab Sci 2003; 33:237-8.
5. Brady G, Barbara M, Iscove NN. Representative in vitro cDNA amplification from individual hemopoietic cells and colonies. Methods Mol Cell Biol 1990; 2:17-25.
6. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009; 6:377-82.
7. Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 2011; 21:1160-7.
8. Ramskold D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 2012; 30:777-82.
9. Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep 2012; 2:666-73.
10. Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol 2013; 14:R31.
11. Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, et al. Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Nat Protoc 2012; 7:813-28.
12. Picelli S, Björklund Å, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 2013; 10:1096-8.
13. Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014; 9:171-81.
14. Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 2010; 5:516-35.
15. Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet 2015; 16:133-45.
16. Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods 2013; 10:1093-5.
17. Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 2015; 33:155-60.
18. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014; 32:381-6.
19. Reiter M, Kirchner B, Müller H, Holzhauer C, Mann W, Pfaffl MW. Quantification noise in single cell experiments. Nucleic Acids Res 2011; 39:e124.
20. Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, et al. Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell Stem Cell 2015; 16:712-24.
21. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 2014; 11:163-6.
22. Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, et al. Normalization and noise reduction for single cell RNA-seq experiments. Bioinformatics 2015; 31:2225-2227.
23. Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, et al. Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. Cell Rep 2014; 7:1130-42.
24. Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 2014; 509:371-5.
25. Talal N. Lymphocyte heterogeneity and function. Arthritis Rheum 1973; 16:422-5.
26. Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol 2004; 4:123-32.
27. Schroeder HW. Similarity and divergence in the development and expression of the mouse and human antibody repertoires. Dev Comp Immunol 2006; 30:119-35.
28. Openshaw P, Murphy EE, Hosken NA, Maino V, Davis K, Murphy K, et al. Heterogeneity of intracellular cytokine synthesis at the single-cell level in polarized T helper 1 and T helper 2 populations. J Exp Med 1995; 182:1357-67.
29. Hussell T, Spender LC, Georgiou A, O'Garra A, Openshaw PJ. Th1 and Th2 cytokine induction in pulmonary T cells during infection with respiratory syncytial virus. J Gen Virol 1996; 77:2447-55.
30. Perfetto SP, Chattopadhyay PK, Roederer M. Seventeen-colour flow cytometry: unravelling the immune system. Nat Rev Immunol 2004; 4:648-55.
31. Reinherz EL, Schlossman SF. The differentiation and function of human T lymphocytes. Cell 1980; 19:821-7.
32. Engleman EG, Benike CJ, Grumet FC, Evans RL. Activation of human T lymphocyte subsets: helper and suppressor/cytotoxic T cells recognize and respond to distinct histocompatibility antigens. J Immunol 1981; 127:2124-9.
33. Mosmann TR, Cherwinski H, Bond MW, Giedlin MA, Coffman RL. Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. J Immunol 1986; 136:2348-57.
34. Mosmann TR. T lymphocyte subsets, cytokines, and effector functions. Ann N Y Acad Sci 1992; 664:89-92.
35. Park H, Li Z, Yang XO, Chang SH, Nurieva R, Wang YH, et al. A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol 2005; 6:1133-41.
36. + effector T cells develop via a lineage distinct from the T helper type 1 and 2 lineages. Nat Immunol 2005; 6:1123-32.
37. Josefowicz SZ, Rudensky A. Control of regulatory T cell lineage commitment and maintenance. Immunity 2009; 30:616-25.
38. Crotty S. Follicular helper CD4 T cells (TFH). Annu Rev Immunol 2011; 29:621-63.
39. Schmitt E, Klein M, Bopp T. Th9 cells, new players in adaptive immunity. Trends Immunol 2014; 35:61-8.
40. Eyerich S, Eyerich K, Pennino D, Carbone T, Nasorri F, Pallotta S, et al. Th22 cells represent a distinct human T cell subset involved in epidermal immunity and remodeling. J Clin Invest 2009; 119:3573-85.
41. Luckheeram RV, Zhou R, Verma AD, Xia B. CD4+ T cells: differentiation and functions. Clin Dev Immunol 2012; 2012:925135.
42. Fang M, Xie H, Dougan SK, Ploegh H, van Oudenaarden A. Stochastic cytokine expression induces mixed T helper cell States. PLoS Biol 2013; 11:e1001618.
43. Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, et al. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. PLoS Biol 2013; 11:e1001616.
44. + Th1/Th2 hybrid cells arise in vivo, can develop directly from naive precursors, and limit immunopathologic inflammation. PLoS Biol 2013; 11:e1001633.
45. Dash P, McClaren JL, Oguin TH, Rothwell W, Todd B, Morris MY, et al. Paired analysis of TCRα and TCRβ chains at the single-cell level in mice. J Clin Invest 2011; 121:288-95.
46. Douek DC, Betts MR, Brenchley JM, Hill BJ, Ambrozak DR, Ngai KL, et al. A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape. J Immunol 2002; 168:3099-104.
47. Zhou J, Dudley ME, Rosenberg SA, Robbins PF. Selective growth, in vitro and in vivo, of individual T cell clones from tumor-infiltrating lymphocytes obtained from patients with melanoma. J Immunol 2004; 173:7622-9.
48. Kim SM, Bhonsle L, Besgen P, Nickel J, Backes A, Held K, et al. Analysis of the paired TCR α- and β-chains of single human T cells. PLoS One 2012; 7:e37338.
49. Miconnet I. Probing the T-cell receptor repertoire with deep sequencing. Curr Opin HIV AIDS 2012; 7:64-70.
50. Newell EW, Davis MM. Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells. Nat Biotechnol 2014; 32:149-57.
51. Han A, Glanville J, Hansmann L, Davis MM. Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat Biotechnol 2014; 32:684-92.
52. Noy R, Pollard JW. Tumor-associated macrophages: from mechanisms to therapy. Immunity 2014; 41:49-61.
53. Deng Q, Ramskold D, Reinius B, Sandberg R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 2014; 343:193-6.
54. Kim JK, Marioni JC. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. Genome Biol 2013; 14:R7.
55. Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 2013; 498:236-40.
56. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 2014; 510:363-9.
57. Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, et al. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 2015; 33:269-76.
58. Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 2015; 17:471-85.
59. Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 2013; 14:618-30.
60. Sakaguchi S, Fukuma K, Kuribayashi K, Masuda T. Organ-specific autoimmune diseases induced in mice by elimination of T cell subset. I. Evidence for the active participation of T cells in natural self-tolerance; deficit of a T cell subset as a possible cause of autoimmune disease. J Exp Med 1985; 161:72-87.
61. Sakaguchi S, Sakaguchi N, Asano M, Itoh M, Toda M. Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor α-chains (CD25). Breakdown of a single mechanism of self-tolerance causes various autoimmune diseases. J Immunol 1995; 155:1151-64.
62. Cua DJ, Sherlock J, Chen Y, Murphy CA, Joyce B, Seymour B, et al. Interleukin-23 rather than interleukin-12 is the critical cytokine for autoimmune inflammation of the brain. Nature 2003; 421:744-8.
63. Langrish CL, Chen Y, Blumenschein WM, Mattson J, Basham B, Sedgwick JD, et al. IL-23 drives a pathogenic T cell population that induces autoimmune inflammation. J Exp Med 2005; 201:233-40.
64. Veldhoen M, Uyttenhove C, van Snick J, Helmby H, Westendorf A, Buer J, et al. Transforming growth factor-β 'reprograms' the differentiation of T helper 2 cells and promotes an interleukin 9-producing subset. Nat Immunol 2008; 9:1341-6.
65. - effector T cells. Nat Immunol 2008; 9:1347-55.