Linking T-cell receptor sequence to functional phenotype at the single-cell level (original) (raw)

• Wills, Q.F. et al. Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat. Biotechnol. 31, 748–752 (2013).
  Article CAS Google Scholar
• Newell, E.W., Sigal, N., Bendall, S.C., Nolan, G.P. & Davis, M.M. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 36, 142–152 (2012).
  Article CAS Google Scholar
• Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618–630 (2013).
  Article CAS Google Scholar
• Bendall, S.C., Nolan, G.P., Roederer, M. & Chattopadhyay, P.K. A deep profiler's guide to cytometry. Trends Immunol. 33, 323–332 (2012).
  Article CAS Google Scholar
• Spurgeon, S.L., Jones, R.C. & Ramakrishnan, R. High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS ONE 3, e1662 (2008).
  Article Google Scholar
• Wu, A.R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11, 41–46 (2014).
  Article CAS Google Scholar
• Newell, E.W. & Davis, M.M. Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells. Nat. Biotechnol. 32, 149–157 (2014).
  Article CAS Google Scholar
• Krogsgaard, M. & Davis, M.M. How T cells 'see' antigen. Nat. Immunol. 6, 239–245 (2005).
  Article CAS Google Scholar
• Murphy, K., Travers, P., Walport, M. & Janeway, C. Janeway's Immunobiology 8th Edn. (Garland Science, 2012).
• Newell, E.W. et al. Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. Nat. Biotechnol. 31, 623–629 (2013).
  Article CAS Google Scholar
• Birnbaum, M.E. et al. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157, 1073–1087 (2014).
  Article CAS Google Scholar
• Hinrichs, C.S. & Restifo, N.P. Reassessing target antigens for adoptive T-cell therapy. Nat. Biotechnol. 31, 999–1008 (2013).
  Article CAS Google Scholar
• Han, A. et al. Dietary gluten triggers concomitant activation of CD4+ and CD8+ alphabeta T cells and gammadelta T cells in celiac disease. Proc. Natl. Acad. Sci. USA 110, 13073–13078 (2013).
  Article CAS Google Scholar
• Kim, S.M. et al. Analysis of the paired TCR alpha- and beta-chains of single human T cells. PLoS ONE 7, e37338 (2012).
  Article CAS Google Scholar
• Dash, P. et al. Paired analysis of TCRalpha and TCRbeta chains at the single-cell level in mice. J. Clin. Invest. 121, 288–295 (2011).
  Article CAS Google Scholar
• Gascoigne, N.R. & Alam, S.M. Allelic exclusion of the T cell receptor alpha-chain: developmental regulation of a post-translational event. Semin. Immunol. 11, 337–347 (1999).
  Article CAS Google Scholar
• Malissen, M. et al. Regulation of TCR alpha and beta gene allelic exclusion during T-cell development. Immunol. Today 13, 315–322 (1992).
  Article CAS Google Scholar
• Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).
  Article CAS Google Scholar
• Glanville, J. et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc. Natl. Acad. Sci. USA 106, 20216–20221 (2009).
  Article CAS Google Scholar
• De Rosa, S.C., Herzenberg, L.A., Herzenberg, L.A. & Roederer, M. 11-color, 13-parameter flow cytometry: identification of human naive T cells by phenotype, function, and T-cell receptor diversity. Nat. Med. 7, 245–248 (2001).
  Article CAS Google Scholar
• Yanagi, Y., Chan, A., Chin, B., Minden, M. & Mak, T.W. Analysis of cDNA clones specific for human T cells and the alpha and beta chains of the T-cell receptor heterodimer from a human T-cell line. Proc. Natl. Acad. Sci. USA 82, 3430–3434 (1985).
  Article CAS Google Scholar
• Nakamura, K. et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 39, e90 (2011).
  Article CAS Google Scholar
• Law, J.P. et al. The importance of Foxp3 antibody and fixation/permeabilization buffer combinations in identifying CD4+CD25+Foxp3+ regulatory T cells. Cytometry A 75, 1040–1050 (2009).
  Article Google Scholar
• Vahedi, G., Kanno, Y., Sartorelli, V. & O'Shea, J.J. Transcription factors and CD4 T cells seeking identity: masters, minions, setters and spikers. Immunology 139, 294–298 (2013).
  Article CAS Google Scholar
• Oestreich, K.J. & Weinmann, A.S. Master regulators or lineage-specifying? Changing views on CD4+ T cell transcription factors. Nat. Rev. Immunol. 12, 799–804 (2012).
  Article CAS Google Scholar
• Wilson, C.B., Rowell, E. & Sekimata, M. Epigenetic control of T-helper-cell differentiation. Nat. Rev. Immunol. 9, 91–105 (2009).
  Article CAS Google Scholar
• Collins, A., Littman, D.R. & Taniuchi, I. RUNX proteins in transcription factor networks that regulate T-cell lineage choice. Nat. Rev. Immunol. 9, 106–115 (2009).
  Article CAS Google Scholar
• Assenmacher, M., Lohning, M. & Radbruch, A. Detection and isolation of cytokine secreting cells using the cytometric cytokine secretion assay. Curr. Protoc. Immunol. 46, 6.27 (2002).
  Google Scholar
• Anderson, P. Post-transcriptional control of cytokine production. Nat. Immunol. 9, 353–359 (2008).
  Article CAS Google Scholar
• Fontenot, J.D., Gavin, M.A. & Rudensky, A.Y. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat. Immunol. 4, 330–336 (2003).
  Article CAS Google Scholar
• Ribas, A. Tumor immunotherapy directed at PD-1. N. Engl. J. Med. 366, 2517–2519 (2012).
  Article CAS Google Scholar
• Sliwkowski, M.X. & Mellman, I. Antibody therapeutics in cancer. Science 341, 1192–1198 (2013).
  Article CAS Google Scholar
• Pagès, F. et al. Effector memory T cells, early metastasis, and survival in colorectal cancer. N. Engl. J. Med. 353, 2654–2666 (2005).
  Article Google Scholar
• Galon, J. et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 313, 1960–1964 (2006).
  Article CAS Google Scholar
• Gerlinger, M. et al. Ultra-deep T-cell receptor sequencing reveals the complexity and intratumour heterogeneity of T-cell clones in renal cell carcinomas. J. Pathol. 231, 424–432 (2013).
  Article CAS Google Scholar
• Sherwood, A.M. et al. Tumor-infiltrating lymphocytes in colorectal tumors display a diversity of T cell receptor sequences that differ from the T cells in adjacent mucosal tissue. Cancer immunol. immunother. 62, 1453–1461 (2013).
  Article CAS Google Scholar
• Sasada, T. & Suekane, S. Variation of tumor-infiltrating lymphocytes in human cancers: controversy on clinical significance. Immunotherapy 3, 1235–1251 (2011).
  Article CAS Google Scholar
• deLeeuw, R.J., Kost, S.E., Kakal, J.A. & Nelson, B.H. The prognostic value of FoxP3+ tumor-infiltrating lymphocytes in cancer: a critical review of the literature. Clin. Cancer Res. 18, 3022–3029 (2012).
  Article CAS Google Scholar
• Scurr, M., Gallimore, A. & Godkin, A. T cell subsets and colorectal cancer: discerning the good from the bad. Cell. Immunol. 279, 21–24 (2012).
  Article CAS Google Scholar
• Tosolini, M. et al. Clinical impact of different classes of infiltrating T cytotoxic and helper cells (Th1, th2, treg, th17) in patients with colorectal cancer. Cancer Res. 71, 1263–1271 (2011).
  Article CAS Google Scholar
• Ladoire, S., Martin, F. & Ghiringhelli, F. Prognostic role of FOXP3+ regulatory T cells infiltrating human carcinomas: the paradox of colorectal cancer. Cancer immunol. immunother. 60, 909–918 (2011).
  Article CAS Google Scholar
• Blatner, N.R. et al. Expression of RORgammat marks a pathogenic regulatory T cell subset in human colon cancer. Sci. Transl. Med. 4, 164ra159 (2012).
  Article Google Scholar
• Gounaris, E. et al. T-regulatory cells shift from a protective anti-inflammatory to a cancer-promoting proinflammatory phenotype in polyposis. Cancer Res. 69, 5490–5497 (2009).
  Article CAS Google Scholar
• Miyara, M. et al. Functional delineation and differentiation dynamics of human CD4+ T cells expressing the FoxP3 transcription factor. Immunity 30, 899–911 (2009).
  Article CAS Google Scholar
• Zhou, L., Chong, M.M. & Littman, D.R. Plasticity of CD4+ T cell lineage differentiation. Immunity 30, 646–655 (2009).
  Article CAS Google Scholar