Order by chance: origins and benefits of stochasticity in immune cell fate control
Tài liệu tham khảo
Gregor, 2007, Stability and nuclear dynamics of the bicoid morphogen gradient, Cell, 130, 141, 10.1016/j.cell.2007.05.026
Gregor, 2005, Diffusion and scaling during early embryonic pattern formation, Proc Natl Acad Sci, 102, 18403, 10.1073/pnas.0509483102
Suda, 1984, Disparate differentiation in mouse hemopoietic colonies derived from paired progenitors, Proc Natl Acad Sci U S A, 81, 2520, 10.1073/pnas.81.8.2520
Weaver, 1998, Heterogeneity in the clonal T cell response: implications for models of T Cell activation and cytokine phenotype development, Immunol Res, 17, 279, 10.1007/BF02786452
Taylor, 2015, Apoptosis and antigen affinity limit effector cell differentiation of a single naive B cell, Science, 347, 784, 10.1126/science.aaa1342
Buchholz, 2013, Disparate individual fates compose robust CD8+ T cell immunity, Science, 340, 630, 10.1126/science.1235454
Hodgkin, 2018, Modifying clonal selection theory with a probabilistic cell, Immunol Rev, 285, 249, 10.1111/imr.12695
Buchholz, 2016, T cell fate at the single-cell level, Annu Rev Immunol, 34, 65, 10.1146/annurev-immunol-032414-112014
Becker, 1963, Cytological demonstration of the clonal nature of spleen colonies derived from transplanted mouse marrow cells, Nature, 197, 452, 10.1038/197452a0
Cho, 2017, TCR signal quality modulates fate decisions of single CD4 + T cells in a probabilistic manner, Cell Rep, 20, 806, 10.1016/j.celrep.2017.07.005
Hawkins, 2009, Hodgkin PD: a single-cell pedigree analysis of alternative stochastic lymphocyte fates, Proc Natl Acad Sci, 106, 13457, 10.1073/pnas.0905629106
Gerlach, 2013, Heterogeneous differentiation patterns of individual CD8+ T cells, Science, 340, 635, 10.1126/science.1235487
Duffy, 2012, Hodgkin PD: activation-induced B cell fates are selected by intracellular stochastic competition, Science, 335, 338, 10.1126/science.1213230
Chang, 2007, Asymmetric T lymphocyte division in the initiation of adaptive immune responses, Science, 315, 1687, 10.1126/science.1139393
Verbist, 2016, Metabolic maintenance of cell asymmetry following division in activated T lymphocytes, Nature, 532, 389, 10.1038/nature17442
Hart, 2014, Paradoxical signaling by a secreted molecule leads to homeostasis of cell levels, Cell, 158, 1022, 10.1016/j.cell.2014.07.033
Tkach, 2014, T cells translate individual, quantal activation into collective, analog cytokine responses via time-integrated feedbacks, eLife, 3, 10.7554/eLife.01944
Nish, 2017, Lymphocyte fate and metabolism: a clonal balancing act, Trends Cell Biol, 27, 946, 10.1016/j.tcb.2017.07.005
Kamiński, 2016, Polarization and asymmetry in T cell metabolism, Semin Immunol, 28, 525, 10.1016/j.smim.2016.10.002
Altan-Bonnet, 2019, Cytokine-mediated communication: a quantitative appraisal of immune complexity, Nat Rev Immunol, 19, 205, 10.1038/s41577-019-0131-x
Walters, 1995, Enhancers increase the probability but not the level of gene expression, Proc Natl Acad Sci, 92, 7125, 10.1073/pnas.92.15.7125
Hume, 2000, Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression, Blood, 96, 2323, 10.1182/blood.V96.7.2323
Weintraub, 1988, Formation of stable transcription complexes as assayed by analysis of individual templates, Proc Natl Acad Sci, 85, 5819, 10.1073/pnas.85.16.5819
Raser, 2004, Control of stochasticity in eukaryotic gene expression, Science, 304, 1811, 10.1126/science.1098641
Bintu, 2005, Transcriptional regulation by the numbers: models, Curr Opin Genet Dev, 15, 116, 10.1016/j.gde.2005.02.007
Estrada, 2016, Information integration and energy expenditure in gene regulation, Cell, 166, 234, 10.1016/j.cell.2016.06.012
Liu, 2018, Visualizing transcription factor dynamics in living cells, J Cell Biol, 217, 1181, 10.1083/jcb.201710038
Coulon, 2013, Eukaryotic transcriptional dynamics: from single molecules to cell populations, Nat Rev Genet, 14, 572, 10.1038/nrg3484
Bintu, 2016, Dynamics of epigenetic regulation at the single-cell level, Science, 351, 720, 10.1126/science.aab2956
Angel, 2011, A Polycomb-based switch underlying quantitative epigenetic memory, Nature, 476, 105, 10.1038/nature10241
Wu, 2017, Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE, J Exp Med, 214, 183, 10.1084/jem.20161056
Ng, 2018, A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment, eLife, 7, 10.7554/eLife.37851
Rhoades, 2000, Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis, Curr Biol, 10, 789, 10.1016/S0960-9822(00)00565-0
Guo, 2005, Probabilistic regulation in TH2 cells accounts for monoallelic expression of IL-4 and IL-13, Immunity, 23, 89, 10.1016/j.immuni.2005.05.008
Mariani, 2010, Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression, Mol Syst Biol, 6, 359, 10.1038/msb.2010.13
Zhao, 2012, Stochastic expression of the interferon-β gene, PLoS Biol, 10, 16, 10.1371/journal.pbio.1001249
Kravitz, 2019, New subtypes of allele-specific epigenetic effects: implications for brain development, function and disease, Curr Opin Neurobiol, 59, 69, 10.1016/j.conb.2019.04.012
Fuxa, 2007, Reporter gene insertions reveal a strictly B lymphoid-specific expression pattern of Pax5 in support of its B cell identity function, J Immunol, 178, 3031, 10.4049/jimmunol.178.5.3031
Ku, 2015, A monoallelic-to-biallelic T-cell transcriptional switch regulates GATA3 abundance, Genes Dev, 29, 1930, 10.1101/gad.265025.115
Regot, 2014, High-sensitivity measurements of multiple kinase activities in live single cells, Cell, 157, 1724, 10.1016/j.cell.2014.04.039
Hughey, 2015, Single-cell variation leads to population invariance in NF-κB signaling dynamics, Mol Biol Cell, 26, 583, 10.1091/mbc.E14-08-1267
Kellogg, 2015, Noise facilitates transcriptional control under dynamic inputs, Cell, 160, 381, 10.1016/j.cell.2015.01.013
Czerkies, 2018, Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nat Commun, 9, 493, 10.1038/s41467-017-02640-8
Feinerman, 2008, Variability and robustness in T cell activation from regulated heterogeneity in protein levels, Science, 321, 1081, 10.1126/science.1158013
Lu, 2016, Systematic analysis of cell-to-cell expression variation of T lymphocytes in a human cohort identifies aging and genetic associations, Immunity, 45, 1162, 10.1016/j.immuni.2016.10.025
Marangoni, 2013, The transcription factor NFAT exhibits signal memory during serial T cell interactions with antigen-presenting cells, Immunity, 38, 237, 10.1016/j.immuni.2012.09.012
Rand, 2012, Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response, Mol Syst Biol, 8, 584, 10.1038/msb.2012.17
Ashouri, 2017, Endogenous Nur77 is a specific indicator of antigen receptor signaling in human T and B cells, J Immunol, 198, 657, 10.4049/jimmunol.1601301
Richard, 2018, T cell cytolytic capacity is independent of initial stimulation strength, Nat Immunol, 19, 849, 10.1038/s41590-018-0160-9
James, 2018, Tuning ITAM multiplicity on T cell receptors can control potency and selectivity to ligand density, Sci Signal, 11, 10.1126/scisignal.aan1088
Lin, 2019, Mapping the stochastic sequence of individual ligand-receptor binding events to cellular activation: T cells act on the rare events, Sci Signal, 12, 10.1126/scisignal.aat8715
Huang, 2013, A single peptide-major histocompatibility complex ligand triggers digital cytokine secretion in CD4+ T cells, Immunity, 39, 846, 10.1016/j.immuni.2013.08.036
Au-Yeung, 2014, A sharp T-cell antigen receptor signaling threshold for T-cell proliferation, Proc Natl Acad Sci U S A, 111, E3679, 10.1073/pnas.1413726111
Das, 2009, Digital signaling and hysteresis characterize ras activation in lymphoid cells, Cell, 136, 337, 10.1016/j.cell.2008.11.051
Altan-Bonnet, 2005, Modeling T cell antigen discrimination based on feedback control of digital ERK responses, PLoS Biol, 3, e356, 10.1371/journal.pbio.0030356
Martins, 2017, Environment tunes propagation of cell-to-cell variation in the human macrophage gene network, Cell Syst, 4, 379, 10.1016/j.cels.2017.03.002
Su, 2016, Phase separation of signaling molecules promotes T cell receptor signal transduction, Science, 352, 595, 10.1126/science.aad9964
Balagopalan, 2015, The linker for activation of T cells (LAT) signaling hub: from signaling complexes to microclusters, J Biol Chem, 290, 26422, 10.1074/jbc.R115.665869
Kagan, 2014, SMOCs: supramolecular organizing centres that control innate immunity, Nat Rev Immunol, 14, 821, 10.1038/nri3757
Larson, 2017, Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin, Nature, 547, 236, 10.1038/nature22822
Plys, 2019, Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2, Genes Dev, 33, 799, 10.1101/gad.326488.119
Dine, 2018, Protein phase separation provides long-term memory of transient spatial stimuli, Cell Syst, 6, 655, 10.1016/j.cels.2018.05.002
Bracha, 2018, Mapping local and global liquid phase behavior in living cells using photo-oligomerizable seeds, Cell, 175, 1467, 10.1016/j.cell.2018.10.048
Hnisz, 2017, A phase separation model for transcriptional control, Cell, 169, 13, 10.1016/j.cell.2017.02.007
Howard, 2001
Banani, 2017, Biomolecular condensates: organizers of cellular biochemistry, Nat Rev Mol Cell Biol, 18, 285, 10.1038/nrm.2017.7
Zikherman, 2015, The role of T cell receptor signaling thresholds in guiding T cell fate decisions, Curr Opin Immunol, 33, 43, 10.1016/j.coi.2015.01.012
Lo, 2019, Slow phosphorylation of a tyrosine residue in LAT optimizes T cell ligand discrimination, Nat Immunol, 20, 1481, 10.1038/s41590-019-0502-2
Cheng, 2017, Themis2 lowers the threshold for B cell activation during positive selection, Nat Immunol, 18, 205, 10.1038/ni.3642
Symmons, 2016, What's luck got to do with it: single cells, multiple fates, and biological nondeterminism, Mol Cell, 62, 788, 10.1016/j.molcel.2016.05.023
Monahan, 2015, Monoallelic expression of olfactory receptors, Annu Rev Cell Dev Biol, 31, 721, 10.1146/annurev-cellbio-100814-125308
Germain, 2001, The art of the probable: system control in the adaptive immune system, Science, 293, 240, 10.1126/science.1062946
Fatehi, 2018, Stochastic effects in autoimmune dynamics, Front Physiol, 9, 45, 10.3389/fphys.2018.00045
Held, 1998, An allele-specific, stochastic gene expression process controls the expression of multiple Ly49 family genes and generates a diverse, MHC-specific NK cell receptor repertoire, Eur J Immunol, 28, 2407, 10.1002/(SICI)1521-4141(199808)28:08<2407::AID-IMMU2407>3.0.CO;2-D
Freund, 2016, Activating receptor signals drive receptor diversity in developing natural killer cells, PLoS Biol, 14
Antebi, 2013, Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates, PLoS Biol, 11, 10.1371/journal.pbio.1001616
Fang, 2017, Dynamic balance between master transcription factors determines the fates and functions of CD4 T cell and innate lymphoid cell subsets, J Exp Med, 214, 1861, 10.1084/jem.20170494
Yang, 2016, Foxp3+ T cells expressing RORγt represent a stable regulatory T-cell effector lineage with enhanced suppressive capacity during intestinal inflammation, Mucosal Immunol, 9, 444, 10.1038/mi.2015.74
Kim, 2017, Generation of RORγt + antigen-specific T regulatory 17 cells from Foxp3 + precursors in autoimmunity, Cell Rep, 21, 195, 10.1016/j.celrep.2017.09.021
Levine, 2017, Stability and function of regulatory T cells expressing the transcription factor T-bet, Nature, 546, 421, 10.1038/nature22360
Eizenberg-Magar, 2017, Diverse continuum of CD4 + T-cell states is determined by hierarchical additive integration of cytokine signals, Proc Natl Acad Sci, 114, E6447, 10.1073/pnas.1615590114
Sugimoto, 2006, Differential cell division history between neutrophils and macrophages in their development from granulocyte–macrophage progenitors, Br J Haematol, 135, 725, 10.1111/j.1365-2141.2006.06367.x
Heinzel, 2017, A Myc-dependent division timer complements a cell-death timer to regulate T cell and B cell responses, Nat Immunol, 18, 96, 10.1038/ni.3598
Elowitz, 2002, Stochastic gene expression in a single cell, Science, 297, 1183, 10.1126/science.1070919
Lo, 2018, Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT, Nat Immunol, 19, 733, 10.1038/s41590-018-0131-1
Simeonov, 2017, Discovery of stimulation-responsive immune enhancers with CRISPR activation, Nature, 549, 111, 10.1038/nature23875
