Partner: William Rowe


Ostatnie publikacje
1.Bagnall J., Rowe W., Alachkar N., Roberts J., England H., Clark C., Platt M., Jackson Dean A., Muldoon M., Paszek P., Gene-Specific Linear Trends Constrain Transcriptional Variability of the Toll-like Receptor Signaling, Cell Systems, ISSN: 2405-4712, DOI: 10.1016/j.cels.2020.08.007, Vol.11, No.3, pp.300-314, 2020

Streszczenie:

Single-cell gene expression is inherently variable, but how this variability is controlled in response to stimulation remains unclear. Here, we use single-cell RNA-seq and single-molecule mRNA counting (smFISH) to study inducible gene expression in the immune toll-like receptor system. We show that mRNA counts of tumor necrosis factor α conform to a standard stochastic switch model, while transcription of interleukin-1β involves an additional regulatory step resulting in increased heterogeneity. Despite different modes of regulation, systematic analysis of single-cell data for a range of genes demonstrates that the variability in transcript count is linearly constrained by the mean response over a range of conditions. Mathematical modeling of smFISH counts and experimental perturbation of chromatin state demonstrates that linear constraints emerge through modulation of transcriptional bursting along with gene-specific relationships. Overall, our analyses demonstrate that the variability of the inducible single-cell mRNA response is constrained by transcriptional bursting.

Słowa kluczowe:

cellular heterogeneity, transcriptional bursting, stochastic gene expression, toll-like receptor, single-cell transcriptomics, stochastic modeling, TNF-α, IL-1β

Afiliacje autorów:

Bagnall J.-other affiliation
Rowe W.-other affiliation
Alachkar N.-other affiliation
Roberts J.-other affiliation
England H.-other affiliation
Clark C.-other affiliation
Platt M.-other affiliation
Jackson Dean A.-other affiliation
Muldoon M.-other affiliation
Paszek P.-other affiliation
200p.
2.Bagnall J., Boddington C., England H., Brignall R., Downton P., Alsoufi Z., Boyd J., Rowe W., Bennett A., Walker C., Adamson A., Patel Nisha M. X., O’Cualain R., Schmidt L., Spiller David G., Jackson Dean A., Müller W., Muldoon M., White Michael R. H.R., Paszek P., Quantitative analysis of competitive cytokine signaling predicts tissue thresholds for the propagation of macrophage activation, Science Signaling, ISSN: 1945-0877, DOI: 10.1126/scisignal.aaf3998, Vol.11, No.540, pp.1-15, 2018

Streszczenie:

Toll-like receptor (TLR) signaling regulates macrophage activation and effector cytokine propagation in the constrained environment of a tissue. In macrophage populations, TLR4 stimulates the dose-dependent transcription of nuclear factor κB (NF-κB) target genes. However, using single-RNA counting, we found that individual cells exhibited a wide range (three orders of magnitude) of expression of the gene encoding the proinflammatory cytokine tumor necrosis factor–α (TNF-α). The TLR4-induced TNFA transcriptional response correlated with the extent of NF-κB signaling in the cells and their size. We compared the rates of TNF-α production and uptake in macrophages and mouse embryonic fibroblasts and generated a mathematical model to explore the heterogeneity in the response of macrophages to TLR4 stimulation and the propagation of the TNF-α signal in the tissue. The model predicts that the local propagation of the TLR4-dependent TNF-α response and cellular NF-κB signaling are limited to small distances of a few cell diameters between neighboring tissue-resident macrophages. In our predictive model, TNF-α propagation was constrained by competitive uptake of TNF-α from the environment, rather than by heterogeneous production of the cytokine. We propose that the highly constrained architecture of tissues enables effective localized propagation of inflammatory cues while avoiding out-of-context responses at longer distances.

Afiliacje autorów:

Bagnall J.-other affiliation
Boddington C.-other affiliation
England H.-other affiliation
Brignall R.-other affiliation
Downton P.-other affiliation
Alsoufi Z.-other affiliation
Boyd J.-other affiliation
Rowe W.-other affiliation
Bennett A.-other affiliation
Walker C.-other affiliation
Adamson A.-other affiliation
Patel Nisha M. X.-other affiliation
O’Cualain R.-other affiliation
Schmidt L.-other affiliation
Spiller David G.-other affiliation
Jackson Dean A.-other affiliation
Müller W.-other affiliation
Muldoon M.-other affiliation
White Michael R. H.R.-University of Manchester (GB)
Paszek P.-other affiliation
40p.
3.Brignall R., Cauchy P., Bevington Sarah L., Gorman B., Pisco Angela O., Bagnall J., Boddington C., Rowe W., England H., Rich K., Schmidt L., Dyer Nigel P., Travis Mark A., Ott S., Jackson Dean A., Cockerill Peter N., Paszek P., Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells, JOURNAL OF IMMUNOLOGY, ISSN: 0022-1767, DOI: 10.4049/jimmunol.1602033, Vol.199, No.8, pp.2652-2667, 2017

Streszczenie:

TCR signaling pathways cooperate to activate the inducible transcription factors NF-κB, NFAT, and AP-1. In this study, using the calcium ionophore ionomycin and/or PMA on Jurkat T cells, we show that the gene expression program associated with activation of TCR signaling is closely related to specific chromatin landscapes. We find that calcium and kinase signaling cooperate to induce chromatin remodeling at ∼2100 chromatin regions, which demonstrate enriched binding motifs for inducible factors and correlate with target gene expression. We found that these regions typically function as inducible enhancers. Many of these elements contain composite NFAT/AP-1 sites, which typically support cooperative binding, thus further reinforcing the need for cooperation between calcium and kinase signaling in the activation of genes in T cells. In contrast, treatment with PMA or ionomycin alone induces chromatin remodeling at far fewer regions (∼600 and ∼350, respectively), which mostly represent a subset of those induced by costimulation. This suggests that the integration of TCR signaling largely occurs at the level of chromatin, which we propose plays a crucial role in regulating T cell activation.

Afiliacje autorów:

Brignall R.-other affiliation
Cauchy P.-other affiliation
Bevington Sarah L.-other affiliation
Gorman B.-other affiliation
Pisco Angela O.-other affiliation
Bagnall J.-other affiliation
Boddington C.-other affiliation
Rowe W.-other affiliation
England H.-other affiliation
Rich K.-other affiliation
Schmidt L.-other affiliation
Dyer Nigel P.-other affiliation
Travis Mark A.-other affiliation
Ott S.-other affiliation
Jackson Dean A.-other affiliation
Cockerill Peter N.-other affiliation
Paszek P.-other affiliation
4.Adamson A., Boddington C., Downton P., Rowe W., Bagnall J., Lam C., Maya-Mendoza A., Schmidt L., Harper Claire V.V., Spiller David G., Rand David A.A., Jackson Dean A., White Michael R. H.R., Paszek P., Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/ncomms12057, Vol.7, pp.12057-1-14, 2016

Streszczenie:

Cells respond dynamically to pulsatile cytokine stimulation. Here we report that single, or well-spaced pulses of TNFα (>100 min apart) give a high probability of NF-κB activation. However, fewer cells respond to shorter pulse intervals (<100 min) suggesting a heterogeneous refractory state. This refractory state is established in the signal transduction network downstream of TNFR and upstream of IKK, and depends on the level of the NF-κB system negative feedback protein A20. If a second pulse within the refractory phase is IL-1β instead of TNFα, all of the cells respond. This suggests a mechanism by which two cytokines can synergistically activate an inflammatory response. Gene expression analyses show strong correlation between the cellular dynamic response and NF-κB-dependent target gene activation. These data suggest that refractory states in the NF-κB system constitute an inherent design motif of the inflammatory response and we suggest that this may avoid harmful homogenous cellular activation.

Afiliacje autorów:

Adamson A.-other affiliation
Boddington C.-other affiliation
Downton P.-other affiliation
Rowe W.-other affiliation
Bagnall J.-other affiliation
Lam C.-other affiliation
Maya-Mendoza A.-other affiliation
Schmidt L.-other affiliation
Harper Claire V.V.-University of Manchester (GB)
Spiller David G.-other affiliation
Rand David A.A.-University of Warwick (GB)
Jackson Dean A.-other affiliation
White Michael R. H.R.-University of Manchester (GB)
Paszek P.-other affiliation
45p.