Partner: Nissrin Alachkar


Doctoral thesis
2023-01-01Understanding heterogeneity of gene expression in the innate immune system through mathematical modelling 
supervisor -- Prof. Paweł Paszek, PhD, DSc, IPPT PAN
1522 
Recent publications
1.Alachkar N., Norton D., Wolkensdorfer Z., Muldoon M., Paszek P., Variability of the innate immune response is globally constrained by transcriptional bursting, Frontiers in Molecular Biosciences, ISSN: 2296-889X, DOI: 10.3389/fmolb.2023.1176107, Vol.10, pp.1176107-1-16, 2023
Abstract:

Transcription of almost all mammalian genes occurs in stochastic bursts, however the fundamental control mechanisms that allow appropriate single-cell responses remain unresolved. Here we utilise single cell genomics data and stochastic models of transcription to perform global analysis of the toll-like receptor (TLR)-induced gene expression variability. Based on analysis of more than 2000 TLR-response genes across multiple experimental conditions we demonstrate that the single-cell, gene-by-gene expression variability can be empirically described by a linear function of the population mean. We show that response heterogeneity of individual genes can be characterised by the slope of the mean-variance line, which captures how cells respond to stimulus and provides insight into evolutionary differences between species. We further demonstrate that linear relationships theoretically determine the underlying transcriptional bursting kinetics, revealing different regulatory modes of TLR response heterogeneity. Stochastic modelling of temporal scRNA-seq count distributions demonstrates that increased response variability is associated with larger and more frequent transcriptional bursts, which emerge via increased complexity of transcriptional regulatory networks between genes and different species. Overall, we provide a methodology relying on inference of empirical mean-variance relationships from single cell data and new insights into control of innate immune response variability.

Affiliations:
Alachkar N.-other affiliation
Norton D.-other affiliation
Wolkensdorfer Z.-other affiliation
Muldoon M.-other affiliation
Paszek P.-IPPT PAN
2.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
Abstract:

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.

Keywords:

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

Affiliations:
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