Biology subjects

Davis, D. M.

Publications and source records attributed to Davis, D. M..

7 recordsLinked to original sources

bioRxiv2026

A Bayesian framework reveals heterogeneous and stochastic decision-making in NK cell cytotoxicity

Natural killer (NK) cells display striking variability in their cytotoxic responses, but whether this variation reflects random events, stable differences between cells, or effects of previous encounters remains unclear. We developed a Bayesian framework that uses single-cell interaction histories to disentangle these sources of variability. The framework models target encounters and killing decisions to quantify population heterogeneity, determine the sample sizes needed to distinguish competing mechanisms, and separate stable cell-to-cell differences from history-dependent behaviour. Synthetic data established when these mechanisms can be reliably distinguished in practice. We tested the framework using time-lapse imaging of NK cells exposed to rituximab or CC-96673, an antibody co-targeting CD20 and CD47. Despite similar overall killing, the framework identified distinct underlying responses: rituximab mainly increased mean killing rate, whereas CC-96673 reduced cell-to-cell variation. Event-count analysis supported continuous population heterogeneity, while ordered interaction histories revealed that both stable differences in killing propensity and previous encounters shape cytotoxic decisions. To make the framework directly usable, we introduce BARRACUDA, an open-source web platform and Python package implementing these analyses, including donor-aware extensions, for single-cell cytotoxicity datasets.

immunology↗

bioRxiv2026

In vivo screening reveals new regulators of Natural Killer cell development and functional response to acute cytomegalovirus infection

Natural killer (NK) cells are critical innate immune effectors in antiviral and antitumour responses. However, the factors governing NK cell development and function remain incompletely understood. To address this, we adopted an in vivo screening approach, generating a panel of mice deficient in genes differentially expressed across NK cell maturation stages or following viral infection. We performed a combinational screen comprising baseline immunophenotyping and mouse cytomegalovirus (MCMV) challenge. We identified novel regulators of NK cell development, including transcriptional regulators and proteins with putative trafficking functions. MCMV challenge studies additionally identified proteins that impacted antiviral immunity independently of NK cell phenotypes, including a novel regulator of NK cell degranulation, Synaptotagmin-like protein 3. Identified genes exhibited reduced tolerance to loss-of-function in large scale human sequencing studies and evidence for reduced NK cell numbers in a cohort of immunodeficiency patients. Together, these findings provide a resource of NK-expressed genes important for NK cell maturation and function, with relevance to human health. SummaryPring et al. conduct an in vivo screen in mice identifying novel regulators of natural killer (NK) cell development and/or antiviral functionality. Large-scale human sequencing and human immunodeficiency patients revealed evidence for the relevance of identified genes in human health.

immunology↗

bioRxiv2025

Inhibitory TIGIT signalling is dependent on T cell receptor activation

TIGIT is an immune checkpoint receptor that can signal via cytoplasmic ITT-like and ITIM motifs to regulate T cell function. The signalling molecules that mediate inhibitory TIGIT signalling in T cells remain poorly defined, and it is not clear how TIGIT activation is regulated. Here, proximity proteomics was employed in Jurkat T cells to identify TIGIT-associating proteins upon engagement with its ligand CD155. This identified several ligation-specific TIGIT interactors, including proteins involved in signalling (Grb2 and SOS1), cytoskeletal regulation (CD2AP and SdcBP), and endocytosis (IST1 and SNX3). A TIGIT mutant (Y225A/Y231A) incapable of signalling via its inhibitory motifs prevented the recruitment of these proteins, indicating inhibitory signalling-specific engagement of these pathways. Strikingly, T cell receptor (TCR) stimulation was also needed for TIGIT to engage with these pathways. Mechanistically, phosphorylation of TIGIT required both CD155 ligation and TCR activation, which resulted in signalling and internalisation. These findings demonstrate that TIGIT signalling is context-dependent and restricted to T cells receiving simultaneous TCR activation. This establishes a regulatory mechanism that limits checkpoint control to when functionally required.

immunology↗

bioRxiv2024

Nano-org, a functional resource for single-molecule localisation microscopy data

We present a publicly accessible, curated, and functional resource, termed "nano-org", containing single-molecule localisation microscopy (SMLM) data representing the nanoscale distributions of proteins in cells. Nano-org is searchable by comparing the statistical similarity of the datasets it contains. This unique functionality allows the resource to be used to understand the relationships of nanoscale architectures between proteins, cell types or conditions, enabling a new field of spatial nano-omics.

biophysics↗

bioRxiv2020

Priming Is Dispensable For NLRP3 Inflammasome Activation In Human Monocytes

Interleukin (IL)-1 family of cytokines modulate immune responses during infection and inflammation. IL-18 and IL-1{beta} are members of the IL-1 family, which contribute to inflammatory conditions such as rheumatoid arthritis and Alzheimers disease. IL-18 and IL-1{beta} are produced as inactive precursors that are activated by large macromolecular complexes called inflammasomes upon sensing damage or pathogenic signals. Canonical NLRP3 inflammasome activation is regarded to require a priming step that causes NLRP3 and IL-1{beta} gene upregulation, and also NLRP3 post-translational licencing. A subsequent activation step leads to the assembly of the inflammasome and the cleavage of pro-IL-18 and pro-IL-1{beta} by caspase-1 into their mature forms, allowing their release. Here we show that in primary human monocytes, the initial priming step is dispensable to form an active NLRP3 inflammasome. We found that, in the absence of priming, the NLRP3 activator nigericin caused the processing and release of constitutively expressed IL-18. Another IL-1 family member, IL-37, is constitutively cleaved but the release of its mature form was mediated by inflammasome activation, also in the absence of a priming step. This NLRP3 activation was characterised by ASC oligomerisation as well as caspase-1 and GSDMD cleavage and was blocked by the NLRP3 inhibitor MCC950 and in NLRP3 deficient cells. IL-18 and IL-37 release were impaired in GSDMD deficient THP-1s, suggesting that pyroptosis is required for release of these cytokines. This work highlights the readiness of the NLRP3 inflammasome to assemble in the absence of priming and hence contribute to sterile inflammatory processes in health and disease. Significance StatementThe NLRP3 inflammasome is a driver of inflammation through the processing of Interleukins (IL)-1{beta} and IL-18. Human monocytes coordinate the innate immune response through inflammasome activation following exposure to pathogens and damage signals. We currently think of NLRP3 activation as a 2 step process: priming (NLRP3 gene upregulation and post-translational licencing) and assembly. Here we show that the priming step is dispensable for NLRP3 inflammasome activation in human monocytes. The second signal alone is sufficient for caspase-1 activation, leading to cell death and the release of the constitutively expressed IL-18 and mIL-37. This reveals that in human monocytes, the NLRP3 inflammasome is already licenced and able to quickly assemble to mount an inflammatory response.

immunology↗

bioRxiv2018

Machine-learning for cluster analysis of localization microscopy data.

Quantifying the clustering of points within single-molecule localization microscopy data is useful to understanding the spatial relationships of the molecules in the underlying sample. The conversion of point pattern data into a meaningful description of clustering is difficult, especially for biologically derived data, as the definitions of clustering are often subjective or simplistic. Many existing computational approaches are also limited in their ability to process large-scale data-sets or to deal effectively with inhomogeneities in clustering. Here we have developed a supervised machine-learning approach to cluster analysis which is fast and accurate. Trained on a variety of simulated clustered data, the network can then classify all points from a typical localization microscopy data-set (several million points from the entire field of view) as being either clustered or not-clustered, with the potential to include additional classifiers to describe different types of clusters. Clustered points can then be further refined into like-clusters for the measurement of cluster area, shape, and point-density. We demonstrate the performance on simulated data and experimental data of the kinase Csk and the adaptor PAG in both naive and pre-stimulated primary human T cell synapses.

cell biology↗

bioRxiv2018

Tunneling nanotubes contribute to the stroma-mediated imatinib resistance of leukemic cells

Intercellular communication within the bone marrow niche significantly influences leukemogenesis and the sensitivity of leukemic cells to therapy. Tunneling nanotubes (TNTs) are a novel mode of intercellular cross-talk. They are long, thin membranous protrusions that enable the direct transfer of various cargo between cells. Here we show that TNTs are formed between leukemic and bone marrow stromal cells. Fluorescence confocal microscopy with 3D reconstructions, correlative light-electron microscopy and electron tomography provided evidence that TNTs transfer cellular vesicles between cells. The quantitative analysis demonstrated that the stromal cells stimulate TNT-mediated vesicle transfer towards leukemic cells. Transfer of vesicular cargo from stromal cells correlated with increased resistance to anti-leukemic treatment. Moreover, specific sets of proteins with a potential role in survival and the drug response were transferred within these vesicles. Altogether, we found that TNTs are involved in the leukemia-stroma cross-talk and the stroma-mediated cytoprotection of leukemic cells. Our findings implicate TNT connections as a possible target for therapeutic interventions within the leukemia microenvironment to attenuate stroma-conferred protection.

cancer biology↗