Biology subjects

Booty, L.

Publications and source records attributed to Booty, L..

3 recordsLinked to original sources

bioRxiv2026

Plate-based ISD-SPE enables dual proteome-secretome concentration-response profiling of TLR signalling in iPSC-derived macrophages

Protein secretion represents a key functional output of cellular signalling, capturing dynamic responses to stimulation and pharmacological perturbation that shape immune behaviour. In macrophages, activation of Toll-like receptors (TLRs) drives tightly regulated secretion programmes that mediate inflammatory responses and provide a biologically meaningful readout of pathway activity. Whilst mass spectrometry (MS)-based secretomics enables unbiased profiling of these processes, broader application in drug discovery remains constrained by sample preparation workflows that limit scalability. Here, we describe a plate-based in-solution digestion and solid-phase extraction (ISD-SPE) workflow that enables 96-well processing of conditioned media for integrated proteome and secretome analysis from the same sample well. Benchmarking against a precipitation-based approach demonstrated comparable proteomic depth with improved quantitative reproducibility and robust performance across multiple plates. Coupled with dia-PASEF acquisition, this workflow enabled in-depth profiling of macrophage responses to TLR activation, resolving receptor-specific secretory programmes following TLR3, TLR4 and TLR7/8 activation. Extension of the approach to concentration-response studies enabled quantitative characterisation of pharmacological perturbation across intracellular and extracellular protein landscapes, revealing both shared and compartment-specific responses to TLR inhibition, as well as differences in apparent potency linked to secretion dynamics. Together, this workflow provides a scalable strategy for integrated analysis of intracellular signalling and downstream protein secretion, enabling systems-level characterisation of inflammatory responses and compound mechanisms of action.

immunology↗

bioRxiv2026

dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights into Cellular Dynamics and Inflammatory Mechanisms

Protein secretion is a fundamental mechanism for cellular coordination and signalling, with its dysregulation leading to widespread physiological dysfunction and disease. Immunoassay formats that utilise secondary antibody readouts are the current gold standard for measuring secreted proteins, offering high specificity and sensitivity, but relying on predefined protein panels that constrain the discovery of novel biology. We present a scalable mass spectrometry-based workflow that combines data-independent acquisition with ion mobility and parallel fragmentation to deliver rapid, global profiling of the secretome. Using a translationally relevant human iPSC-derived macrophage model, our approach identified over 1200 proteins in under 15 minutes of acquisition time, delivering exceptional reproducibility across a large sample set. We applied this approach to profile pro-inflammatory phenotypes, confirming robust identification of key cytokines and chemokines whilst revealing non-canonical immune responses absent from both targeted panels and the intracellular proteome. In particular, we identified a unique cholesterol efflux signature, marked by the secretion of APOA1 and PON1, in response to Mycobacterium Tuberculosis, consistent with the metabolic reprogramming that takes place during infection. Furthermore, temporal profiling of macrophage responses to lipopolysaccharide over 24 hours resolved dynamic secretion trajectories that distinguish between acute and chronic inflammatory states. The extended time period facilitated the observation of distinct cytokine-dependent secretion phenotypes, with early secretion of TNF and IL6 initiating downstream signalling cascades that resulted in the delayed secretion of chemokines such as CXCL10 and CCL8. Collectively, these findings establish a robust, scalable platform for global characterisation of secretory networks. Beyond macrophage biology, this workflow offers broad utility for biomarker discovery, mechanistic studies of disease progression and evaluation of new therapeutic interventions, providing a powerful tool for advancing precision medicine.

immunology↗

bioRxiv2025

Pulmonary macrophage subsets display distinct metabolic responses to polarising stimuli in vivo

Macrophage activation is underpinned by metabolic changes required to fight infection, resolve inflammation and enable effective wound healing. While metabolic control of macrophage activation is increasingly understood in culture systems in vitro, it remains poorly understood in more complex in vivo settings, like the lung. Here we applied novel flow cytometry based immunometabolic techniques to profile immune cell metabolism in the murine lung. We revealed a surprising role for glucose in naive alveolar macrophages (AMs) that was retained by AMs polarised in vivo with either interleukin-4 (IL-4) or lipopolysaccharide (LPS). We identified that naive interstitial macrophages (IMs) were dependent on mitochondrial and glucose metabolism, IMs polarised with IL-4 failed to induce metabolic alterations but displayed a glycolytic phenotype following LPS exposure as they adopted an M1 like metabolic profile. We also demonstrated that AMs were metabolically less responsive than IMs to intranasal delivery of LPS, but upregulated glycolysis and metabolic features of M2 polarisation (defined in vitro) in response to intranasal IL-4, including oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO) and arginine metabolism. Finally, we identified AM M2 polarisation as highly sensitive to glucose inhibition ex vivo. Thus, lung macrophage subsets display distinct metabolic responses to polarising stimuli in vivo. HighlightsO_LINaive alveolar macrophages require glucose metabolism despite residing in a low glucose environment. C_LIO_LIAlveolar macrophages are more responsive to IL-4 in vivo than LPS upregulating oxidative metabolism, lipid metabolism and glycolysis. C_LIO_LIInterstitial macrophages adopt a glycolytic phenotype characteristic of M1 BMDMs in vitro following in vivo LPS administration. C_LIO_LIAlternatively activated alveolar macrophages are extremely sensitive to glucose inhibition ex vivo. C_LI

immunology↗