Alhendi, A. S. N. | Search bioRxiv

bioRxiv2026

Multi-omics reveals a monocyte-macrophage-fibroblast axis in post-COVID-19 fibroinflammatory lung remodelling

Post-COVID-19 residual lung abnormalities (RLA) are associated with persistent respiratory symptoms and radiological changes, yet the underlying mechanisms remain unclear. We performed integrated multi-omic profiling of paired bronchoalveolar lavage and blood samples from patients with post-COVID-19 RLA and healthy controls, combining single-cell RNA sequencing, CITE-seq, single-cell T cell receptor sequencing, bronchoalveolar lavage fluid proteomics and functional fibroblast assays. In post-COVID-19 RLA lungs, we identified an increased abundance of profibrotic SPP1hi monocyte-derived alveolar macrophages, arising from an expanded circulating HLA-DRlowCD163+PDE4Dhi classical monocyte progenitor population, supporting a blood-lung myeloid axis. Cell-cell communication modelling positioned macrophages as central hubs of immune-stromal crosstalk, promoting monocyte recruitment with profibrotic priming, and fibroblast activation. Proteomic analysis of bronchoalveolar lavage fluid from post-COVID-19 RLA and idiopathic pulmonary fibrosis, compared with healthy controls, revealed shared and distinct signatures. These alveolar proteins in post-COVID-19 RLA were predominantly attributed to myeloid cells and predicted to engage fibroblast receptors. Bronchoalveolar lavage fluid induced fibroblast proliferation, differentiation and collagen deposition in vitro, with proliferation attenuated by the antifibrotic drug nintedanib. We also identified compartment-specific lymphoid dysregulation, including depletion of mucosal-associated invariant T (MAIT) cells in both the lung and blood, decreased natural killer (NK) cells with oligoclonal T cell expansion in the lung, and expansion of regulatory and cytotoxic T cells in the blood. These findings support a persistent monocyte-macrophage-fibroblast axis linking immune dysregulation to fibroproliferative remodelling after COVID-19 and highlights candidate therapeutic targets for post-viral lung fibrosis. We provide a publicly available atlas (on publication).

systems biology↗

bioRxiv2025

Recovery of human upper airway epithelium after smoking cessation is driven by a slow-cycling stem cell population and immune surveillance

The upper airway epithelium in humans is maintained in homeostasis by a resident population of basal stem cells. In the presence of tobacco smoke these gain mutations that significantly increase their risk of transformation to lung squamous cell carcinoma. Previous studies show that a small proportion of stem cells avoid the mutational damage caused by carcinogens in tobacco and are more abundant in the lungs of former smokers than ongoing smokers, indicating unexplained tissue-level genomic recovery. This mirrors epidemiological risk, which falls rapidly after quitting smoking. Somatic evolutionary mechanistic hypotheses have been proposed to explain these observations. Here, we present a computational framework to model each of these hypotheses within the upper airway epithelial stem cell population over the entire patient lifetimes of a cohort with diverse smoking histories. Applying a mechanistic learning approach based on a set of biologically informed metrics to single cell-derived whole-genome sequencing data, we identified subtle differences between epithelia modelled under different combinations of hypotheses. A slow-cycling subpopulation of stem cells, combined with suppression of immune predation of highly mutated stem cells while smoking, best matched observed data, a result converged upon by multiple distinct machine learning methodologies. Our findings, drawing on an evolutionary model of mutagen exposure at a whole-lifetime scale that is not feasible to model in vivo, reveal the mechanisms behind reduction in lung squamous cell carcinoma risk on cessation of smoking and inform future therapeutic interventions to prevent lung cancer initiation.

evolutionary biology↗