Biology subjects

Pennycuick, A.

Publications and source records attributed to Pennycuick, A..

7 recordsLinked to original sources

bioRxiv2026

Persistence of tobacco-mutated alveolar progenitor cells after smoking cessation mirrors long term risk of lung adenocarcinoma

Tobacco smoke shapes mutations, selection and clonal expansion in lung epithelial cells. Smoking cessation leads to divergent epidemiology in the two most common lung cancers: squamous cell carcinoma risk declines sharply, while adenocarcinoma risk is preserved. To investigate this discrepancy, we analysed 806 genomes of alveolar type II (AT2) cells and found persistently elevated mutation burdens after cessation. In contrast, in the proximal airway, rare basal stem cells with near-normal mutation burden expand after cessation, protecting against squamous cell carcinoma. Targeted single-molecule DNA sequencing of AT2 cells revealed positive selection for TP53 and cell cycle and MAPK genes, supporting continued cancer risk. A multistage carcinogenesis model emphasised the importance of a small population of hypermutated cells in the alveoli and reproduced the divergent epidemiological trajectories following cessation due to distinct regenerative dynamics. Our findings suggest that differences in mutational burden and clonal regeneration explain post-cessation trends in lung cancer subtypes. One sentence summaryCancer risk reflects not only cumulative exposure to toxins, but the capacity of tissues to erase genomic damage through regeneration from protected cells with clonal advantage.

genomics↗

bioRxiv2025

Podoplanin expression identifies human airway basal cells with higher progenitor cell potential

Basal cells are key to maintaining and repairing a functioning airway epithelium. Understanding how basal cells maintain normal airways provides a foundation for interpreting their dysfunction in disease states and for the development of novel therapies. The airway epithelium exists in a dynamic state in which basal stem cells replace lost luminal mucosecretory and multiciliated cell types via an intermediate suprabasal cell state. The ability to isolate basal cells with high progenitor cell potential would be beneficial in regenerative medicine applications, but the molecular identity of this population is unclear. Here, we evaluate candidate surface markers to isolate human basal cells. As an individual marker, we found that podoplanin (PDPN) had a favorable sensitivity and specificity compared with integrin alpha 6 (ITGA6) or nerve growth factor receptor (NGFR). We found that KRT5-expressing basal cells could be subdivided into those with high or low PDPN expression; KRT5-negative cells did not express PDPN. In vitro, PDPN-high basal cells had higher colony-forming capacity, increased population doubling potential and formed larger colonies than PDPN-low basal cells. PDPN-high basal cells expressed higher levels of TP63, as well as other genes expressed by quiescent or resting basal cells identified in single cell RNA sequencing studies. PDPN-low basal cells expressed genes associated with a differentiating basal cell state, including KRT4, NOTCH3 and serpin B family genes. Our results demonstrate that PDPN expression can identify basal cells with high progenitor cell potential, enabling high efficiency sorting of airway stem cells.

cell 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↗

bioRxiv2021

Toll-like receptor 2 orchestrates a potent anti-tumor response in non-small cell lung cancer

Targeting early-stage lung cancer is vital to improve overall survival. We previously identified Toll-like receptor 2 (TLR2) as a regulator of oncogene-induced senescence (OIS) and the senescence-associated secretory phenotype (SASP), both key for tumor suppression. Here, we demonstrate that TLR2 is widely expressed in human lung tumor epithelium where it correlates with improved survival and clinical regression. Using genetically engineered mouse models of lung cancer we have shown that Tlr2 is a tumor suppressor in lung cancer initiation via regulation of proliferation and the SASP. The SASP is integral in the regulation of immune surveillance of premalignant cells, and we observe impaired myeloid derived immune surveillance following Tlr2 loss. Lastly, we show that administration of a synthetic Tlr2 agonist significantly reduces preinvasive lung tumor growth. Our data highlight an unexpected tumor surveillance pathway in early-stage lung cancer with therapeutic potential. Statement of significanceLung cancer is a major cancer of unmet need. This study identifies a novel tumor suppressor mechanism in lung cancer. Not only does this highlight a potential therapeutic target for early-stage disease but also multiple secreted candidate biomarkers that could be exploited to augment lung cancer screening approaches.

cancer biology↗

bioRxiv2020

BAP1 and YY1 regulate expression of death receptors in malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a rare, aggressive, and incurable cancer arising from the mesothelial lining of the lungs with few treatment options. We recently reported loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1), a frequent event in MPM, is associated with sensitivity to tumour necrosis factor-related apoptosis-inducing ligand (TRAIL). As a potential underlying mechanism, here we report that BAP1 negatively regulates the expression of TRAIL receptors: death receptors 4 (DR4) and 5 (DR5). Using tissue microarray (TMAs) of tumour samples from MPM patients, we found a strong inverse correlation between BAP1 and TRAIL receptors. BAP1 knockdown increased DR4 and DR5 expression, whereas overexpression of BAP1 had the opposite effect. Reporter assays confirmed wild-type BAP1, but not catalytically-inactive mutant BAP1, reduced promoter activities of DR4 and DR5, suggesting deubiquinase activity plays an important role in the regulation of gene expression. Co-IP studies demonstrated direct binding of BAP1 and the transcription factor Ying Yang 1 (YY1) and ChIP assays revealed BAP1 and YY1 to be enriched in the promoter regions of DR4 and DR5. Notably, shRNA knockdown of YY1 also increased DR4 and DR5 expression, and sensitivity to TRAIL. These results demonstrate that BAP1 and YY1 together negatively regulate transcriptional activity of TRAIL receptors. BAP1 and YY1 may both therefore be strong therapeutic targets to enhance the efficacy of TRAIL-induced apoptosis. Statement of significanceWe describe how the most-frequently mutated tumour suppressor gene in mesothelioma regulates the response to TNF-related apoptosis-inducing ligand (TRAIL). These findings will accelerate a biomarker-driven cancer therapy.

cancer biology↗

bioRxiv2020

Cell-intrinsic differences between human airway epithelial cells from children and adults

The airway epithelium is a key protective barrier, the integrity of which is preserved by the self-renewal and differentiation of basal stem cells. Epithelial cells are central to the pathogenesis of multiple lung diseases. In chronic lung diseases, increasing age is a principle risk factor. Few studies have explored the differences between airway epithelial cells in children and adults and how the function of basal stem cells changes during ageing is poorly understood. Here, we analyze airway epithelial cells from children and adults in homeostatic conditions (laser capture-microdissected whole epithelium and fluorescence-activated cell-sorted basal cells) and in proliferation-inducing cell culture conditions. We find that, while the cellular composition of the pediatric and adult tracheobronchial epithelium is broadly similar, in cell culture, pediatric airway epithelial cells displayed higher colony-forming ability, sustained in vitro growth and outcompeted adult cells in competitive proliferation assays. In RNA sequencing experiments, we observed potentially important differences between epithelium from children and adults, including higher baseline interferon-associated gene expression in pediatric epithelium. Our results demonstrate cell-intrinsic differences in transcriptional profile and regenerative capacity between proximal airway epithelial cells of children and adults. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/027144v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@b7a680org.highwire.dtl.DTLVardef@1145543org.highwire.dtl.DTLVardef@1e9a86aorg.highwire.dtl.DTLVardef@12fe0bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Immune surveillance in clinical regression of pre-invasive squamous cell lung cancer

Before squamous cell lung cancer develops, pre-cancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. While recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of pre-cancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in-situ lesions harbour more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, TGF-beta signalling is overactive, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the CIS lesions as the adjacent stroma of progressive and regressive lesions are transcriptomically similar. This study identifies mechanisms by which pre-cancerous lesions evade immune detection during the earliest stages of carcinogenesis and forms a basis for new therapeutic strategies that treat or prevent early stage lung cancer.

cancer biology↗