Biology subjects

Cox, M. J.

Publications and source records attributed to Cox, M. J..

10 recordsLinked to original sources

bioRxiv2026

Macrophage Phagocytic Impairment is associated with Dysbiosis of the Respiratory Microbiome in Frail older adults

Advanced age and frailty are risk factors for pulmonary infections, which are the leading cause of death in older adults. The mechanism behind increased susceptibility to infection is poorly understood, but interactions between innate immunity and the respiratory microbiome may be implicated. We investigated changes to monocyte-derived macrophage function, and the respiratory microbiome in healthy young adults, healthy older adults, and frail older adults. We found that macrophage phagocytosis and efferocytosis is impaired in frail older adults, associated with elevated pro-inflammatory cytokine secretion and a failure to regulate expression of phagocytic receptors CD14 and CD36. Pre-treatment of macrophages with a PPAR{gamma} agonist restored phagocytosis, implicating this pathway in cellular dysfunction. Accompanying respiratory microbiome showed reduced bacterial diversity and richness in older adults, which was more advanced in frail older adults. These results are consistent with a macrophage predation defect in the lungs during frailty which may impact bacterial diversity, and may be improved via manipulation of the PPAR{gamma} pathway. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/703495v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1c53e8forg.highwire.dtl.DTLVardef@8e34bcorg.highwire.dtl.DTLVardef@28345dorg.highwire.dtl.DTLVardef@185d93d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation

Unfolded protein response (UPR) promotes protein homeostasis under endoplasmic reticulum stress. UPR signaling has numerous functions in metabolism, cancer, immunology, and neurodegenerative diseases. Recent studies also showed that UPR signaling has important roles in hematopoietic stem and progenitor cell biology. However, whether UPR signaling regulates hematopoietic lineage fate decision remains elusive. Here, we found that Fc{gamma}R- MPP3 generates erythroid lineage and Jak2V617F mutation leads to overproduction of erythroid cells by expanding Fc{gamma}R- MPP3. We showed that UPR signaling increases myeloid cell production through promoting Fc{gamma}R- MPP3 transition to granulocyte/macrophage progenitor producing Fc{gamma}R+ MPP3 at the expense of erythroid lineage via the XBP1 pathway. Under a disease condition, UPR signaling cooperates with Jak2V617F mutation and exacerbates disease phenotype in a mouse model of polycythemia vera (PV) through the ATF4 pathway. Activation of UPR signaling also increased myeloid output in healthy donor bone marrow MPP cells while skewing the output towards erythroid lineage in PV patient bone marrow MPP cells. Together, our results identify a novel function of UPR signaling in hematopoietic lineage specification and provide critical insights into targeting UPR signaling in hematological malignancies. Key pointsO_LIUPR signaling promotes myeloid cell production at the expense of erythroid lineage in steady state. C_LIO_LIUPR signaling collaborates with Jak2V617F mutation and increases red blood cell production. C_LI

cell biology↗

bioRxiv2024

Microbiome diversity, intra-mucosal bacteria and immune integration within normal and asthmatic airway mucosa

Asthma is characterized by reduced bronchial bacterial diversity and airway mucosal disruption. We examined spatial distributions of microbial sequences and host mucosal transcripts in bronchial biopsies from healthy controls and adult asthmatics. Bacteria were discovered by 16S ribosomal RNA staining in the lamina propria of all biopsies, with counts positively associated to lumenal bacterial diversity. Weighted correlation network analysis identified fifteen co-expression networks, including distinct programs of adaptive and innate immunity in differing spatial distributions. Stromal bacterial counts correlated significantly with eight of the network eigenvectors in directions compatible with beneficial relationships. The results suggest that dysbiosis may affect mucosal immunity through impaired interactions beneath the epithelial border. Intra-mucosal companion bacteria may be a potential substrate for selective management of immunity in a wide range of diseases. One-Sentence SummaryThe lung microbiome extends within the airway mucosa and associates spatially and functionally with immune networks.

microbiology↗

bioRxiv2023

The Identification of IL-4 as a Regulator of Chimeric Antigen Receptor T Cell Exhaustion

Durable response to chimeric antigen receptor T (CART) cell therapy remains limited in part due to CART cell exhaustion. We investigated the regulation of CART cell exhaustion with three independent approaches including: a genome-wide CRISPR knockout screen using a validated in vitro model for exhaustion, RNA and ATAC sequencing on baseline and chronically stimulated CART cells, and RNA and ATAC sequencing on pre-infusion CART cell products from responders and non-responders in the ZUMA-1 clinical trial. Each of these approaches identified IL-4 as a key regulator of CART cell dysfunction. Further, when CART cells were treated with IL-4, they developed signs of exhaustion, but when CART cells were treated with an IL-4 monoclonal antibody, they showed improved antitumor efficacy and reduced signs of exhaustion in preclinical models. Therefore, our study identified both a novel role for IL-4 on CART cells and the improvement of CART cell therapy through IL-4 neutralization. Statement of SignificanceIdentifying regulators of CART cell exhaustion will not only enhance the fields understanding of therapeutic failure, but it will also provide avenues to enhance CART cell efficacy. This study reveals both a novel role for IL-4 in exhaustion and a strategy to improve CART cell activity through IL-4 neutralization.

immunology↗

bioRxiv2022

Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms

Platelets from patients with myeloproliferative neoplasms (MPNs) exhibit a hyperreactive phenotype. Here, we found elevated P-selectin exposure and platelet-leukocyte aggregates indicating activation of platelets from essential thrombocythemia (ET) patients. Single cell RNA-seq analysis of primary samples revealed significant enrichment of transcripts related to platelet activation, mTOR and oxidative phosphorylation (OXPHOS) in ET patient platelets. These observations were validated via proteomic profiling. Platelet metabolomics revealed distinct metabolic phenotypes consisting of elevated ATP generation, accompanied by increases in the levels of multiple intermediates of the tricarboxylic acid (TCA) cycle, but lower alpha-ketoglutarate (-KG) in MPN patients. Inhibition of PI3K/AKT/mTOR signaling significantly reduced metabolic responses and hyperreactivity in MPN patient platelets, while -KG supplementation markedly reduced oxygen consumption and ATP generation. Ex vivo incubation of platelets from both MPN patients and Jak2 V617F mice with -KG significantly reduced platelet activation responses. Oral -KG supplementation of Jak2 V617F mice decreased splenomegaly and reduced hematocrit, monocyte and platelet counts. Finally, -KG incubation significantly decreased proinflammatory cytokine secretion from MPN CD14+ monocytes. Our results reveal a previously unrecognized metabolic disorder in conjunction with aberrant PI3K/AKT/mTOR signaling, contributing to platelet hyperreactivity in MPN patients.

cancer biology↗

bioRxiv2022

Genomic and ecologic characteristics of the airway microbial-mucosal complex

SO_SCPLOWUMMARYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWPARAGRAPHC_SCPLOWLung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide1-4. Microbial communities at the airway mucosal barrier are conserved and highly ordered5, reflecting symbiosis and co-evolution with human host factors6. Freed of selection to digest nutrients for the host, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species, identifying abundant novel organisms within the genera Streptococcus, Pauljensenia, Neisseria and Gemella. Bacterial genomes were enriched for genes encoding antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. RNA-targeting CRISPR elements in some taxa suggest the potential to prevent or treat specific viral infections. Homologues of human RO60 present in Neisseria spp. provide a possible respiratory primer for autoimmunity in systemic lupus erythematosus (SLE) and Sjogren syndrome. We interpret the structure and biogeography of airway microbial communities from clinical surveys in the context of whole-genome content, identifying features of airway dysbiosis that may presage breakdown of homeostasis during acute attacks of asthma and chronic obstructive pulmonary disease (COPD). We match the gene content of isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

microbiology↗

bioRxiv2022

Machine learning for exploring microbial inter-kingdom associations in Cystic Fibrosis and Bronchiectasis

BackgroundCystic fibrosis (CF) and non-CF bronchiectasis (BX) are characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Little however is known about how fungal and bacterial organisms interact and whether these interactions impact on disease outcomes. MethodsQuantitative PCR and next-generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF or BX with clinically defined fungal infection status for all patients. The relationship between fungal and bacterial community composition was extensively explored using: random forest modelling, correlation network analysis, multi-omics factor analysis, and sample-wise clustering, to understand associations both within and between the microbial communities and their relationship to respiratory disease. ResultsRandom forest modelling demonstrated distinct fungal and bacterial communities within CF and BX patients. The inclusion of both kingdoms in the models did not improve discrimination between the two diseases. Within the CF patients, bacterial community composition was independent of clinical fungal disease status. Bacterial and fungal communities did not relate to the presence of CF pulmonary exacerbations (CFPE). Correlation network analysis found intra-kingdom interactions were predominant in the data. Multi-omics factor analysis (MOFA) revealed latent factors corresponding to single kingdoms. Thus, in the bacterial community we identified two distinct clusters characterised by the presence or absence of Pseudomonas-domination. This was independent of fungal community which was characterised by a second set of independent clusters dominated by Saccharomycetes. ConclusionsIn this study we were unable to detect clear evidence of clinically significant inter-kingdom interactions between the bacterial and fungal communities. While further work is required to fully understand microbial interaction within the lung, our data suggests that interkingdom interactions may not be the primary driver of patient outcomes, particularly in the context of fungal infection.

molecular biology↗

bioRxiv2020

Tales of 1,008 Small Molecules: Phenomic Profiling through Live-cell Imaging in a Panel of Reporter Cell Lines

Phenomic profiles are high-dimensional sets of readouts that can comprehensively capture the biological impact of chemical and genetic perturbations in cellular assay systems. Phenomic profiling of compound libraries can be used for compound target identification or mechanism of action (MoA) prediction and other applications in drug discovery. To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and well-characterized tool compounds manually annotated to 218 unique MoAs, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. For 41 of 83 testable MoAs, phenomic profiles accurately ranked the reference compounds (AUC-ROC [≥]0.9). MoAs could be better resolved by screening compounds at multiple concentrations than by including replicates at a single concentration. Screening additional cell lineages and fluorescent markers increased the number of distinguishable MoAs but this effect quickly plateaued. There remains a substantial number of MoAs that were hard to distinguish from others under the current studys conditions. We discuss ways to close this gap, which will inform the design of future phenomic profiling efforts.

pharmacology and toxicology↗

bioRxiv2019

Distinctive airway microbial ecology of smokers and asthmatics

BackgroundNormal airway microbial communities play a central role in respiratory health but are poorly characterized. Cigarette smoking is the dominant global environmental influence on lung function, and asthma has become the most prevalent chronic respiratory disease worldwide. Both conditions have major microbial components that are also poorly defined. MethodsWe investigated airway bacterial communities in a general population sample of 529 Australian adults. Posterior oropharyngeal swabs were analysed by sequencing of the 16S rRNA and methionine aminopeptidase genes. The microbiota were characterised according to their prevalence, abundance, and network memberships. FindingsMicrobial communities were similar across the population and were strongly organized into co-abundance networks. Smoking associated with diversity loss, negative effects on abundant taxa, profound alterations to network structure and expansion of Streptococcus spp. By contrast, the asthmatic microbiota were selectively affected by an increase in Neisseria spp. and by reduced numbers of low abundance but prevalent organisms. InterpretationOur study shows healthy airway microbiota are contained within a highly structured ecosystem, indicating balanced relationships between the microbiome and human host factors. The marked abnormalities in smokers may be pathogenic for chronic obstructive pulmonary disease (COPD) and lung cancer. The narrow spectrum of abnormalities in asthmatics encourages investigation of damaging and protective effects of specific bacteria. FundingThe study was funded by the Asmarley Trust and a Wellcome Senior Investigator Award to WOCC and MFM (P46009). The Busselton Healthy Ageing Study is supported by the Government of Western Australia (Office of Science, Department of Health) the City of Busselton, and private donations.

ecology↗

bioRxiv2018

Haemophilus, antibiotic therapy and the airway microbiome in chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a smoking-related illness affecting 64 million people worldwide. Airway infection drives recurrent exacerbations and lung function decline. Prophylactic antibiotics may prevent exacerbations but their use is a significant cause of population antimicrobial resistance.\n\nWe characterised the sputum microbiome by 16S rRNA gene analysis using 138 samples collected during a randomised controlled trial of prophylactic antibiotics in 71 patients with stable COPD. On comparing the profile of the microbiome obtained by sequencing to the isolates grown from samples using standard culture, there were similarities overall, although with a much narrower spectrum of genera on culture with under-representation of certain genera including Veillonella and Prevotella. There was concordance in the most abundant genera within samples and the number of isolates cultured reflected the measured bacterial diversity.\n\nWe found that at baseline the microbiota of 17 (24%) patients were dominated by Haemophilus influenzae, accompanied by narrowed microbial diversity and higher levels of sputum inflammatory cytokines. Different H. influenzae strains co-existed within individuals. Opportunistic whole genome sequencing of six H. influenzae isolates obtained during the study revealed that all were non-typeable H. influenzae (NTHI), with a range of different antibiotic resistance gene profiles, but an identical complement of virulence genes.\n\nAdministration of 13 weeks prophylaxis with moxifloxacin, azithromycin or doxycycline revealed distinctive changes in microbial communities for each group. Haemophilus numbers reduced by 90% compared to placebo only after moxifloxacin, and significant reduction in sputum cytokines occurred in patients dominated by Haemophilus at baseline. Haemophilus influenzae dominance defines COPD patients with active disease who may particularly benefit from antibiotics or vaccination.

microbiology↗