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Parsons, D.

Publications and source records attributed to Parsons, D..

12 recordsLinked to original sources

Gene-Corrected Basal Cells Restore CFTR In Vitro; Transplants Regenerate Epithelium in a Preclinical Sinus Model

BackgroundCystic fibrosis (CF) is caused by mutations in the CFTR gene, leading to epithelial dysfunction and progressive lung disease. Although CFTR modulators have transformed care, [~]10% of people with CF remain without effective therapy. Durable, mutation-agnostic approaches are urgently needed. MethodWe used a lentiviral (LV) vector to deliver wild-type CFTR to airway basal cells derived from 13 paediatric CF participants with a range of genotypes. Transduced cells were assessed for transgene expression, epithelial differentiation, and CFTR function using air-liquid interface (ALI) cultures. Separately, to evaluate regenerative capacity in vivo, LVGFP-transduced rabbit airway basal cells were transplanted into the denuded nasal septum of healthy New Zealand white rabbits using a biocompatible scaffold. ResultsTransduced basal cells retained multilineage differentiation capacity, forming well-organized, pseudostratified epithelium with intact barrier function and ciliary activity. CFTR channel activity was restored to levels comparable to or exceeding those achieved with elexacaftor/tezacaftor/ivacaftor (ETI), including in individuals with nonsense mutations. Combined CFTR transduction plus ETI treatment showed additive benefit. In vivo, transplanted rabbit basal cells engrafted and differentiated to regenerate a mucociliary epithelium, with improved nasal potential difference and mucociliary clearance compared to scaffold-only controls. ConclusionOur study demonstrates that LV-mediated CFTR gene addition restores CFTR function in vitro across genotypes and supports epithelial regeneration in a clinically relevant animal airway model. This two-part platform offers a scalable path toward cell therapies for all people with CF and may have broader applications in upper airway epithelial repair.

cell biology↗

A longitudinal evaluation of localised chronic Pseudomonas aeruginosa infection in cystic fibrosis rat models

Recurrent bacterial infections with Pseudomonas aeruginosa result in chronic airway inflammation, lung damage and eventual respiratory failure, and are the major cause of morbidity and mortality in people with cystic fibrosis (CF). Animal models are essential for understanding disease progression and assessing potential treatments in the presence of infection. Previously reported P. aeruginosa lung infection rodent models for CF research have some weakness, including acute infection rather than chronic, associated mortality, use of laboratory strains of P. aeruginosa and the use of non-CF rodents. The aim of this study was to create a localised P. aeruginosa infection in wildtype and two CF rat models, by delivering bacteria embedded agar beads using a miniature bronchoscope. The resulting infection was well tolerated by all animals of all genotypes with no mortality associated with the procedure or infection. Histologically the affected regions were localised to the right lung, with bronchopneumonia present. Bacteria persisted for 9 weeks (63 days) in all genotypes, with lung function changes observed by day 63 of the infection.

pathology↗

Aevol-9: A simulation platform to decipher the evolution of genome architecture

Aevol is a forward-in-time simulator of genome architecture. It simulates a population of individuals, each with an explicit genome whose sequence and architecture can be modified by various mutational operators, including substitutions, indels, and large-scale chromosomal rearrangements. This enables performing in silico experiments to decipher the effects of evolutionary conditions (e.g. population size, selection strength, mutation rates, and biases) on genome organization.

evolutionary biology↗

CFTR High Expresser BEST4+ cells are pH-sensing neuropod cells: new implications for intestinal physiology and Cystic Fibrosis disease

Single-cell RNA sequencing (scRNA-seq) studies identified a novel subpopulation of epithelial cells along the rostrocaudal axis of human intestine specifically marked by bestrophin 4 (BEST4) that are enriched for genes regulating pH, GPCR acid-sensing receptors, satiety, cGMP signaling, HCO3- secretion, ion transport, neuropeptides, and paracrine hormones. Interestingly, BEST4+ cells in the proximal small intestine express CFTR but have not been linked to the previously described CFTR High Expresser Cell (CHE) subpopulation in rat and human intestine. ScRNA-seq studies in rat jejunum identified CHEs and a gene expression profile consistent with human small intestinal BEST4+ and neuropod cells. Protein immunolocalization confirmed that CHEs express CFTR, BEST4, neuropod proteins, high levels of intracellular uroguanylin (UGN), guanylyl cyclase-C (GC-C), and the proton channel otopetrin 2 (OTOP2), and display long basal processes connecting to neurons. OTOP2, GC-C, and CFTR traffic robustly into the apical domain of CHEs in response to acidic luminal conditions, indicating their roles in luminal pH regulation. In the {Delta}F508 cystic fibrosis (CF) rat jejunum, the loss of apical CFTR did not affect BEST4 protein expression in CHEs. However, there was an increased abundance of CHE cells in the {Delta}F508 rat jejunum compared to wild-type animals. Furthermore, {Delta}F508 rat CHEs expressed higher levels of GC-C at the apical domain compared to wild-type. These data implicate CHEs in intestinal CF disease pathogenesis. NEW & NOTEWORTHYThis is the first study to identify CFTR High Expresser cells in the rat small intestine as neuropod cells capable of sensing and responding to luminal pH. This study also provides the first characterization of CFTR and relevant mRNA and proteins in CHEs in CF rat models that provide insights into the significance of CHEs to CF intestinal disease.

physiology↗

HIV broadly neutralizing antibody escapability drives the therapeutic efficacy of vectored immunotherapy

Broadly neutralizing antibodies (bNAbs) have shown promise for prevention and treatment of HIV. Potency and breadth measured in vitro are often used as predictors of clinical potential; however, human studies demonstrate that clinical efficacy of bNAbs can be undermined by both pre-existing and de novo resistance. Here we find that HIV-infected humanized mice receiving bNAbs delivered via AAV as Vectored ImmunoTherapy (VIT) can be used to identify antibody escape paths, which are largely conserved for each bNAb. Path selection, and consequent therapeutic success, is driven by the fitness cost and resistance benefit of emerging mutations. Applying this framework, we independently modulated bNAb resistance or the fitness cost of escape mutants, resulting in enhanced efficacy of VIT. This escape path analysis successfully explains the therapeutic efficacy of bNAbs, and enables a tractable means of quantifying and comparing the potential for viral escape from therapeutics in vivo. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/603156v4_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@180c86borg.highwire.dtl.DTLVardef@1e6108dorg.highwire.dtl.DTLVardef@148bac7org.highwire.dtl.DTLVardef@1de93ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Functional lung imaging identifies peripheral ventilation changes in mice with muco-obstructive lung disease

{beta}-ENaC-Tg mice serve as a relevant model of muco-obstructive lung disease, with impaired mucociliary clearance, mucus obstruction, chronic airway inflammation, structural lung damage, and altered lung function. The aim of this study was to undertake a comprehensive lung function and mechanics analysis of the adult {beta}-ENaC-Tg model. {beta}-ENaC-Tg and wild-type littermates underwent X-ray Velocimetry (XV) scans using a Permetium XV scanner (4DMedical, Melbourne, Australia). For comparative lung mechanics, lung function assessments were conducted with a flexiVent system. XV imaging demonstrated elevated ventilation defect percentage, mean specific ventilation, and ventilation heterogeneity in {beta}-ENaC-Tg mice. Spatial analysis of ventilation maps indicated increased ventilation variability in the peripheral lung regions, as well as an increased proportion of under-ventilated areas. The flexiVent analysis indicated that compared to wild-types, {beta}-ENaC-Tg mice have a significantly more compliant lungs with increased inspiratory capacity, reduced tissue elastance and increased hysteresivity (heterogeneity), suggesting loss of parenchymal integrity. This research highlights the utility of XV imaging in evaluating ventilation defects in the {beta}-ENaC-Tg model and provides a comprehensive lung function analysis.

physiology↗

Ribose lowers RpoS translation through RbsD mRNA

The Escherichia coli sigma factor RpoS accumulates during starvation, activates transcription of the general stress response, and then rapidly returns to low levels upon nutrient replenishment. Sugar levels modulate RpoS levels by signaling though central metabolism, ATP and the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) transport system, which favors glucose. However, there have been few examples of dedicated control pathways for specific sugars regulating RpoS. We screened an overexpression library with a RpoS- LacZ reporter and found that overexpressing the ribose metabolism rbsD gene reduced RpoS levels. A functional RbsD ribose pyranase protein was not necessary for the effect, suggesting that the RbsD mRNA was responsible for the effect. We used a series of LacZ fusions and RT-qPCR to determine how RbsD mRNA affects RpoS and found that regulation of RpoS occurred at the level of translation. Furthermore, the effect of rbsD overexpression was diminished in strain that did not have the RpoS untranslated hairpin loop or the small RNA chaperone Hfq. RbsD mRNA has previously been shown to bind to the sRNA DsrA. We demonstrated that the effect of RbsD on RpoS was dependent on the sRNAs DsrA and ArcZ and Hfq. Finally, we showed that the sugar ribose lowers RpoS levels in a manner that requires RbsD. In summary, our results demonstrate that RpoS levels respond specifically to ribose though a component of the ribose metabolism pathway and the main player, RbsD, acts as dual function mRNA that has a regulatory role by interacting with the sRNAs that control RpoS.

genetics↗

Antibody-mediated prevention of vaginal HIV transmission is dictated by IgG subclass in humanized mice

HIV broadly neutralizing antibodies (bNAbs) are capable of both blocking viral entry and recruiting innate immunity to HIV-infected cells through their fragment crystallizable (Fc) region. Vaccination or productive infection results in a polyclonal mixture of class-switched IgG antibodies comprised of four subclasses, each encoding distinct Fc regions that differentially engage innate immune functions. Despite evidence that innate immunity contributes to protection, the relative contribution of individual IgG subclasses is unknown. Here we use vectored immunoprophylaxis (VIP) in humanized mice to interrogate the efficacy of individual IgG subclasses during prevention of vaginal HIV transmission by VRC07, a potent CD4-binding site directed bNAb. We find that VRC07-IgG2, which lacks Fc-mediated functionality, exhibits significantly reduced protection in vivo relative to other subclasses. However, even low concentrations of highly functional VRC07-IgG1 yields substantial protection against vaginal challenge, suggesting that interventions capable of eliciting modest titers of functional subclasses may provide meaningful benefit against infection.

immunology↗

phylogatR: Phylogeographic data aggregation and repurposing

Patterns of genetic diversity within species contain information about the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyze sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR, large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology and student- or citizen-science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalyzed and increase accessibility to big data for research labs and classroom instructors with limited computational expertise and resources.

bioinformatics↗

Survey data on European organic multi-species livestock farms

While there is increasing evidence of the sustainability benefits of diversified systems in the organic cropping sector, this has been much less investigated with organic livestock farming. To fill this knowledge gap, we surveyed a sample of 128 European organic multi-species livestock farms located across seven countries - Austria, Belgium, France, Germany, Italy, Sweden and Switzerland - and covering a large range of livestock species combinations. We recorded 1574 variables as raw data out of which we calculated 107 indicators describing farm structure, management and several sustainability dimensions: resource use efficiency and conservation, animal, land and work productivities, animal and human welfare. After technical validation of the data, we withdrew 26 farms and the database covers 102 farms. This database is well suited to unveil relationships between various dimensions of organic multi-species livestock farm sustainability and their structure and management. It can help reveal sustainable strategies for organic multi-species livestock farming systems and understand levers or barriers to their development.

ecology↗

TMPRSS2 structure-phylogeny repositions Avoralstat for SARS-CoV-2 prophylaxis in mice

Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS-CoV-2 viral entry and may represent such a target.1-3 We hypothesized drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. We created a structure-based phylogenetic computational tool 3DPhyloFold to systematically identify structurally similar serine proteases with known therapeutic inhibitors and demonstrated effective inhibition of SARS-CoV-2 infection in vitro and in vivo.4,5 Several candidate compounds, Avoralstat, PCI-27483, Antipain, and Soybean-Trypsin-Inhibitor, inhibited TMPRSS2 in biochemical and cell infection assays. Avoralstat, a clinically tested Kallikrein-related B1 inhibitor,6 inhibited SARS-CoV-2 entry and replication in human airway epithelial cells. In an in vivo proof of principle,5 Avoralstat significantly reduced lung tissue titers and mitigated weight-loss when administered prophylactically to SARS-CoV-2 susceptible mice indicating its potential to be repositioned for COVID-19 prophylaxis in humans.

microbiology↗

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

MotivationGene and species tree reconciliation methods are used to interpret gene trees, root them and correct uncertainties that are due to scarcity of signal in multiple sequence alignments. So far, reconciliation tools have not been integrated in standard phylogenetic software and they either lack performance on certain functions, or usability for biologists. ResultsWe present Treerecs, a phylogenetic software based on duplication-loss reconciliation. Treerecs is simple to install and to use. It is fast and versatile, has a graphic output, and can be used along with methods for phylogenetic inference on multiple alignments like PLL and Seaview. AvailabilityTreerecs is open-source. Its source code (C++, AGPLv3) and manuals are available from https://project.inria.fr/treerecs/ Contacteric.tannier@inria.fr or david.parsons@inria.fr

bioinformatics↗