Biology subjects

Pickles, R. J.

Publications and source records attributed to Pickles, R. J..

6 recordsLinked to original sources

bioRxiv2025

Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes

The long-term pulmonary sequelae of SARS-CoV-2 respiratory infections reflect infection severity, innate and adaptive immunity, and respiratory epithelial repair. This study investigated the acute and reparative responses as a function of age and sex in primary human bronchial epithelial (HBE) cultures utilizing a 14-day SARS-CoV-2 infection protocol. SARS-CoV-2 infection peaked at 3 days post-infection (dpi) with an [~] 2 log titer suppression at 14 dpi. SARS-CoV-2 infection induced interferon, interferon-induced gene, and cell damage responses. No age- or sex-dependent effects on SARS-CoV-2 infection were detected. Airway epithelia repaired to an abnormal mucus metaplastic/inflammatory state that reflected potentially beneficial and adverse consequences at 14 dpi. Repair processes were infection severity-dependent, not sex-dependent, and were more robust in young donor cultures. Analyses of long-COVID subjects with persistent pulmonary fibrosis or persistent bronchitic airway diseases exhibited expression of HBE 14 dpi failed repair gene signatures, including ISG gene signatures. Human airway epithelial repair post-SARS-CoV-2 is prolonged and incomplete in vitro over 14 days, and persistently abnormal repair may contribute to phenotypes of people with long-COVID pulmonary syndrome.

cell biology↗

bioRxiv2024

Temporal High-Resolution Atlas of Human Blood Leukocyte Composition in Response to Respiratory Virus Inoculation

BackgroundRespiratory viral infections produce highly variable clinical outcomes, even after controlled exposure. Human viral challenge studies are well suited to study this variation because they capture immune profiles before inoculation and across defined post-challenge intervals. However, how circulating immune-cell populations change over time, and which responses are shared or virus-specific across respiratory viruses, remains incompletely defined. MethodsWe leveraged HR-VILAGE-3K3M, a curated human respiratory viral challenge transcriptomic resource, to analyze longitudinal whole-blood profiles from H1N1, H3N2, RSV, and HRV challenge studies. Using statistical deconvolution and xCell-based digital sorting, we estimated changes in major leukocyte populations and 28 immune-cell subtypes in symptomatic infected (Sx/Inf) and asymptomatic uninfected (Asx/Uninf) participants. Across viruses, symptomatic infection was marked by a broad shared pattern of innate immune activation together with reduced circulating lymphocyte enrichment. Activated dendritic cells, monocytes, and neutrophils increased following challenge, whereas strong pDC activation was observed primarily in influenza studies. Most T-cell and B-cell populations decreased after challenge. Plasma-cell enrichment increased progressively over time. Despite this shared architecture, response timing differed by virus: H3N2 showed the earliest changes, followed by H1N1, whereas RSV responses were delayed and HRV showed more distinct immune-cell trajectories. Migration-associated transcriptional programs were detected across both innate and adaptive immune-cell populations, supporting coordinated immune-cell trafficking during infection. Baseline immune composition also differed between outcome groups, suggesting that pre-existing immune-state differences may influence infection outcomes. ConclusionsThese findings define a cellular atlas of human respiratory viral challenge responses and show that respiratory viruses induce a broadly conserved immune-response program with distinct virus-specific kinetics. This framework may help clarify immune features associated with natural resistance, symptomatic infection, and vaccine-relevant antiviral immunity.

genomics↗

bioRxiv2024

A curated collection of transcriptome datasets to study the transcriptional response in blood and nasal samples following viral respiratory inoculation and vaccination

Our understanding of the human immune systems response to viral respiratory tract infections (VRTIs) and vaccines, including the molecular mechanisms and correlates of protection, remains incomplete. Extensive transcriptomic data from inoculation and vaccination studies have been deposited in publicly available databases. However, these studies are often separate and difficult to locate. We provide a curated compendium of public gene expression data repositories for researchers to reanalyze transcriptomes from human whole blood, peripheral blood mononuclear cells (PBMCs), and nasal swab samples. This enables the study of transcriptional responses to viral inoculation or vaccination. This collection includes 18 datasets from inoculation studies and 37 datasets from vaccination studies, sourced from the NCBI Gene Expression Omnibus (GEO), ImmPort Shared Data, and ArrayExpress.

genomics↗

bioRxiv2024

Prolonged airway explant culture enables study of health, disease, and viral pathogenesis

In vitro models play a major role in studying airway physiology and disease. However, the native lungs complex tissue architecture and non-epithelial cell lineages are not preserved in these models. Ex vivo tissue models could overcome in vitro limitations, but methods for long-term maintenance of ex vivo tissue has not been established. We describe methods to culture human large airway explants, small airway explants, and precision-cut lung slices for at least 14 days. Human airway explants recapitulate genotype-specific electrophysiology, characteristic epithelial, endothelial, stromal and immune cell populations, and model viral infection after 14 days in culture. These methods also maintain mouse, rabbit, and pig tracheal explants. Notably, intact airway tissue can be cryopreserved, thawed, and used to generate explants with recovery of function 14 days post-thaw. These studies highlight the broad applications of airway tissue explants and their use as translational intermediates between in vitro and in vivo studies.

bioengineering↗

bioRxiv2022

Viral Airway Injury Promotes Cell Engraftment in an In Vitro Model of Cystic Fibrosis Cell Therapy

Cell therapy is a potential treatment for cystic fibrosis (CF). However, cell engraftment into the airway epithelium is challenging. Here, we model cell engraftment in vitro using the air-liquid interface (ALI) culture system by injuring well-differentiated CF ALI cultures and delivering non-CF cells at the time of peak injury. Engraftment efficiency was quantified by measuring chimerism by droplet digital PCR and functional ion transport in Ussing chambers. Using this model, we found that human bronchial epithelial cells (HBECs) engraft more efficiently when they are cultured by conditionally reprogrammed cell (CRC) culture methods. Cell engraftment into the airway epithelium requires airway injury, but the extent of injury needed is unknown. We compared three injury models and determined that severe injury with partial epithelial denudation facilitates long-term cell engraftment and functional CFTR recovery up to 20% of wildtype function. The airway epithelium promptly regenerates in response to injury, creating competition for space and posing a barrier to effective engraftment. We examined competition dynamics by time-lapse confocal imaging and found that delivered cells accelerate airway regeneration by incorporating into the epithelium. Irradiating the repairing epithelium granted engrafting cells a competitive advantage by diminishing resident stem cell proliferation. Intentionally causing severe injury to the lungs of people with CF would be dangerous. However, naturally occurring events like viral infection can induce similar epithelial damage with patches of denuded epithelium. We found that viral preconditioning promoted effective engraftment of cells primed for viral resistance.

cell biology↗

bioRxiv2021

Thiol-based mucolytics exhibit antiviral activity against SARS-CoV-2 through allosteric disulfide disruption in the spike glycoprotein

Small molecule therapeutics targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lagged far behind the development of vaccines in the fight to control the COVID-19 pandemic. Here, we show that thiol-based mucolytic agents, P2119 and P2165, potently inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity of repurposed mucolytic agents to the reduction of key disulfides, specifically, by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif (RBM) in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol warhead pointed directly towards Cys432. These collective findings establish the vulnerability of human coronaviruses to repurposed thiol-based mucolytics and lay the groundwork for developing these compounds as a potential treatment, preventative and/or adjuvant against infection.

microbiology↗