Biology subjects

Nichols, D.

Publications and source records attributed to Nichols, D..

7 recordsLinked to original sources

bioRxiv2026

Clade B serpins promote direct basal-to-goblet cell differentiation in airways of patients with chronic obstructive pulmonary disease

Goblet cell hyperplasia (GCH) is a hallmark of chronic obstructive pulmonary disease (COPD) and contributes to morbidity and mortality. We investigated the cellular and molecular origins of GCH in COPD using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and in vitro models. We identified "basal-to-goblet transitional cells" (BGTC) which are transcriptionally and physically located between basal and goblet cells and are characterized by expression of clade B serpins. In vitro studies indicate that inflammatory cytokines, including IL-1{beta}, stimulate basal-to-goblet differentiation through a SERPINB3/4+ intermediate and SERPINB3 overexpression induces differentiation of airway basal cells into IL1B-producing inflammatory goblet cells. In addition, we identified a subset of SERPINB4+ "goblet-variant basal cells" from lungs of COPD patients that express goblet cell and inflammatory genes ex vivo. Together, these results indicate clade B serpins contribute to altered epithelial differentiation and inflammatory signaling in COPD and support therapeutic targeting of clade B serpins to reduce GCH.

cell biology↗

bioRxiv2025

Loss of Regulator of telomere elongation helicase (Rtel1) impairs alveolar epithelial cell progenitor function but does not exacerbate experimental fibrosis

Inherited loss-of-function mutations in the replication-associated helicase Regulator of telomere elongation helicase (RTEL1) are among the most frequent monogenic causes of familial pulmonary fibrosis (FPF), but the specific functional role of RTEL1 in lung development, homeostasis, and injury-repair has not been determined. Using single-cell RNA-sequencing to define the cellular diversity and molecular programs following intratracheal bleomycin injury in mice, we observed that Rtel1 was most highly expressed in the lung epithelium, and its expression was reduced in PF epithelial cells compared to nonfibrotic controls. While global deletion of Rtel1 leads to embryonic lethality, constitutive deletion of Rtel1 in the lung epithelium (Rtel{Delta}epi) led to normal lung structure and architecture. Rtel1{Delta}epi mice exhibited accelerated telomere attrition and impaired AEC progenitor potential ex-vivo. Despite decreased AEC progenitor function, no differences in lung fibrosis were observed in Rtel{Delta}epi mice compared to controls following single-dose or repetitive intratracheal bleomycin. Together, these data implicate RTEL1 as a regulator of AEC progenitor function but this level of progenitor dysfunction is not alone sufficient to cause or exacerbate experimental lung fibrosis.

cell biology↗

bioRxiv2023

Hypoxia-inducible factor-2 (HIF2) regulates alveolar regeneration after repetitive injury

Idiopathic Pulmonary Fibrosis (IPF) is a progressive and often fatal chronic respiratory disease thought to result from repetitive injury and failed repair of the lung alveoli, and recent studies have identified a number of disease-emergent intermediate/transitional cell states in the IPF lung supporting this concept. In this study, we found that persistent activation of hypoxia-inducible factor (HIF)-signaling in airway-derived, repair-associated cell types/states is a hallmark of dysfunctional epithelial repair in the IPF lung epithelium and experimental models of recurrent lung epithelial injury. Disrupting Hif-signaling attenuated experimental lung fibrosis, reduced mucous-secretory cell polarization, and promoted functional alveolar regeneration following repetitive injury. Mouse and human organoid studies demonstrated that small-molecule-based HIF2 inhibition promoted alveolar epithelial cell proliferation and maturation while preventing the emergence of maladaptive intermediate/transitional states analogous to those in IPF. Together, these studies indicate that targeted HIF2-inhibition represents a novel and effective therapeutic strategy to promote functional lung regeneration, and could be readily translated into human studies of IPF and other chronic interstitial lung diseases with disease modifying effect. One sentence summaryInhibiting hypoxia-inducible-factor 2 (HIF2) promotes functional lung alveolar epithelial repair following recurrent injury.

cell biology↗

bioRxiv2022

Epithelial Outgrowth Through Mesenchymal Rings Drives Alveologenesis

Determining how alveoli are formed and maintained is critical to understanding lung organogenesis and regeneration after injury. While technological barriers have heretofore limited real-time observation of alveologenesis, we have now used scanned oblique plane illumination microscopy of living lung slices to observe specific cellular behaviors at high resolution over several days. Contrary to the prevailing paradigm that alveoli form by airspace subdivision via ingrowing septa, we find that alveoli form by ballooning epithelial outgrowth supported by stable mesenchymal ring structures. Our systematic analysis allowed creation of a computational model of finely-timed cellular structural changes that drive alveologenesis under normal conditions or with perturbed intercellular Wnt signaling. This new paradigm and platform can be leveraged for mechanistic studies and screening for therapies to promote lung regeneration. One-Sentence SummaryLong-term live analysis of neonatal lungs supports a dynamic epithelial outgrowth model for alveologenesis.

developmental biology↗

bioRxiv2021

Club cells are the primary source of pIgR in small airways

BackgroundLoss of secretory immunoglobulin A (SIgA) is common in COPD small airways and likely contributes to disease progression. We hypothesized loss of SIgA results from reduced expression of pIgR, a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. MethodspIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in-situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice utilized immunostaining, primary murine tracheal epithelial cell (MTEC) culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from non-typeable Haemophilus influenzae (NTHi) was evaluated in vitro. ResultsWe found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and NTHi-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD. InterpretationLoss of the SIgA immunobarrier in small airways of patients severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation. Key MessagesWhat is the key question? Localized SIgA deficiency in small airways is an established driver of COPD pathogenesis, but the mechanism of loss remains unclear. We hypothesized loss of SIgA is due to reduced numbers of pIgR-expressing cells in SIgA-deficient small airways. What is the bottom line? pIgR is primarily expressed by secretory cells in human and murine airways. Although numbers of secretory cells are similar between SIgA-deficient and SIgA-replete airways in COPD, there is reduced expression of pIgR protein, but not mRNA, in SIgA-deficient airways. Additionally, host and bacterial proteases degrade SIgA in vitro, suggesting loss of SIgA may relate to both impaired transcytosis and increased degradation. Why read on? This study highlights the complexity of SIgA immunobarrier maintenance and suggests that strategies aimed at restoring the SIgA immunobarrier will need to account for both impaired transcytosis and degradation by host and/or bacterial proteases.

cell biology↗

bioRxiv2021

A Single Cell Atlas of Lung Development

Lung organogenesis requires precisely timed shifts in the spatial organization and function of parenchymal cells, especially during the later stages of lung development. To investigate the mechanisms governing lung parenchymal dynamics during development, we performed a single cell RNA sequencing (scRNA-seq) time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14) in mice. We combined new computational analyses with RNA in situ hybridization to explore transcriptional velocity, fate likelihood prediction, and spatiotemporal localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of type 1 pneumocyte function during the saccular and alveolar stages, and we demonstrate an integrated view of the cellular dynamics during lung development.

developmental biology↗

bioRxiv2018

A Chemogenetic Platform for Spatio-temporal Control of β-arrestin Translocation and Signaling at G protein-Coupled Receptors

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/251769_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@1e4bf96org.highwire.dtl.DTLVardef@de4937org.highwire.dtl.DTLVardef@198dd33org.highwire.dtl.DTLVardef@e26f46_HPS_FORMAT_FIGEXP M_FIG C_FIG Although ligand-activated GPCRs induce both G-protein and {beta}-arrestin dependent signaling, gaining precise spatio-temporal control of {beta}-arrestin signaling has proven elusive. Here we describe a platform for specifically activating {beta}-arrestin-dependent signaling in situ. The platform, which we have dubbed \"GA-PAIR\" (GPCR/{beta}-Arrestin -Plant protein and Abscisic acid Induced Recruitment), can be controlled by the inert phytochemical S-(+)-abscisic acid (ABA). ABA induces interaction between ABI1 (ABA Insensitive 1) and PYL1 (Pyrabactin Resistance (PYR) 1-Like), two plant proteins with no mammalian counterparts. We fused ABI to the engineered human muscarinic M3 G protein-coupled receptor (hM3Dq) and PYL1 to {beta}-arrestin2. Addition of ABA induced rapid and nearly complete translocation of the PYL-{beta}-arrestin fusion protein and, importantly, induced both ERK and Akt signaling. Photo-uncaging a new photo-caged ABA analogue allowed us to gain relatively precise spatio-temporal control over {beta}-arrestin translocation. Because GA-PAIR facilitates the exclusive activation of endogenous {beta}-arrestin signaling pathways in the absence of a GPCR ligand or G protein, the GA-PAIR system will facilitate deconvoluting GPCR signaling in situ.

synthetic biology↗