Biology subjects

Walker, N. M.

Publications and source records attributed to Walker, N. M..

6 recordsLinked to original sources

bioRxiv2026

Longitudinal Single-Cell RNA-seq Profiling of Lung Cell Phenotypes, Signaling, and Cross-talk During Fibrosis Resolution

Resolution of fibrosis following lung injury is distinguished from persistent/progressive parenchymal scarring through the timely clearance of aberrant cell types, removal of excess collagens, and regeneration of alveolar structure. The requisite signaling pathways, cellular cross-talk, and phenotypic shifts associated with, and required for, resolution of established lung fibrosis have not been well characterized. To address this critical knowledge gap, we performed longitudinal single-cell RNA sequencing of whole mouse lung digests obtained during spontaneously resolving fibrosis. We observed a putatively pro-fibrotic macrophage population emerge during peak fibrosis and undergo partial clearance during resolution. Our study also revealed conspicuous shifts in well-established pathways associated with tissue repair and fibrosis among immune, mesenchymal, and epithelial cells during spontaneous resolution. In addition to a decline in pro-fibrotic driver pathways, the putative anti-fibrotic pathways cAMP, HGF/MET, and TWEAK were enriched in several cell types during spontaneous resolution. CellChat analysis was used to predict the cellular senders and recipients of each pathway and characterize their longitudinal changes. Our characterization of the cellular and molecular dynamics in whole lungs during spontaneous fibrosis resolution provides a foundation for the identification of endogenous pathways that might be leveraged to treat pulmonary fibrosis.

cell biology↗

bioRxiv2025

Characterization of bronchovascular-bundle mesenchymal stromal cells regulating antibody-secreting cell niche in rejecting lung allografts

A transplanted lung offers a permissive milieu for local adaptive immune cell responses. Here, we characterize a transcriptionally and anatomically distinct adult lung-resident mesenchymal stromal population (MSC) that supports a pro-survival niche for antibody-secreting cells in rejecting lung allografts through a novel IL-6 trans-signaling/CXCL12 axis. By using a mouse orthotopic lung transplant model and Blimp1EYFP recipients, we identify spatial localization of antibody-secreting cells (ASCs) and terminally differentiated plasma cells (PCs) along the bronchovascular bundles (BVBs). A previously described Foxf1+Gli1+Itga8- subset of collagen- expressing MSCs, which forms a 3-dimensional network along the bronchovascular bundles (BVB-MSCs), was found to be the major source of the PC survival factors CXCL12 and IL-6. Cxcl12iCre/ERT2Rosa26tdTomatomice utilized as donors, validated the expansion of this population in a rejecting graft and their intimate association with ASCs. CXCL12 expression was increased in murine allografts and in Foxf1+ mesenchymal cells (MCs) isolated from human CLAD patients. IL-6 trans-signaling/STAT3 signaling axis was shown to upregulate CXCL12 secretion in human MCs, and Olamkicept-mediated neutralization of IL-6 trans-signaling in murine RAS attenuates CXCL12 expression, intra-graft ASC population, and fibrogenesis. Our findings represent the first delineation of specialized CXCL12-expressing mesenchymal stromal cells in adult lungs and the contribution of IL-6 trans-signaling driven CXCL12 expression to sustaining intra-graft ASC niches and allograft fibrogenesis. One Sentence SummaryWe characterize CXCL12-expressing mesenchymal cells and their role in a pro-survival niche for antibody-secreting cells in rejecting lung allografts.

pathology↗

bioRxiv2024

Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and putative regulators of lung fibrosis

Survival after lung transplantation is limited by chronic progressive graft failure, termed chronic lung allograft dysfunction (CLAD). Graft-resident mesenchymal cells (MCs) drive CLAD pathogenesis and exhibit stable, dysregulated signaling; however, the transcriptomic and epigenomic drivers behind this fibrogenic transformation remain elusive. Here, we utilize single-cell multi-omic technologies to study gene expression and chromatin accessibility of MCs from the lavage fluid of lung transplant recipients with and without CLAD, obtained either early post-transplantation or after disease onset. MCs obtained after CLAD onset (CLAD-MCs) demonstrated a unique transcriptomic signature compared to non-CLAD controls; a logistic regression model trained on these profiles classified the disease status of individual cells with > 98% accuracy using a set of signature genes. Chromatin accessibility and motif scan analysis identified the CCAAT-enhancer-binding proteins family of transcription factors, specifically CEBPD, as a key marker of the CLAD-enriched subtype. Footprint analysis of early time-point MCs revealed minimal differences in accessibility, suggesting that CEBPD-associated regulatory changes emerge over time after transplantation. Integration and unsupervised clustering identified 8 distinct cell states, and a compositional shift was noted uniquely in CLAD-MCs. Knocking down CEBPD with siRNA in CLAD-MCs partially reverted the CLAD transcriptomic signature, confirming its importance in the dysregulated molecular state of CLAD-associated MCs. scRNA-seq analysis on human lung CLAD tissue provided in situ validation of key genes and CEBPD expression changes noted in CLAD-MCs. Our results provide deeper insights into the transcriptomic and epigenomic changes in post-transplant MCs, nominating biomarkers and disease-associated factors with implications for future therapeutic efforts.

bioinformatics↗

bioRxiv2017

Targeting regulatory T cells with Interleukin-2 treatment in type 1 diabetes: a response-adaptive, non-randomised, open-label trial of repeat doses of Aldesleukin (DILfrequency)

BackgroundType 1 diabetes (T1D) results from loss of immune regulation leading to the development of autoimmunity to pancreatic beta-cells, involving autoreactive T effector cells (Teffs). Regulatory T cells (Tregs), that prevent autoimmunity, require Interleukin-2 (IL-2) for maintenance of immunosuppressive functions and, alterations in the IL-2 pathway predispose to T1D. Using an adaptive trial design we aimed to determine the optimal regimen of aldesleukin (recombinant human IL-2) to physiologically enhance Tregs while limiting expansion of autoreactive Teffs.\n\nMethodsDILfrequency is a single-center, non-randomised, open-label, response-adaptive study of participants aged 18 to 70 years with T1D. The initial learning phase allocated 12 participants to six different predefined dose-frequency regimens. Then, three cohorts of 8 participants were sequentially allocated dose-frequencies, based on repeated interim analyses of all accumulated trial data. The co-primary endpoints were percentage change in Tregs, Teffs and, CD25 ( subunit of the IL-2 receptor) expression by Tregs, from baseline to steady state. Trial registration ISRCTN40319192 and ClinicalTrials.gov (NCT02265809).\n\nFindings115 participants were assessed between November 17th 2014 and May 22nd 2016, 38 participants were enrolled with 36 completing treatment. The optimal regimen to maintain a steady state increase in Tregs of 30% and CD25 expression of 25% without Teff expansion is 0.26 x 106 IU/m2 (95% CI (-0.007 to 0.485)) every 3 days (1.3 to 4.4). Tregs and CD25 were dose-frequency responsive, while Teffs were not. The commonest adverse event was injection site reaction (464/694 events), with a single participant developing transient eosinophilia at the highest dose (0.47 x 106 IU/m2).\n\nInterpretationThis response-adaptive trial defined a well-tolerated aldesleukin regimen that specifically induces Treg expansion that can now be trialled to treat T1D.\n\nFundingSir Jules Thorn Trust, Wellcome, JDRF, SNSF, NIHR

clinical trials↗

bioRxiv2017

CFTR Modulates Wnt/β-Catenin Signaling and Stem Cell Proliferation in Murine Intestine

Background & AimsCystic fibrosis (CF) patients and CF mouse models have increased risk for gastrointestinal tumors. CF mice exhibit augmented intestinal proliferation of unknown etiology and an altered intestinal environment. We examined the role of Cftr in Wnt/{beta}-catenin signaling, stem cell proliferation and its functional expression in the active intestinal stem cell (ISC) population. Dysregulation of intracellular pH (pHi) in CF ISCs was investigated for facilitation of Wnt/{beta}-catenin signaling.\n\nMethodsCrypt epithelia from wild-type (WT) and CF mice were compared ex vivo and in intestinal organoids (enteroids) for proliferation and Wnt/{beta}-catenin signaling by standard assays. Cftr in ISCs was assessed by immunoblot of sorted Sox9EGFP intestinal epithelia and pHi regulation by confocal microfluorimetry of Lgr5+-EGFP ISCs. Plasma membrane association of the Wnt transducer Disheveled 2 (Dvl2) was assessed by fluorescence imaging of live enteroids from WT and CF mice crossed with Dvl2-EGFP/RosamT/mG mice.\n\nResultsRelative to WT, CF intestinal crypts showed a ~30% increase in epithelial and Lgr5+ ISC proliferation and increased Wnt/{beta}-catenin signaling. Cftr was expressed in Sox9EGFPLo ISCs and loss of Cftr induced an alkaline pHi in Lgr5+-EGFP ISCs. CF crypt-base columnar cells (CBCs) demonstrated a generalized increase in plasma membrane Dvl2-EGFP association as compared to WT. Dvl2-EGFP membrane association was charge- and pH-dependent and increased in WT CBCs by Cftr inhibition.\n\nConclusionsCF intestine exhibits increased ISC proliferation and Wnt/{beta}-catenin signaling. Loss of Cftr increases pHi in ISCs which stabilizes the plasma membrane association of the Wnt transducer Dvl, likely facilitating Wnt/{beta}-catenin signaling. Absence of Cftr-dependent suppression of ISC proliferation in the CF intestine may contribute to increased risk for intestinal tumors.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC=\"FIGDIR/small/156562_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@cf807forg.highwire.dtl.DTLVardef@fd24baorg.highwire.dtl.DTLVardef@176497dorg.highwire.dtl.DTLVardef@d2b265_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

physiology↗

bioRxiv2016

All or Nothing: the False Promise of Anonymity

In early 2016, the International Committee of Medical Journal Editors (ICMJE) proposed that responsible sharing of de-identified individual-level data be required for clinical trials published in their affiliated journals. There would be a delay in implementing this policy to allow for the necessary informed consents to work their way through ethical review. Meanwhile, some researchers and policy makers have conflated the notions of de-identification and anonymity. The former is a process that seeks to mitigate disclosure risk though careful application of rules and statistical analysis, while the latter is an absolute state. The consequence of confusing the process and the state is profound. Extensions to the ICMJE proposal based on the presumed anonymity of data include: sharing unconsented data; sharing data without managing access, as Open Data; and proposals to sell data. This essay aims to show that anonymity (the state) cannot be guaranteed by de-identification (the process), and so these extensions to the ICMJE proposal should be rejected on governance grounds, if no other. This is not as negative a position as it might seem, as other disciplines have been aware of these limitations and concomitant responsibilities for many years. The essay concludes with an example from social science of managed access strategies that could be adopted by the medical field.

scientific communication and education↗