Biology subjects

Manning, E.

Publications and source records attributed to Manning, E..

9 recordsLinked to original sources

bioRxiv2026

A Time-Resolved Single-Cell Atlas Reveals Infection-Status, Age-, and Sex-Dependent Immune Responses Drive Viral Disease Severity

The majority of mortality during viral infections occurs in older males; however, underlying mechanisms by which age and sex shape antiviral immunity and pathological inflammatory responses remain incompletely understood. Here, we performed time-resolved single-cell RNA sequencing across 16 conditions spanning age, sex, and four stages of influenza infection in mice, generating a high-resolution atlas. Aged mice demonstrate delayed antiviral and inflammatory responses in multiple myeloid cells, impairing viral clearance, which delays recovery. Similarly, endothelial cells from aging mice show prolonged inflammatory and antiviral gene signatures. Altered gene signatures in immune and endothelial cells result in a shift in endothelial-immune interactions in the aged lung. Further, the infection status of the cell is a major driver of transcriptional state, with infected myeloid cells exhibiting broad upregulation of genes, including interferon-stimulated, inflammatory, complement, and oxidative stress-related genes. To assess whether these age-associated transcriptional patterns are conserved in humans, we examined BAL cells obtained from healthy individuals and COVID-19 patients, and found that immune cells from aged COVID-19 patients had elevated antiviral and pro-inflammatory gene expression compared to cells from young patients. Our analyses of sex differences identified that multiple myeloid cell types in aged male mice, but not in young male mice, show persistent inflammatory responses at later stages of infection, a likely mechanism contributing to elevated mortality in older males. These data reveal how infection status of the cell, age, and sex interact to drive persistent inflammation and impaired resolution, providing a foundational resource for designing age- and sex-specific therapeutic strategies.

immunology↗

bioRxiv2026

Alveolar niche disruption and aberrant epithelial reprogramming are early hallmarks of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease in which the earliest cellular events driving fibrosis remain poorly defined. Here, we analyzed lung samples from three independent and unique cohorts of patients with early disease and preserved lung function (Florence, NIH, Forli), applying an integrated multi-modal approach combining single-nucleus RNA sequencing, bulk transcriptomics, immunostaining, and spatial transcriptomics. Single nuclear RNA sequencing of samples obtained by diagnostic bronchoscopic cryobiopsy (Florence, n= 22) revealed that early IPF is characterized by a marked shift in alveolar epithelial composition, with loss of AT1 and AT2 cells and the emergence of aberrant basaloid cells and alveolar epithelial intermediate cells. These populations exhibited transcriptional programs associated with epithelial plasticity and profibrotic signaling and closely resembled those observed in end-stage IPF. Higher proportions of aberrant basaloid and alveolar epithelial intermediate cells were associated with subsequent disease progression, whereas AT2 cell abundance correlated with preserved lung function. Fibrotic CTHRC1+ fibroblasts are largely restricted to advanced disease, while endothelial remodeling and inflammatory fibroblast states are already evident in early IPF. Spatial transcriptomic analyses confirmed early disruption of the alveolar niche, with replacement of normal epithelial-capillary interactions by aberrant epithelial and venous endothelial cells (Forli, n= 24); the findings were replicated through single cell RNA sequencing of samples obtained by video assisted thoracoscopy two decades earlier (NIH n=9). Together, these findings identify that alveolar niche remodeling with loss of its normal components, and emergence of aberrant basaloid cells are features of early IPF, highlighting epithelial dysfunction as a key potential target for therapeutic interventions in early disease.

genomics↗

bioRxiv2025

Growth Arrest of Thoracic Aortic Aneurysms in Aging Marfan Mice

There is a pressing need to identify pathologic mechanisms that render a thoracic aortic aneurysm susceptible to continued enlargement, dissection, or rupture, but additional insight can be gleaned by understanding potential compensatory mechanisms that prevent disease progression and thereby stabilize a lesion. Our biomechanical data suggest that the ascending aorta within a common mouse model of Marfan syndrome, Fbn1C1041G/+, exhibits progressive disease from 12 weeks to 1 year of age, but near growth arrest from 1 to 2 years of age. Comparison of the biomechanical phenotype, histological characteristics, proteomic signature, and transcriptional profile from 12 weeks to 1 year to 2 years suggests that numerous differentially expressed genes (including downregulated Ilk, Ltbp3, and Rictor) and associated proteins may contribute to late-term growth arrest. There is also a conspicuous absence of proteins associated with inflammation from 1 to 2 years of age. Although there is a need to understand better the interconnected roles of temporal changes in differential gene expression and protein abundance, reducing mTOR signaling and reducing excessive inflammation appears to merit increased attention in preventing continued aneurysmal expansion in Marfan syndrome.

bioengineering↗

bioRxiv2025

Resolving forebrain developmental organisation by analysis of differential growth patterns

The forebrain is the most complex region of the vertebrate CNS, and its developmental organisation is controversial. We fate-mapped the embryonic chick forebrain using lipophilic dyes and Cre-recombination lineage tracing, and built a 4D model of brain growth. We reveal modular patterns of anisotropic growth, ascribed to progenitor regions through multiplex HCR. Morphogenesis is dominated by directional growth towards the eye, more isometric expansion of the prethalamus and dorsal telencephalon, and anterior movement of ventral cells into the hypothalamus. Fate conversion experiments in chick and comparative gene expression analysis in chick and mouse support placement of the hypothalamus ventral to structures extending from the telencephalon up to and including the zona limitans intrathalamica (ZLI), with the dorsoventral axis becoming distorted at the base of the ZLI. Our findings challenge the widely accepted prosomere model of forebrain organisation, and we propose an alternative tripartite hypothalamus model.

developmental biology↗

bioRxiv2024

The role of GPR87 in Pulmonary Fibrosis

RationaleG- protein coupled receptor 87 (GPR87), an alternative lysophosphatidic acid (LPA) receptor previously implicated in cancer, is highly expressed in basal and aberrant basaloid cells in idiopathic pulmonary fibrosis (IPF). We sought to determine whether signaling through GPR87 is important to the development of pulmonary fibrosis. MethodsReanalysis of bulk and single cell RNA sequencing dataset was performed to confirm the increased expression of GPR87 in pulmonary fibrosis. The role of GPR87 in fibrosis in-vivo was assessed using global GPR87 knockout (GPR87-/-) and wildtype mice in the bleomycin model of pulmonary fibrosis, in-vitro in induced pluripotent stem cells (iPSCs) derived airway basal cells (iBC) using GPR87 siRNAs, and ex-vivo in human precision cut slices using disease free tissues in the fibrotic cocktail model as well as IPF tissues treated with GPR87 siRNA. ResultsGPR87 is highly expressed in IPF lungs, and its expression correlates with disease severity. Furthermore, It is highly expressed in basal and aberrant basaloid cells. GPR87-/- mice are protected against bleomycin induced pulmonary fibrosis. GPR87 knockdown is protective against fibrosis development in normal PCLS treated with fibrotic cocktail and leads to fibrosis regression in IPF PCLS. In iBC, GPR87 knockdown leads to decreased expression of fibrosis related genes, proteins and microRNAs. GPR87 stimulation with LPA leads to the opposite results. The main downstream pathways are PI3K, mTOR, and TNF/NFkB; stimulation or inhibition of PI3K pathway mimics GPR87 stimulation or inhibition responses, respectively. ConclusionGPR87 is highly expressed in basal and aberrant basaloid cells in IPF lungs and seems to mediate profibrotic effects based on in-vivo, ex-vivo and in-vitro models of disease, suggesting that it should be studied as a potential epithelial specific therapeutic target in pulmonary fibrosis.

cell biology↗

bioRxiv2024

Epidermal Growth Factor Receptor Regulates Beclin-1 in Hyperoxia

While delivery of supplemental oxygen is a life-saving therapy, exposure to high levels of oxygen, called hyperoxia, is associated with increased mortality in the intensive care unit (ICU). Hyperoxia leads to oxidant-mediated acute lung injury (ALI) and pulmonary cell death, called hyperoxic acute lung injury (HALI). Elucidation of molecular mechanisms in HALI could identify therapeutic targets in ALI. In the current study, we examined in vivo effects of HALI on Beclin-1 (BCN1), a molecule that regulates autophagy and cell death. Effects of HALI on BCN1 and autophagy markers were examined in wildtype mice. Analysis of BCN1 and autophagy was completed via Western blot, RT-qPCR, and immunohistochemistry. In wildtype mice, HALI led to increased BCN1 in the lung and in the alveolar epithelium. HALI resulted in significant alterations in markers of autophagy in the lung, including reduced microtubule-associated protein 1B-light chain (LC3B)-II/-I ratios, suggesting reduced autophagic flux. HALI caused increased LDH release in human alveolar type-II cells derived from induced pluripotent stem cells (AT2siPSC), as well as reduced LC3B-II/-I ratios. We previously showed that inhibition of the tyrosine kinase receptor epidermal growth factor receptor (EGFR) is protective in HALI. EGFRWa5/+ mice, which have genetically reduced EGFR activity and improved survival in HALI, showed increased total BCN1, reduced phosphorylated-(p-)/total BCN1 ratios, and decreased LC3B-II/-I ratios in the lung in HALI compared with wildtype. Administration of wortmannin, a phosphatidylinositol-3 kinase (PI3K) inhibitor which decreases BCN1-mediated autophagy, led to increased mortality in HALI in wildtype mice. These data support that regulation of BCN1 and autophagy by EGFR is a protective mechanism in HALI, a pathway which warrants further study for its therapeutic potential. KEY MESSAGESHALI is associated with increased mortality in the ICU and causes alveolar epithelial cell death, but the role of BCN1 in HALI is not well defined. This study shows that BCN1, a molecule involved in autophagy and cell death, is regulated by EGFR in HALI in vivo. These results are significant because regulation by BCN1 and autophagy by EGFR is a novel pathway in HALI with therapeutic potential that warrants further study.

cell biology↗

bioRxiv2022

A neuroepithelial wave of BMP signalling drives anteroposterior specification of the tuberal hypothalamus

The tuberal hypothalamus houses several major hypothalamic nuclei, dozens of transcriptionally distinct cell types, and clinically relevant cell populations implicated in obesity and related metabolic disorders. Building on recent advances in the field, here we draw upon transcriptional, signalling, and fate mapping analyses of chicken embryos and neuroepithelial explants to analyze tuberal hypothalamic development. We show that a wave of BMP signalling sweeps through early floor plate-like progenitors overlying prospective Rathkes pouch as they track anteriorly. The timing of BMP signalling correlates with cell fate, with anterior tuberal specification complete by Hamilton-Hamburger (HH) stage 10 but posterior tuberal progenitors requiring BMPs after this point. scRNA-Seq profiling of FGF10-expressing cells, a proxy for cells with active BMP signalling, through HH8-21 reveals transcriptional differences that may underlie their differing response to BMPs, and the switch from neuroepithelial progenitors to stem-like radial glial cells. This study provides an integrated account of the development of the tuberal hypothalamus.

developmental biology↗

bioRxiv2021

Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors.

The hypothalamus is an evolutionarily ancient brain region that regulates many innate behaviors, but its development is still poorly understood. To identify molecular mechanisms controlling hypothalamic specification and patterning, we used single-cell RNA-Seq to profile multiple stages of early hypothalamic development in the chick. We observe that hypothalamic neuroepithelial cells are initially induced from prethalamic-like cells. Two distinct hypothalamic progenitor populations emerge later, which give rise to paraventricular/mammillary and tuberal hypothalamus. At later developmental stages, the regional organization of the chick and mouse hypothalamus closely resembles one another. This study identifies selective markers for major subdivisions of the developing chick hypothalamus and many uncharacterized candidate regulators of hypothalamic patterning and neurogenesis. As proof of concept for the power of the dataset, we demonstrate that follistatin, a novel prethalamic progenitor-like marker, inhibits hypothalamic induction. This study both clarifies the organization of the early developing hypothalamus and identifies novel molecular mechanisms controlling hypothalamic induction, regionalization, and neurogenesis. HighlightsO_LIEarly hypothalamic development was profiled in chick using scRNA-Seq and multiplexed HCR. C_LIO_LIHypothalamic cells are induced from prethalamic-like neuroepithelial cells. C_LIO_LIDistinct paraventricular/mammillary and tuberal progenitor populations emerge later, and hypothalamic organization is evolutionarily conserved. C_LIO_LIPrethalamic progenitor-derived follistatin inhibits hypothalamic specification. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/438683v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@18ac4c2org.highwire.dtl.DTLVardef@17bb90aorg.highwire.dtl.DTLVardef@1b17cceorg.highwire.dtl.DTLVardef@178e769_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2020

Integrated Single Cell Atlas of Endothelial Cells of the Human Lung

BackgroundDespite its importance in health and disease, the cellular diversity of the lung endothelium has not been systematically characterized in humans. Here we provide a reference atlas of human lung endothelial cells (ECs), to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium, both in health and disease. MethodsWe reprocessed control single cell RNA sequencing (scRNAseq) data from five datasets of whole lungs that were used for the analysis of pan-endothelial markers, we later included a sixth dataset of sorted control EC for the vascular subpopulation analysis. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by immunohistochemistry and in situ hybridization. Signaling network between different lung cell types was studied using connectomic analysis. For cross species analysis we applied the same methods to scRNAseq data obtained from mouse lungs. ResultsThe six lung scRNAseq datasets were reanalyzed and annotated to identify over 15,000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including pan-endothelial, pan-vascular and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial and venous ECs we found previously indistinguishable subpopulations; among venous EC we identified two previously indistinguishable populations, pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary EC we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1 and TBX2 and general capillary EC. We confirmed that all six endothelial cell types, including the systemic-venous EC and aerocytes are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-Receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. Our manuscript is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). ConclusionOur integrated analysis provides the comprehensive and well-crafted reference atlas of lung endothelial cells in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.

cell biology↗