Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell atlas of the aging mouse trachea

ABSTRACT: The airways conduct gases to and from the gas-exchanging alveoli of the lung and are the site of age-related diseases, such as chronic obstructive pulmonary disease, asthma, and bronchogenic carcinoma. Here we set out to study the effects of aging on the cellular composition and gene expression of murine airway. We present a comprehensive single-cell RNA-sequencing atlas of tracheas from young (2 month) and aged (24 month) mice, comprising diverse populations of cells, including epithelial, endothelial, immune, fibroblast, and cartilage cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE244215 | GEO | 2024/03/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:We report here senescent changes in the structure and organization of the mucociliary pseudostratified epithelium of the mouse trachea and the main stem bronchi. We confirm previous reports of the graduate appearance of age-related, gland-like structures (ARGLS) in the submucosa, espeically in the intercartilage regions and carina. Immunohistochemistry shows these structures contain ciliated and secretory cells and Krt5+ basal cells, but not the myoepithelial cells or ciliated ducts typical of normal submucosal glands. Data suggests they arise de novo by budding from teh surface epithelium rather than by delayted growth of small or cryptic submucosal glands. In old mice the surface epithelium contains fewer cells per unit length than in young mice and the proportion of Krt5+, p63+ basal cells is reduced in both males and females. However, there appears to be no significant difference in the ability of basal stem cells isolated from individual young and old mice to form clonal tracheospheres in culture or in the ability of the pithelium to repair after damage by inhaled sulfur dioxide. Gene expression analysis by Affymetrix microarray and quantitative PCR, as well as immunohistochemistry and flow sorting studies, are consistent with low-grade chronic inflammation in the tracheas of old versus young mice. The significance of these changes for ARGL formation are not clear since several treatments that induce acute inflammation in young mice did not result in budding of the surface epithelium. Total RNA from distal tracheas and carinas of four young (2 month) and four older (14 month) C57Bl/6 female mice was extracted using QIAshredder and RNeasy Micro Kits (QIAGEN). The quality was checked with a 2100 Bioanalyzer (Agilent Technologies). Total RNA was processed using Ambion MessageAmpTM Premier by the Duke Microarray Facility. Standard Affymetrix protocols and Affymetrix GeneChip® Mouse Genome 430 2.0 Array chips were used to generate .cel files.

2014-02-20 | E-GEOD-55162 | biostudies-arrayexpress

The human respiratory airways contain a distinct multipotent secretory cell lineage that can regenerate lung alveoli

Project description:The human lung differs substantially from its murine counterpart, resulting in a distinct distal airway architecture affected by disease pathology in chronic obstructive pulmonary disease. In humans, the distal branches of the airway interweave with the alveolar gas exchange niche, forming an anatomical structure known as the respiratory airways. Due to the lack of a murine counterpart, the cellular and molecular characterization of the respiratory airways in the human lung remains an enigma. We show that human respiratory airways contain a unique secretory cell population that is distinct from cells in larger proximal airways. Stem cell modeling reveal that these respiratory airway secretory cells (RASCs) act as unidirectional progenitors for alveolar type 2 cells, which are essential for maintaining and regenerating the alveolar niche. RASC lineage differentiation into AT2 cells is regulated, in part, by Notch signaling. In COPD, RASCs are altered transcriptionally, corresponding to abnormal AT2 cell states. These data identify a distinct progenitor in a region of the human lung not found in mouse that plays a critical role in maintaining the gas exchange compartment and is altered in chronic lung disease.

2021-12-09 | GSE168191 | GEO

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

Project description:Airways conduct gases to the lung and are disease sites of asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells by proximodistal location; a distinct cell type in high turnover squamous epithelial structures that we term 'hillocks'; and disease-relevant subsets of tuft and goblet cells. We developed 'pulse-seq' , combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that characterize cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.

2018-07-30 | GSE103354 | GEO

Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.

Project description:As observed in mice with genetic depletion of stem cells, epithelial plasticity is a critical component of tissue repair in response to injury; however, the physiological relevance of this process and the involved progenitor populations are not well understood. Severe respiratory viral infection and chronic lung disease share pathological features including stem cell loss in the gas-exchange regions, basal cell (BC) hyperplasia in small airways, and innate immune activation. Collectively, these processes contribute to epithelial remodeling and loss of diffusion capacity. Here, we show that small airways harbor a previously undescribed lineage of secretory cells, intralobar serous (IS) cells, that are activated to assume BC fates following influenza virus infection. Nascent BC were distinguished from pre-existing BC by high expression of IL-22Ra1 and a dependency on innate immune activation and local IL-22 production for self-renewal and colonization of injured alveoli. Resolution of virus-elicited inflammation and the associated decline in IL-22 signaling resulted in basal to serous re-differentiation in repopulated alveoli, and increased local expression of antimicrobial factors, but failed to replace normal alveolar epithelium. We define a mechanism whereby epithelial plasticity confers protection against mortality from acute respiratory viral infection but has potential to contribute to progressive lung remodeling and life-threatening declines in lung function among patients with chronic lung disease.

2023-08-08 | GSE184384 | GEO

Measurement and Analysis of Gas Composition in Digestive Tract

Project description:The purpose of this study is to detect the concentration of various gases，including hydrogen, methane, hydrogen sulfide, nitric oxide in different parts of the digestive tract by a safe and direct method, and to establish a human digestive tract gas profiles. Analyze the differences in gas components in different segments of the digestive tract in patients with different diseases, and analyze the correlation between specific gases and digestive tract diseases and non-specific symptoms.

| 14702 | ecrin-mdr-crc

Autoantibody profiles in patients with COPD and non-COPD smokers

Project description:Chronic obstructive pulmonary disease (COPD) is a highly prevalent disease leading to irreversible airflow limitation and is characterized by chronic pulmonary inflammation，obstructive bronchiolitis and emphysema. Etiologically, COPD is mediated by toxic gases and particles, e.g. cigarette smoke, while the pathogenesis of the disease is largely unknown. Several lines of evidence indicate a link between COPD and autoimmunity but comprehensive studies are lacking. By using a protein microarray assaying more than 19,000 human proteins we determined in this study the autoantibody profiles of COPD and non-COPD smokers.

2019-06-21 | GSE133096 | GEO

Transcription profiling of branching and non-branching regions of the mouse embryonic lung.

Project description:During development, the proximal and distal regions of respiratory tract undergo distinct processes that ultimately give rise to conducting airways and alveoli. To gain insights into the genetic pathways differentially activated in these regions when branching morphogenesis is initiating, we characterized their transcriptional profiles in murine rudiments isolated at embryonic day 11.5.

2007-09-29 | E-GEOD-1423 | biostudies-arrayexpress

Context-Dependent Roles of Mitochondrial LONP1 in Orchestrating the Balance between Airway Progenitor versus Progeny Cells

Project description:While all eukaryotic cells are dependent on mitochondria for function, in a complex tissue, which cell type and which cell behavior are more sensitive to mitochondrial deficiency remains unpredictable. Here we show that in the mouse airway, compromising mitochondrial function by inactivating mitochondrial protease gene Lonp1 led to reduced progenitor proliferation and differentiation during development; apoptosis of terminally differentiated ciliated cells and their replacement by basal progenitors and goblet cells during homeostasis; and failed airway progenitor migration into damaged alveoli following influenza infection. ATF4 and the integrated stress response (ISR) pathway are elevated and responsible for airway phenotypes. Such context dependent sensitivities are predicted by the selective expression of Bok, which is required for ISR activation. Reduced LONP1 expression is found in chronic obstructive pulmonary disease (COPD) airways with squamous metaplasia. These findings illustrate a cellular energy landscape whereby compromised mitochondrial function could favor the emergence of pathological cell types.

2024-08-23 | GSE230334 | GEO

Global analysis of genes differentially expressed in branching and non-branching regions of the mouse embryonic lung

2004-05-23 | GSE1423 | GEO

Transcription profiling of human atrial tissue from patients undergoing coronary artery bypass graft surgery to determine the effect of anesthesia on gene expression

Project description:Anesthetic gases elicit organ protection in patients undergoing coronary artery bypass graft (CABG) surgery. This study aimed at identifying myocardial transcriptional phenotypes and anesthetic-induced changes in gene expression to predict cardiovascular biomarkers and cardiac function after off-pump CABG. Experiment Overall Design: Patients scheduled for off-pump CABG were randomized into a group with the anesthetic gas sevoflurane (n=10) or the intravenous anesthetic propofol (n=10). Atrial samples were collected at the beginning and end of bypass surgery to determine gene expression profiles.

2008-11-22 | E-GEOD-4386 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data