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Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scATAC-Seq)

ABSTRACT: The pulmonary capillary endothelial cells (ECs) consist of two populations, CAP1 and CAP2; how each population reacts to diverse tissue injury is incompletely understood. Using single-cell multiome and genetic lineage tracing, we characterize the induction and function of a truncated isoform of Ntrk2, Ntrk2-tk (lacking the tyrosine kinase domain), in multiple lung injury models in mice. Upon Sendai parainfluenza infection, Ntrk2-tk is activated in CAP1 across the whole lung after the initial interferon response, associated with increased intronic accessibility, and persists for weeks after injury. Ntrk2-tk ECs arise from CAP1 but not CAP2, traced by KitCreER and Car4CreER, respectively, and proliferate and give rise to CAP1 but not CAP2, as traced by Ntrk2CreER. EC-specific deletion of Ntrk2 has little molecular and cellular consequences in response to Sendai and H3N2 viral infection. Our data identifies Ntrk2-tk as an EC marker of lung injury-repair and enhances our understanding of EC heterogeneity. 

ORGANISM(S): Mus musculus

PROVIDER: GSE261081 | GEO | 2025/06/20

REPOSITORIES: GEO

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Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scRNA-Seq)

Project description:The pulmonary capillary endothelial cells (ECs) consist of two populations, CAP1 and CAP2; how each population reacts to diverse tissue injury is incompletely understood. Using single-cell multiome and genetic lineage tracing, we characterize the induction and function of a truncated isoform of Ntrk2, Ntrk2-tk (lacking the tyrosine kinase domain), in multiple lung injury models in mice. Upon Sendai parainfluenza infection, Ntrk2-tk is activated in CAP1 across the whole lung after the initial interferon response, associated with increased intronic accessibility, and persists for weeks after injury. Ntrk2-tk ECs arise from CAP1 but not CAP2, traced by KitCreER and Car4CreER, respectively, and proliferate and give rise to CAP1 but not CAP2, as traced by Ntrk2CreER. EC-specific deletion of Ntrk2 has little molecular and cellular consequences in response to Sendai and H3N2 viral infection. Our data identifies Ntrk2-tk as an EC marker of lung injury-repair and enhances our understanding of EC heterogeneity. 

2025-06-20 | GSE261082 | GEO

Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scRNA-Seq)

Project description:Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scRNA-Seq)

| PRJNA1085255 | ENA

Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scATAC-Seq)

Project description:Mouse lung injury-repair induces Ntrk2-tk in CAP1 endothelial cells (scATAC-Seq)

| PRJNA1085254 | ENA

mRNA aging shapes the Cap2 methylome in mammalian mRNA

Project description:The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2’-O-methylation on the first, or both the first and second transcribed nucleotide, respectively. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-Seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. We find that large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions where RIG-I expression is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG-I. We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.

2022-12-12 | GSE196043 | GEO

Truncated NTRK2 is induced in CAP1 endothelial cells during mouse lung injury-repair

Project description:Truncated NTRK2 is induced in CAP1 endothelial cells during mouse lung injury-repair

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Histone lactylation drives endothelial activation-mediated lung injury in sepsis-associated ARDS via promoting ferroptosis

Project description:The activation of pulmonary endothelial cells (ECs) triggers the occurrence of lung injury and is a hallmark of sepsis-associated acute respiratory distress syndrome(ARDS). Aberrant metabolism favoring glycolysis plays a pivotal role in the pathogenesis of sepsis-induced EC activation. Herein we demonstrate that glycolysis-related histone lactylation, represented by H3K14 lactylation (H3K14la), drives sepsis-associated EC activation and lung injury. Accordingly, H3K14la level is elevated in injured lung tissue and activated ECs. Inhibition of lactate production suppresses both H3K14la levels and EC activation in response to lipopolysaccharide (LPS). We also show that lactate-dependent H3K14la is enriched at the promoters of ferroptosis-related genes, thereby inducing ferroptosis in ECs, and inhibiting ferroptosis effectively ameliorates EC activation. Taken together, elevated lactate in sepsis modulates EC activation and lung injury via histone lactylation and manipulation of glycolysis/H3K14la/ferroptosis axis may provide novel therapeutic approaches for the treatment of sepsis-associated ARDS.

2023-01-01 | GSE212087 | GEO

H3K14la drives endothelial dysfunction in sepsis-induced ARDS via promoting SLC40A1/TFR-mediated ferroptosis

Project description:Background: Pulmonary endothelial cell (EC) activation is a key factor in acute respiratory distress syndrome (ARDS). In sepsis, increased glycolysis leads to lactate buildup, which induces lysine lactylation (Kla) on histones and other proteins. However, the role of protein lactylation in EC dysfunction during sepsis-induced ARDS remains unclear. Methods: Integrative lactylome and proteome analysis was performed to identify the global lactylome profiling in lung tissues of septic mice. Cut&Tag analysis were used to identify the transcriptional targets of histone H3 lysine 14 lactylation (H3K14la) in ECs. Results: Septic mice exhibited elevated levels of lactate and H3K14la in lung tissues, particularly in pulmonary ECs. Suppressing glycolysis reduced both H3K14la and EC activation, suggesting a link between glycolysis and lactylation. Moreover, H3K14la was found to be enriched at promoter regions of ferroptosis-related genes such as transferrin receptor (TFRC) and solute carrier family 40 member 1 (SLC40A1), which contributed to EC activation and lung injury under septic conditions. Conclusions: We for the first time reported the role of lactate-dependent H3K14 lactylation in regulating EC ferroptosis to promote vascular dysfunction during sepsis-induced lung injury. Our findings suggest that manipulation of glycolysis/H3K14la/ferroptosis axis may provide novel therapeutic approaches for sepsis-associated ARDS.

2025-05-07 | PXD056805 | Pride

A single cell transcriptome atlas of murine endothelial cells

Project description:The heterogeneity of endothelial cells (ECs), lining blood vessels, across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomic data from 11 tissues of the model organism Mus musculus. We propose a new classification of EC phenotypes based on transcriptome signatures and inferred putative biological features. We identified top-ranking markers for ECs from each tissue. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) resembled each other across tissues, but only arterial, venous and lymphatic (not capillary) ECs shared markers, illustrating a greater heterogeneity of capillary ECs. We identified high-endothelial-venule and lacteal-like ECs in the intestines, and angiogenic ECs in healthy tissues. Metabolic transcriptomes of ECs differed amongst spleen, lung, liver, brain and testis, while being similar for kidney, heart, muscle and intestines. Within tissues, metabolic gene expression was heterogeneous amongst ECs from different vascular beds, altogether highlighting large EC heterogeneity.

2020-02-13 | E-MTAB-8077 | biostudies-arrayexpress

Endothelial cell heterogeneity in pathological angiogenesis characterized by metabolic transcriptome diversity

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2020-03-31 | E-MTAB-8604 | biostudies-arrayexpress

CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster

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2021-12-18 | GSE181321 | GEO

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