Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [II]

ABSTRACT: Cellular atlases reveal diverse cellular phenotypes, but how cells traverse this phenotypic landscape to impact tissues requires systematic study. We present an alveolosphere screening platform for investigating interactions between lung epithelial stem cells and their fibroblast niche. We assessed the role of 201 candidate genes in stem cells via imaging, then used RNAseq analysis for a transcriptome-wide understanding of cell-autonomous effects on stem cells and non-cell-autonomous effects on the niche. This phenome-transcriptome map uncovered new cellular states and pathways regulating stem cell growth, metabolism, and immune signaling. Notably, stem cells influenced scar-forming and immune programs in fibroblasts. This injury response was dependent on stem cell identity; loss of Nkx2.1, the transcription factor conferring lung epithelial identity, disrupted stem cell-niche interactions and had a greater non-cell-autonomous effect than eliminating the cancer genes Trp53, Egfr, or Cdkn2b. Our study highlights how functional atlases complement the cellular diversity revealed by descriptive methods.

ORGANISM(S): Mus musculus

PROVIDER: GSE307128 | GEO | 2026/06/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [I]

Project description:Cellular atlases reveal diverse cellular phenotypes, but how cells traverse this phenotypic landscape to impact tissues requires systematic study. We present an alveolosphere screening platform for investigating interactions between lung epithelial stem cells and their fibroblast niche. We assessed the role of 201 candidate genes in stem cells via imaging, then used RNAseq analysis for a transcriptome-wide understanding of cell-autonomous effects on stem cells and non-cell-autonomous effects on the niche. This phenome-transcriptome map uncovered new cellular states and pathways regulating stem cell growth, metabolism, and immune signaling. Notably, stem cells influenced scar-forming and immune programs in fibroblasts. This injury response was dependent on stem cell identity; loss of Nkx2.1, the transcription factor conferring lung epithelial identity, disrupted stem cell-niche interactions and had a greater non-cell-autonomous effect than eliminating the cancer genes Trp53, Egfr, or Cdkn2b. Our study highlights how functional atlases complement the cellular diversity revealed by descriptive methods.

2026-06-29 | GSE307112 | GEO

Recombinant FGF10-induced de novo alveologenesis in neonatal mice after hyperoxia exposure is associated with enhanced AT2’s resident mesenchymal cell niche activity

Project description:Recombinant FGF10 improved hemodynamic measurements and alveologenesis. Alveolosphere assays indicate that the activity of rMC-Sca1Pos is negatively impacted by HYX and partially rescued by FGF10 treatment. scRNAseq results identified clusters expressing Fgf10, Fgf7, Pdgfra, Axin2 which could represent the rMC niche cells for the AT2 stem cells. In this syudy, we demonstrate that FGF10 administration is curative for BPD and identified a subpopulation of rMC-Sca1Pos niche cells which could represent its cellular target.

2022-06-29 | GSE190934 | GEO

Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions

Project description:Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions

| PRJNA1315700 | ENA

Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [I]

Project description:Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [I]

| PRJNA1314575 | ENA

Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [II]

Project description:Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [II]

| PRJNA1314603 | ENA

Differential expression of stem cell-specific genes in P7 and P28 dentate gyrus neural progenitors

Project description:In order to identify cell-autonomous factors that might be regulating the neurogenic niche, type 1 and 2 progenitors were FACS sorted from P7 and P28 animals and their cDNA was hybridized to a stem cell-specific microarray. Keywords: differential gene expression analysis Two samples per microarray (P7 and P28). Each microarray experiment was done in triplicate. P7 is the control sample.

2009-03-10 | E-GEOD-15085 | biostudies-arrayexpress

Old mitochondria regulate niche renewal via stem cell metabolism

Project description:Cellular metabolism is emerging as a potent regulator of cell fate, raising the possibility that the recently discovered metabolic heterogeneity between newly synthesized and chronologically old organelles may impact stem cell fate in mammalian tissues. The small intestine is maintained by actively cycling intestinal stem cells (ISCs) that give rise to metabolically distinct progeny, including their Paneth cell niche. Here, we find that asymmetric cell division generates a subset of ISCs enriched for old mitochondria (ISCmito-O). Although ISCmito-O lack characteristics of reserve stem cells, they form organoids niche-independently, owing to their ability to recreate the Paneth cell niche. Mechanistically, mitochondria in ISCmito-O generate more alpha-ketoglutarate (aKG), driving ten-eleven translocation (Tet) methylcytosine dioxygenase-mediated epigenetic changes that are associated with differentiation towards the Paneth cell fate. aKG supplementation in vivo promotes Paneth cell turnover leading to niche renewal, which promotes recovery from chemotherapy-induced damage in aged animals. Our results reveal a subpopulation of intestinal stem cells whose old mitochondria metabolically regulate cell fate, and provide proof-of-principle for metabolically promoted replacement of specific aged cell types in vivo.

2025-04-24 | MTBLS12349 | MetaboLights

RNA-Seq of single cells from the Arabidopsis root

Project description:The definition of cell identity is a central problem in biology. Single-cell RNA-seq provides a wealth of information regarding the developmental state of individual cells. However, better methods are needed to map the identity of single cells, especially during identity transitions. We have developed a quantitative classification method that is robust to expression noise and can detect primary and chimeric identities from single-cell RNA sequencing profiles. The method uses existing transcriptome repositories of grouped cell-types to define a set of optimal cell-identity markers, which are then used to define a cell identity metric. This metric accurately classified diverse cell identities in Arabidopsis root tips and human glioblastoma cells. We demonstrate the strength of the approach to resolve a dynamic developmental process by analyzing the identity of single cells captured from regenerating Arabidopsis roots following removal of their stem-cell-niche. We discover that, apart from new niche formation at the vicinity of the cut site, cells that are distant from the injury site also undergo a transient, partial collapse of identity during the regeneration and reorganization of the root, demonstrating the usefulness of a quantitative cell identity metric. Overall design: 4 Technical replicates (pooled-and-split single QC cells), 23 cells from the QC, 3 cells from the Stele, and 4 cells from the stele, 16h following root tip decapitation

2015-03-12 | E-MTAB-4125 | biostudies-arrayexpress

A dual genetic constraint underlies the conservation of early brains in vertebrates

Project description:As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplan’s power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint—neuromeric identity and pleiotropic stemness—that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems.

2026-03-15 | E-MTAB-16735 | biostudies-arrayexpress

Differential expression of stem cell-specific genes in P7 and P28 dentate gyrus neural progenitors

2009-03-11 | GSE15085 | GEO