Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA648429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12319600_1.fastq.gz | Fastqsanger.gz | |||
| SRR12319600_2.fastq.gz | Fastqsanger.gz | |||
| SRR12319700_1.fastq.gz | Fastqsanger.gz | |||
| SRR12319700_2.fastq.gz | Fastqsanger.gz | |||
| SRR12319800_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1536 |
Similar Datasets
Project description:Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, we perform single cell RNA-sequencing of 26,515 cells (including 8,433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-gamma and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4,648 BC patients reveals that treatment with metformin (an indirect PPAR-gamma agonist) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-gamma link for BC treatment.
2022-08-02 | GSE155109 | GEO
Project description:Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, here we perform single cell RNA-sequencing of 26,515 cells (including 8433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-γ and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4648 BC patients reveals that treatment with metformin (an indirect PPAR-γ signaling activator) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-γ link for BC treatment.
| S-EPMC9489707 | biostudies-literature
Project description:Distinct immunomodulatory pathways mediate radiotherapy response in malignant peripheral nerve sheath tumors [scRNA-Seq]
| PRJNA1221551 | ENA
Project description:Distinct immunomodulatory pathways mediate radiotherapy response in malignant peripheral nerve sheath tumors [sgRNA library]
| PRJNA1221552 | ENA
Project description:<p>The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.</p>
2026-02-28 | MTBLS13927 | MetaboLights
Project description:Lipid metabolism plays a critical role in the progression of cancers, including glioblastoma (GBM). Tumor necrosis factor-α (TNF-α) exhibits a dual role in the tumor microenvironment: at high concentrations, it induces cell death and exerts anti-tumor effects, while at low doses, it demonstrates pro-tumorigenic activity. This study investigates the regulatory effects of low-dose TNF-α on the malignant behavior and lipid metabolism of GBM. The results show that low-dose TNF-α (10 ng/mL) significantly promotes GBM cell Malignant phenotypes and lipid droplet accumulation via the TNFR signaling pathway, a process dependent on its downstream adaptor protein, Tumor necrosis factor receptor-associated factor 2 (TRAF2). Mechanistically, TRAF2 interacts with Fatty acid synthase (FASN) through its TRAF domain and, serving as an E3 ubiquitin ligase, leverages its RING domain to mediate K63-linked polyubiquitination of FASN. This enhances FASN protein stability, promotes lipid synthesis, and ultimately drives tumor progression. Furthermore, through virtual screening, the small-molecule compound Jionoside B1 was identified to target the RING domain of TRAF2, effectively inhibiting K63-linked ubiquitination of FASN and disrupting the TRAF2–FASN interaction and protein accumulation. In both in vitro and in vivo experiments, Jionoside B1 significantly suppressed lipid synthesis and attenuated tumor growth. This study systematically elucidates the mechanism by which low-dose TNF-α regulates lipid metabolism and promotes GBM malignant progression via the TRAF2–FASN axis, providing not only new insights into the "double-edged sword" role of TNF-α in the tumor microenvironment but also a potential novel therapeutic strategy for targeting this pathway in GBM treatment.
2026-02-04 | GSE318064 | GEO
Project description:Maternal obesity and gestational diabetes mellitus (GDM) are associated with adverse intrauterine environments that are high in circulating nutrients. These adverse environments facilitate impairments in placental mitochondrial function and nutrient processing that ultimately leads to an increased risk of the exposed offspring developing non-communicable cardiometabolic health disorders (e.g. obesity, type 2 diabetes, metabolic syndrome). Analysis of fasting serum lipid levels in the third trimester has highlighted that Palmitate (PA) and oleate (OA) are the most abundance non-esterified fatty acids (NEFAs) in circulation. More importantly, these important NEFAs are elevated in both obese and GDM pregnancies. As PA and OA are the most abundant NEFAs in the typical “Westernized Diet” they elevated levels in obese and GDM pregnancies may highlight increased maternal consumption of these fats and could be a link between poor diet and abberant placental function. However, the independent and combined impacts of dietary PA and OA on mitochondrial function and nutrient processing in placental trophoblast cells remains poorly defined. Thus, in this study we sought to utilize a multi-omics approach (combining transcriptomics with untargeted metabolomics and lipidomics) to elucidate the underlying impacts of elevated NEFA levels on BeWo placental trophoblast cells. We highlighted a significant enrichment in the Wikipathways Fatty Acid Biosynthesis Pathway in BeWo cytotrophoblast cells treated with a combination of PA and OA (P/O; 50 µM each). Further, we identified differential expression of genes involved in lipid processing (e.g. ACADVL, ACACB, ACSL5, CREB3L3, PLIN2, and SCD) in BeWo cytotrophoblast cells treated with dietary NEFA species. Overall, these data highlighted that alterations in lipid processing, storage, and oxidation are implicated in the development of placental dysfunction in response to elevated lipid levels.
2023-08-30 | GSE197385 | GEO
Project description:The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.
2026-02-16 | GSE319369 | GEO
Project description:The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.
2026-02-20 | GSE319557 | GEO
Project description:Cell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex [Patch-seq]
| PRJNA1423173 | ENA