Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376708 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ribosomal protein (RP) L23 is a negative regulator of cell apoptosis. RPL23 overexpression is associated with abnormal apoptotic resistance in CD34+ cells derived from patients with higher-risk myelodysplastic syndrome (MDS). However, the mechanism underlying RPL23-induced apoptotic resistance in higher-risk MDS patients is poorly understood. Gene microarray analysis between RPL23-knockdown (RPL23-KD) and matched control cells (RPL23-NC) was performed to detail global gene expression profiles and to identify differentially expressed genes and potentially involved pathways associated with RPL23 knockdown.
2017-02-25 | GSE95348 | GEO
Project description:Beta-hydroxybutyrate (BHB) is a ketone body synthesized during fasting or strenuous exercise. Our previous study demonstrated that a cyclic ketogenic diet (KD), which induces BHB levels similar to fasting every other week, reduces midlife mortality and improves memory in aging mice. BHB actively regulates gene expression and inflammatory activation through non-energetic signaling pathways. Neither of these activities has been well-characterized in the brain and they may represent mechanisms by which BHB affects brain function during aging. First, we analyzed hepatic gene expression in an aging KD-treated mouse cohort using bulk RNA-seq. In addition to the downregulation of TOR pathway activity, cyclic KD reduces inflammatory gene expression in the liver. We observed via flow cytometry that KD also modulates age-related systemic T cell functions. Next, we investigated whether BHB affects brain cells transcriptionallyin vitro. Gene expression analysis in primary human brain cells (microglia, astrocytes, neurons) using RNA-seq shows that BHB causes a mild level of inflammation in all three cell types. However, BHB inhibits the more pronounced LPS-induced inflammatory gene activation in microglia. Furthermore, we confirmed that BHB similarly reduces LPS-induced inflammation in primary mouse microglia and bone marrow-derived macrophages (BMDMs). BHB is recognized as an inhibitor of histone deacetylase (HDAC), an inhibitor of NLRP3 inflammasome, and an agonist of the GPCR Hcar2. Nevertheless, in microglia, BHB's anti-inflammatory effects are independent of these known mechanisms. Finally, we examined the brain gene expression of 12-month-old male mice fed with one-week and one-year cyclic KD. While a one-week KD increases inflammatory signaling, a one-year cyclic KD reduces neuroinflammation induced by aging. In summary, our findings demonstrate that BHB mitigates the microglial response to inflammatory stimuli, like LPS, possibly leading to decreased chronic inflammation in the brain after long-term KD treatment in aging mice.
2024-01-31 | GSE252513 | GEO
Project description:Counterintuitively, increased tumour predisposition is associated with ribosomal protein (RP) loss. Here, we provide the first evidence that RP depletion can directly drive tissue overgrowth. Haematopoietic compartment-specific knockdown (KD) of RpS19a in the Drosophila lymph gland not only results in haematopoietic stem and progenitor cell (HSPC) loss but also drives excess proliferation and tissue overgrowth. In accordance with continued ribosome assembly and protein synthesis, actively translating ribosomes (polysomes) are detected in RpS19a KD Drosophila S2 cells. The RpS19a KD ribosomes do, however, display heterogeneity and significantly altered stoichiometry of the associated translation initiation factors eIF4A and eIF5. Consistent with altered translation, in addition to increased association between polysomes and mRNA encoding growth promoting genes (e.g. Ras), we observe increased abundance of the ortholog of ribosomal (r)RNA small subunit methyltransferase NEP1. Although uncharacterised in Drosophila, in yeast and human NEP1 is implicated in methylation of 18S rRNA and, thus, 40S assembly and 80S ribosome stability. Moreover, NEP1 (EMG1) mutations in humans underpin Bowen-Conradi syndrome, a ribosomopathy associated with developmental defects, growth failure, and infantile death. Remarkably, NEP1 depletion suppresses the RpS19a KD phenotype, restoring both stem and progenitor cells and suppressing lymph gland overgrowth. We further demonstrate NEP1 depletion significantly decreases methylation of the 18S rRNA residue (Ψ1,279) that is implicated in ribosome assembly. Together, these data suggest the increased NEP1 expression associated with RpS19a KD promotes assembly of pro-proliferative “onco-ribosomes” to drive haematopoietic compartment overgrowth.
2024-06-30 | GSE236310 | GEO
Project description:Counterintuitively, increased tumour predisposition is associated with ribosomal protein (RP) loss. Here, we provide the first evidence that RP depletion can directly drive tissue overgrowth. Haematopoietic compartment-specific knockdown (KD) of RpS19a in the Drosophila lymph gland not only results in haematopoietic stem and progenitor cell (HSPC) loss but also drives excess proliferation and tissue overgrowth. In accordance with continued ribosome assembly and protein synthesis, actively translating ribosomes (polysomes) are detected in RpS19a KD Drosophila S2 cells. The RpS19a KD ribosomes do, however, display heterogeneity and significantly altered stoichiometry of the associated translation initiation factors eIF4A and eIF5. Consistent with altered translation, in addition to increased association between polysomes and mRNA encoding growth promoting genes (e.g. Ras), we observe increased abundance of the ortholog of ribosomal (r)RNA small subunit methyltransferase NEP1. Although uncharacterised in Drosophila, in yeast and human NEP1 is implicated in methylation of 18S rRNA and, thus, 40S assembly and 80S ribosome stability. Moreover, NEP1 (EMG1) mutations in humans underpin Bowen-Conradi syndrome, a ribosomopathy associated with developmental defects, growth failure, and infantile death. Remarkably, NEP1 depletion suppresses the RpS19a KD phenotype, restoring both stem and progenitor cells and suppressing lymph gland overgrowth. We further demonstrate NEP1 depletion significantly decreases methylation of the 18S rRNA residue (Ψ1,279) that is implicated in ribosome assembly. Together, these data suggest the increased NEP1 expression associated with RpS19a KD promotes assembly of pro-proliferative “onco-ribosomes” to drive haematopoietic compartment overgrowth.
2024-06-30 | GSE236307 | GEO
Project description: Not available
| S-EPMC2531291 | biostudies-literature
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have challenged this dogma by preserving ribosomal RNA (rRNA) in our samples and by lowering the minimal RNA size window of our small RNA-Seq analyses to 8 nt
2022-09-01 | GSE179678 | GEO
Project description: Not available
| S-EPMC4686780 | biostudies-literature
Project description: Not available
| S-EPMC3743458 | biostudies-literature
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
2010-09-25 | GSE24338 | GEO