Similar Datasets
Project description:Metabolomics and metagenomics-combined study to diagnose colorectal cancer using gut-microbiome-secreted extracellular vesicles
2020-01-14 | ST001307 | MetabolomicsWorkbench
Project description:Human neurodevelopment requires differentiating neurons to establish large networks of connections in a highly stereotyped manner. Neuronal differentiation in particular requires RNA-binding proteins to spatiotemporally regulate thousands of different mRNAs. Yet how these proteins precisely relate to neuronal development and coordinate the expression of functionally coherent genes in a cell type specific manner is only partially understood. To address this, we sought to clarify how the paradigmatic RNA-binding protein IMP1/IGF2BP1, an essential developmental factor, selects and regulates its RNA targets transcriptome-wide during the differentiation of human pluripotent stem cell-derived neural precursor cells to their neuronal counterparts. We used a combination of systemic and molecular analyses to show that IMP1 directly binds to and regulates the expression of a large sets of mRNAs.
2024-04-13 | GSE203570 | GEO
Project description:Human neurodevelopment requires differentiating neurons to establish large networks of connections in a highly stereotyped manner. Neuronal differentiation in particular requires RNA-binding proteins to spatiotemporally regulate thousands of different mRNAs. Yet how these proteins precisely relate to neuronal development and coordinate the expression of functionally coherent genes in a cell type specific manner is only partially understood. To address this, we sought to clarify how the paradigmatic RNA-binding protein IMP1/IGF2BP1, an essential developmental factor, selects and regulates its RNA targets transcriptome-wide during the differentiation of human pluripotent stem cell-derived neural precursor cells to their neuronal counterparts. We used a combination of systemic and molecular analyses to show that IMP1 directly binds to and regulates the expression of a large sets of mRNAs.
2024-04-13 | GSE203569 | GEO
Project description:Human neurodevelopment requires differentiating neurons to establish large networks of connections in a highly stereotyped manner. Neuronal differentiation in particular requires RNA-binding proteins to spatiotemporally regulate thousands of different mRNAs. Yet how these proteins precisely relate to neuronal development and coordinate the expression of functionally coherent genes in a cell type specific manner is only partially understood. To address this, we sought to clarify how the paradigmatic RNA-binding protein IMP1/IGF2BP1, an essential developmental factor, selects and regulates its RNA targets transcriptome-wide during the differentiation of human pluripotent stem cell-derived neural precursor cells to their neuronal counterparts. We used a combination of systemic and molecular analyses to show that IMP1 directly binds to and regulates the expression of a large sets of mRNAs.
2024-04-13 | GSE203568 | GEO
Project description:Isolation of IMP1 bound mRNAs. Flag-tagged IMP1 was expressed in HEK293 cells. Flag tagged IMP1 was immunoprecipitated and mRNAs isolated. As controls HEK293 cells that do not express Flag-tagged IMP1 was included.
2006-12-31 | E-MEXP-841 | biostudies-arrayexpress
Project description:ZBP1/IMP1 is a RNA binding protein that post-transcriptionally regulates the expression of a handful mRNAs, implicated in maintaining cell polarity and adhesion. We have previously shown that ZBP1 was able to inhibit proliferation and invasiveness of breast carcinoma cells in vitro. To determine important LncRNA for breast tumor growth and metastasis in response to IMP1 expression, LncRNA expression data were obtained from, and compared between the breast cancer cell line MDA231-IMP1 and MDA231/GFP.
2016-12-09 | GSE91057 | GEO
Project description:Long noncoding RNAs (lncRNAs) have been shown to play important roles in diverse biological process, including embryonic development and cell differentiation. Extensive studies have revealed the function and mechanism of those lncRNAs adjacent to protein-coding genes (PCGs), but there are relatively fewer reports about the lncRNAs within gene desert, particularly in human early germ layer differentiation. Here based on transcriptome analysis during human definitive endoderm (DE) differentiation, we identified a “desert” lncRNA named CTD-2501M5.1, a cytoplasm-located transcript with no protein-coding gene nearby within the 50 kb genomic region, highly expressed in human definitive endoderm. Depletion of CTD-2501M5.1 by either shRNA or promoter deletion could cause the deficiency of DE differentiation from human pluripotent stem cells (PSCs). The biochemical analysis showed that CTD-2501M5.1 functionally interacted with insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1, also named IMP1), which is necessary for endoderm differentiation demonstrated by loss-of-function assay. We further found depletion of CTD-2501M5.1 could result in reduced WNT signaling activities. More importantly, manipulating WNT activity by chemicals could rescue the phenotype of DE deficiency due to the depletion of CTD-2501M5.1 or IMP1. Mechanistically, CTD-2501M5.1 facilitated the interaction between IMP1 and FZD5 mRNA, stabilizing FZD5 which is required for WNT signaling activation and DE differentiation. Ultimately, our study not only revealed the biological function of a novel desert lncRNA CTD-2501M5.1 in human DE differentiation, but also underlined lncRNA-mediated mRNA stability regulation via IMP1.
2023-03-30 | GSE188501 | GEO
Project description:Extracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. We studied the gene expression changes in fibroblasts in the presence and absence pf CRC-derived EVs.
2019-02-25 | GSE114979 | GEO
Project description:Our study demonstrated that the expression of Igf2bp1 in activated microglia was significantly up-regulated, implying a role of Igf2bp1 in LPS-induced m6A modifications in microglia. To understand the roles of Igf2bp1 on LPS-induced m6A modification in microglia, we performed Igf2bp1 loss-of-function (LOF) approach. Microglia stimulated by LPS were transfected with either scrambled siRNA control or Igf2bp1 siRNA for 48 hours. To m6A modification profiles in control and Igf2bp1 LOF microglia were determined by MeRIP-seq analysis.
2022-12-31 | E-MTAB-11411 | biostudies-arrayexpress
Project description:Background: There is some evidence demonstrating the effect of psychological interventions in improvements in health biological parameters. To best of our knowledge, no study had addressed the impact of any psychological intervention on extracellular vesicles. In addition, Mindfulness-Based Cognitive Therapy (MBCT) and Emotion Focused Therapy for Cancer Recovery (EFT-CR) in the group have never been explored regarding extracellular vesicles and the effectiveness of these was not compared yet.
Objectives:
1. To explore and compare the effect of MBCT and EFT-CR on biological parameters and psychological variables in distressed people who have had breast, prostate and colorectal cancer;
2. In addition, we will explore the acceptability through recruitment and retention rates of MBCT and EFT-CR in group and evaluate whether these interventions are appropriate for a larger clinical trial.
Methods: The design of this study is a parallel randomized controlled trial. Participants will be randomized into MBCT, EFT-CR or usual care. Outcome measures will be assessed before, at the end of the intervention (8 weeks) and follow-ups (24 and 52 weeks from the baseline moment).
Hypotheses: The researchers expected that both interventions will have an effect on extracellular vesicles and other study biomarkers as well as improvements in psychological outcomes, compared to treatment as usual (TAU) group. Regarding the comparative effectiveness, we did not have evidence to hypothesize which one of the interventions will be superior in both biological (extracellular vesicles) and psychological outcomes.
Contribution for practice: The results of this preliminary study would permit to know if there are benefits of these psychological interventions on changes in extracellular vesicles and on psychological outcomes related to health. In addition, this study will permit to determine the acceptability of conducting a larger randomized controlled trial.
| 2332322 | ecrin-mdr-crc