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Mouse HSC proteomics in basal or 5FU activated conditions

ABSTRACT: Proteomics of hemaopoietic stem cells under basal or 5FU activated conditions

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Blood Cell, Bone Marrow

SUBMITTER: Ana Maria Cuervo

LAB HEAD: Ana Maria Cuervo

PROVIDER: PXD021340 | Pride | 2022-02-16

REPOSITORIES: Pride

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	proteomicsexp2.xlsx	Xlsx
	proteomicsexp3.xlsx	Xlsx

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Publications

Chaperone-mediated autophagy sustains haematopoietic stem-cell function.

Dong Shuxian S Wang Qian Q Kao Yun-Ruei YR Diaz Antonio A Tasset Inmaculada I Kaushik Susmita S Thiruthuvanathan Victor V Zintiridou Aliona A Nieves Edward E Dzieciatkowska Monika M Reisz Julie A JA Gavathiotis Evripidis E D'Alessandro Angelo A Will Britta B Cuervo Ana Maria AM

Nature 20210113 7848

The activation of mostly quiescent haematopoietic stem cells (HSCs) is a prerequisite for life-long production of blood cells<sup>1</sup>. This process requires major molecular adaptations to allow HSCs to meet the regulatory and metabolic requirements for cell division<sup>2-4</sup>. The mechanisms that govern cellular reprograming upon stem-cell activation, and the subsequent return of stem cells to quiescence, have not been fully characterized. Here we show that chaperone-mediated autophagy ( ...[more]

PMID: 33442062

Similar Datasets

Chaperone-mediated autophagy sustains hematopoietic stem cell function

Project description:Activation of mostly quiescent hematopoietic stem cells (HSC) is a prerequisite for life-long blood production1, 2. This process requires major molecular adaptations to meet the regulatory and metabolic requirements for cell division3-8. The mechanisms governing cellular reprograming upon stem cell activation and their subsequent return to quiescence are still not fully characterized. Here, we describe a role for chaperone-mediated autophagy (CMA)9, a selective form of lysosomal protein degradation, in sustaining adult HSC function. CMA is required for stem cell protein quality control and upregulation of fatty acid metabolism upon HSC activation. We identify that CMA activity decreases with age in HSC and show that genetic or pharmacological activation of CMA can restore functionality of old HSC. Together, our findings provide mechanistic insights into a new role for CMA in sustaining quality control, appropriate energetics and overall long-term hematopoietic stem cell function. Our work supports that CMA may be a promising therapeutic target to enhance hematopoietic stem cell function in conditions such as aging or stem cell transplantation.

2021-03-05 | PXD022196 | Pride

Transcription profiling of yeast with Anc1p or without under basal or MMS exposed conditions

Project description:We are investigating the transcriptional response of Anc1 deficient yeast under basal and MMS exposed conditions; We used microarrays to detail the global programme of gene expression underlying the MMS response in WT and Anc1 deficient yeast Experiment Overall Design: Yeast strains either WT or Anc1 deficient were exposed or unexposed to MMS

2008-11-13 | E-GEOD-12150 | biostudies-arrayexpress

basal

Project description:basal

| OEX00003098 | NODE

Proximity biotinylation of the Toxoplasma gondii basal complex

Project description:During T. gondii cell division (endodyogeny) the basal complex acts as the cytokinetic ring by preserving daughter bud integrity and executing the tapering and basal constriction of nascent parasites. Its molecular composition, order of assembly and mode of action are incompletely understood but differ substantially from final cytokinesis events described in other organisms. In order to identify new proteins of the basal complex we used proximity biotinylation (BioID) and fused the small biotin ligase BioID2 (Kim et al., 2016) to basal complex components (BCCs). We endogenously tagged MORN1, Centrin2 (Cen2), IMC8, MyoJ, BCC1 (TGGT1_232780) and BCC2 (TGGT1_231070) with BioID2 and used an YFP-BioID2 fusion protein as a cytosolic control. Our reciprocal BioID approach identifies several novel BCCs that resolve into four basal complex sub clusters (BCSC1-4). Together with the functional characterization of critical BCCs our data uncover a novel dimension to the hierarchy and structure of daughter budding.

2022-08-09 | PXD031116 | Pride

RNA-seq of mouse prostate basal cell organoids treated under different androgen and Wnt signaling conditions

Project description:To determine the role of Wnt and AR signaling pathway crosstalk on prostate basal stem cells, RNA-seq was performed for mouse prostate basal cell organoids treated under three conditions.

2023-06-28 | GSE220499 | GEO

Cargo and lipid profiling of isolated autophagosomes upon basal autophagy, starvation, and proteasome inhibition

Project description:Autophagy is responsible for degradation of an extensive portfolio of cytosolic cargoes that are engulfed in autophagosomes to facilitate their transport to lysosomes. Besides basal autophagy, which constantly degrades cellular material, the pathway is dynamically altered by different conditions, resulting in enhanced autophagosome formation and cargo turnover. The extensive profile of autophagosome content as well as the phospholipid composition of human autophagosome membranes remains elusive. Here, we introduce a novel FACS-based approach for isolation of native autophagosomes and confirm the quality and specificity of the preparations. Employing quantitative proteomics and lipidomics, we obtained a profound cargo and lipid profile of autophagosomes isolated upon basal autophagy conditions, nutrient deprivation, and proteasome inhibition. This resource will allow to identify the impact of different autophagy conditions on the degradation of distinct proteins and to dissect the phospholipid composition of the human autophagosome membrane in detail.

2022-10-06 | PXD024419 | Pride

Transcriptomic profiles of OASL knockdown HUVECs under basal or activated condition

Project description:Purpose: The goal of this study is to compare endothelial transcriptome affected by OASL knockdown under basal or stimulated conditions by utilizing RNA-seq. Methods: Endothelial mRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. Following an optimized data analysis workflow, RNA sequence reads were counted using StringTie-2.1.3b and used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs treated with or without TNFα and IFNγ. Results: DESeq2 was used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs under basal or stimulated conditions. Genes showing <10 read counts total were pre-filtered. Conclusions: Our study represents the first analysis of endothelial mRNA affected by OASL knockdown with biologic replicates, generated by RNA-seq.

2022-09-06 | GSE186352 | GEO

Correlation of global micro RNA expression with basal cell carcinoma subtype

Project description:Basal cell carcinomas (BCCs) are the most common cancers in the US. Histologic appearance distinguishes several subtypes, each of which can have a different biologic behavior. In this study global miRNA expression was quantified by high throughput sequencing in nodular BCCs, a subtype that is slow growing, and infiltrative BCCs, aggressive tumors that extend through the dermis and invade structures such as cutaneous nerves. Principal components analysis correctly classified seven out of eight infiltrative tumors on the basis of miRNA expression. The remaining tumor, on pathology review, contained a mixture of nodular and infiltrative elements. Nodular tumors did not cluster tightly, likely reflecting broader histopathologic diversity in this class, but trended toward forming a group separate from infiltrative BCCs. qPCR assays were developed for six of the miRNAs that showed significant differences between the BCC subtypes, and five of these six were validated in a replication set of four infiltrative and three nodular tumors. The expression level of miR-183, a miRNA that inhibits invasion and metastasis in several types of malignancies, was consistently lower in infiltrative than nodular tumors and could be one element underlying the difference in invasiveness. These results represent the first miRNA profiling study in BCCs and demonstrate that miRNA gene expression may be involved in tumor pathogenesis and particularly in determining the aggressiveness of these malignancies. Total RNA was extracted from eight nodular and eight infiltrative basal cell carcinomas. miRNA was then processed into libraries using the Illumina Small RNA Ver 1.5 protocol. Samples were then sequenced on the Illumina GAII system

2012-02-01 | E-GEOD-33665 | biostudies-arrayexpress

Frequent PTEN genomic alterations and activated PI3K pathway in basal-like breast cancer

Project description:Introduction Basal-like (BLCs) and epidermal growth factor receptor 2 overexpressing (HER2+) carcinomas are the subgroups of breast cancers which have the more aggressive clinical behavior. In contrast to HER2+ carcinomas, no targeted therapy is currently available for the treatment of patients with BLCs. In order to discover potential therapeutic targets, we searched for deregulated signaling pathways in human BLCs. Methods In this study, we focused on the oncogenic phosphatidylinositol 3-kinase (PI3K) pathway in twelve BLCs, and compared it to a control series of eleven hormonal receptor negative- and grade III- matched HER2+ carcinomas. The two tumor populations were first characterized by immunohistochemistry and gene expression. The PI3K pathway was then investigated by gene copy-number analysis, gene expression profiling and at a proteomic level using reverse phase protein array technology and tissue microarray. The effects of PI3K inhibition pathway on proliferation and apoptosis was further analyzed in three human basal-like cell lines. Results The PI3K pathway was found to be activated in BLCs and up-regulated compared to HER2+ tumors as shown by a significantly increased activation of the downstream targets Akt and mTOR. BLCs expressed significantly lower levels of the tumor suppressor PTEN and PTEN levels correlated negatively in a significant manner with Akt activity within that population. PTEN protein expression correlated significantly with PTEN DNA copy number and more importantly, reduced PTEN DNA copy numbers were observed specifically in BLCs. Similarly to human samples, basal-like cell lines exhibited an activation of PI3K / Akt pathway and low/lack PTEN expression. Both PI3K and mTOR inhibitors led to basal-like cell growth arrest. However, apoptosis was observed specifically after PI3K inhibition.

2008-12-03 | GSE13787 | GEO

Analysis of global gene expression profiles of A549 cells treated with TOP1 siRNA under basal conditions

Project description:Untransfected (no siRNA), control siRNA or TOP1 siRNA treated A549 cells were analyzed for gene expression differences under basal conditions

2016-07-11 | GSE52931 | GEO