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A combined N-terminomics and shotgun proteomics approach to investigate the responses of human cells to rapamycin and zinc at the mitochondrial level

ABSTRACT: This study aims at investigating the impact of rapamycin and zinc at subtoxic doses on the human mitochondrial proteome. Experiments were performed on U397 monocytic cells. A dN-TOP strategy, combining shotgun proteomics and N-terminomics, was applied to study both internal and N-terminal peptides of the mitochondrial proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Monocyte, Cell Culture

SUBMITTER: Joanna Bons

LAB HEAD: Christine CARAPITO

PROVIDER: PXD010220 | Pride | 2019-05-14

REPOSITORIES: pride

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Publications

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level.

Bons Joanna J Macron Charlotte C Aude-Garcia Catherine C Vaca-Jacome Sebastian Alvaro SA Rompais Magali M Cianférani Sarah S Carapito Christine C Rabilloud Thierry T

Molecular & cellular proteomics : MCP 20190315 6

All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coupled with the cleavage of a presequence called the transit peptide, and the formation of a new N-terminus. Determination of the neo N-termini has been investigated by proteomic approaches in several systems, but generally in a static way to compile as many N-termini as possi ...[more]

PMID: 31154437

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A combined N-terminomics and shotgun proteomics approach to investigate the responses of human cells to rapamycin and zinc at the mitochondrial level

Project description:This study aims investigating the impact of rapamycin and zinc at subtoxic doses on the human mitochondrial proteome. Experiments were performed on U397 monocytic cells. A dN-TOP strategy, combining shotgun proteomics and N-terminomics, was applied to study both internal and N-terminal peptides of the mitochondrial proteins.

2019-05-14 | PXD010572 | Pride

RNA-sequencing of 465 lymphoblastoid cell lines from the 1000 Genomes

Project description:10.1038/nature12531

2012-11-06 | E-GEUV-1 | biostudies-arrayexpress

RNA-sequencing and small RNA-sequencing of 465 lymphoblastoid cell lines from the 1000 Genomes

Project description:This RNA sequencing data set of 465 human lymphoblastoid cell line samples from the CEU, FIN, GBR, TSI and YRI populations from the 1000 Genomes sample collection was created by the Geuvadis consortium (www.geuvadis.org, http://www.geuvadis.org/web/geuvadis/our-rnaseq-project). The data is under embargo until the first publication by the investigators in early 2013. This accession contains all mRNA and small RNA sequencing data, clean data that passed QC and other filters are available under accession E-GEUV-1, E-GEUV-2.

2012-12-06 | E-GEUV-3 | biostudies-arrayexpress

Effect of rapamycin on murine subcutaneous MC38 tumor cell populations

Project description:To determine differential metabolic gene expression in distinct cell populations from subcutaneous MC38 tumors at baseline and in response to rapamycin, tumors from mice treated with vehicle or rapamycin were harvested, reconstituted to single cell suspensions, and flow sorted into cancer cell (CD45-), tumor-associated macrophage (TAM, CD45+ CD11b+ Ly6G- Ly6C lo F4/80 hi), monocytic myeloid-derived suppressor cell (M-MDSC, CD45+ CD11b+ Ly6G- Ly6C hi), CD8 T cell (CD45+ CD3+ CD8a+), and CD4 T cell (CD45+ CD3+ CD8a-) populations. RNA was extracted and transcripts were quantified by the NanoString nCounter Metabolic Pathways Panel.

2021-02-26 | GSE165223 | GEO

Gene expression profile of TRAIL-sensitive and -resistant H460 cells

Project description:We generated H460 cells with acquired TRAIL resistance by exposing the parental sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the gene expression profile of the sensitive versus the resistant cells. We generated acquired TRAIL-resistant H460 cells from the sentisitve cells by treating subtoxic range of TRAIL for 6 month. And we tried to compare the expressional profile of the genes between two cell types to isolate genes regulating acquired TRAIL-resistance H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the gene expression profile was analyzed.

2014-09-01 | E-GEOD-55859 | biostudies-arrayexpress

Gene expression profile of TRAIL-sensitive and -resistant H460 cells

2014-09-01 | GSE55859 | GEO

Gene regulation in Arabidopsis by isothiocyanates

Project description:in Brassicaceae isothiocyanates are generated by metabolism of endogenous glucosinulates regulation of gene expression by subtoxic concentrations of isothiocyanates was investigated

2020-06-14 | GSE117869 | GEO

MicroRNA expression profile in TRAIL-sensitive and -resistant H460 cells

Project description:We generated H460 cells with acquired TRAIL resistance by exposing the parental sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the microRNA expression profile in the sensitive versus resistant cells. H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the microRNA expression profile was analyzed using the NanoString technology.

2014-09-01 | E-GEOD-55821 | biostudies-arrayexpress

Cross-species transcriptional networks in Diabetic Glomerulopathy in mouse and man

Project description:Murine models have been valuable instruments in defining the pathogenesis of diabetic nephropathy (DN), but they only partially recapitulate disease manifestations of human DN, limiting their utility . In order to define the molecular similarities and differences between human and murine DN, we performed a cross-species comparison of glomerular transcriptional networks. Glomerular gene expression was profiled in patients with early type 2 DN and in three mouse models (streptozotocin DBA/2 mice, db/db C57BLKS, and eNOS-deficient C57BLKS db/db mice). Species-specific transcriptional networks were generated and compared with a novel network-matching algorithm. Three shared, human-mouse cross-species glomerular transcriptional networks containing 143 (Human-STZ), 97 (Human- db/db), and 162 (Human- eNOS-/- db/db) gene nodes were generated. Shared nodes across all networks reflected established pathogenic mechanisms of diabetic complications, such as elements of JAK-STAT and VEGFR signaling pathways . In addition, novel pathways not formally associated with DN and cross-species gene nodes and pathways unique to each of the human-mouse networks were discovered. The human-mouse shared glomerular transcriptional networks will assist DN researchers in the selection of mouse models most relevant to the human disease process of interest. Moreover, they will allow identification of new pathways shared between mice and humans. We used microarrays to analyze the transcriptome of three different diabetic mouse models Glomerular RNA was extracted using the RNeasy Mini Kit and processed for hybridization on Affymetrix GeneChip Mouse Genome 430 2.0 microarrays.

2012-12-10 | E-GEOD-33744 | biostudies-arrayexpress

Investigating HMGB1 as a Potential Serum Biomarker for Early Diabetic Nephropathy Monitoring by Quantitative Proteomics

Project description:Current diagnostic methods for diabetic nephropathy (DN) lack precision, especially in early stages and monitoring progression. This study aims to find potential biomarkers for DN progression and evaluate their accuracy. Using serum samples from healthy controls (NC), diabetic patients (DM), early-medium stage DN (DN-EM), and late-stage DN (DN-L), researchers employed quantitative proteomics and Mfuzz clustering analysis revealed 15 proteins showing increased expression during DN progression, hinting at their biomarker potential. Combining Mfuzz clustering with weighted gene co-expression network analysis (WGCNA) highlighted five candidates (HMGB1, CD44, FBLN1, PTPRG, and ADAMTSL4). HMGB1 emerged as a promising biomarker, closely correlated with renal function changes. Experimental validation supported HMGB1’s upregulation under high glucose conditions, reinforcing its potential as an early detection biomarker for DN. This research advances DN understanding and identifies five potential biomarkers, notably HMGB1, as a promising early monitoring target. These findings set the stage for future clinical diagnostic applications in DN.

2023-12-28 | PXD047872 | Pride

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