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Proteomic profile of the early transition from naïve to primed pluripotency in mouse ES cells

ABSTRACT: We describe here the proteome of mouse embryonic stem cells growth in complete media (KSR, LIF/2i) or media without 2i for 24h and 48h.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Stem Cell

SUBMITTER: Rui Vitorino

LAB HEAD: Bruno Jesus

PROVIDER: PXD033005 | Pride | 2025-06-23

REPOSITORIES: Pride

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			Action	DRS
	2021MQ038_BRBE_001_01_1ug.raw	Raw
	2021MQ038_BRBE_002_01_1ug.raw	Raw
	2021MQ038_BRBE_003_01_1ug.raw	Raw
	2021MQ038_BRBE_004_01_1ug.raw	Raw
	2021MQ038_BRBE_005_01_1ug.raw	Raw

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1 - 5 of 14

Publications

Claudin-6 mediates an embryonic stem cell-driven antitumor response against breast cancer.

Correia Magda M Tavares-Marcos Carlota C Pessoa João J Casanova Miguel M Cavadas Bruno B Vitorino Rui R Tavares E Silva Júlia J Mateus Francisca F Espadas Guadalupe G Pinheiro Mariana M Alves-Vale Catarina C Sabidó Eduard E Neves Bruno B Nóbrega-Pereira Sandrina S Bernardes de Jesus Bruno B

iScience 20250516 6

Stem cells are emerging sources of antigens for cancer immunotherapy. Here, we used TNG-A mouse embryonic stem cells to trigger an anticancer response against tumors derived from E0771 mouse breast cancer cells, possibly mediated by the mouse immune system. TNG-A cells were cultured in the presence or absence of two specific kinase inhibitors. While the inhibitors preserved TNG-A pluripotency, their removal altered the morphology, transcriptome, and proteome of TNG-A cells, increasing their simi ...[more]

PMID: 40520090

Similar Datasets

Diabetes disturbs protein secretome of human adipose-derived stem cells and promotes tumorogenesis in hepatic cancer cells

Project description:Metabolic disorders impact adipose-derived stem cells (ASCs), which play a central role in adipose tissue (AT) homeostasis but might also regulate tumour microenvironments via paracrine signalling routes. Here, we aimed to determine whether type 2 diabetes (T2D) disturbs the protein secretome of human ASCs, and its potential relevance for their pro-tumoral activity. An untargeted proteomics approach by liquid chromatography coupled to tandem mass spectrometry was used to analyse the secretome of ASCs isolated from the subcutaneous AT of subjects with and without T2D. Out of 231 quantified proteins, 52 factors were found differentially secreted on T2D-ASCs. In silico studies revealed that only 46,7% of the total proteins identified used the conventional secretory pathway. Network analysis showed up-secreted factors in T2D were implicated in immune system processes, extracellular matrix organization and endoplasmic reticulum stress. We found that diabetic ASCs secretome increases some inflammatory-, invasiveness- and epithelial-to-mesenchymal transition-related markers in HepG2 cells, an effect that was blocked with an anti-SUB1 antibody. Remarkably, SUB1 neutralization also inhibited invasive capacities of HepG2 in response to T2D-ASCs secretome. Overall, our study demonstrates that T2D-ASCs show an aberrant protein secretome and although further studies will be needed to understand the pathogenic consequences of this disturbance, our findings suggest that SUB1 might serve as a novel molecular link in the interplay between ASCs and tumor cells.

2022-06-03 | PXD029829 | Pride

New ruthenium-cyclopentadienyl complexes affect colorectal cancer hallmarks showing high therapeutic potential

Project description:Colorectal cancer (CRC) is one of the most lethal cancers worldwide. Current therapeutic strategies are accompanied by low success rates and several side effects, representing a relevant clinical problem and requiring the discovery of new and more effective therapeutic alternatives. Ruthenium drugs emerged as one of the most promising metallodrugs due to their high selectivity to cancer cells. In this work, we studied for the first time the anticancer properties and mechanisms of action of four lead Ru-cyclopentadienyl compounds, namely PMC79, PMC78, LCR134 and LCR220, in CRC-derived cell lines. Biological assays were performed in CRC cell lines to evaluate cellular distribution, colony formation, cell cycle, proliferation, apoptosis, motility as well as cytoskeleton and mitochondrial alterations. Our results showed that all compounds displayed high bioactivity and selectivity, as shown by low IC50 concentrations against CRC cells. We observed that all Ru compounds had different intracellular distributions and inhibited to a high extent the clonogenic ability and proliferation of CRC cells. In addition, PMC79, LCR134 and LCR220 induced apoptosis, increased the levels of reactive oxygen species, induced mitochondrial alterations and affected F-actin cytoskeleton organization and cellular motility. A proteomic analysis showed that these compounds induce alterations in several cellular proteins related to the phenotypic alterations induced. Overall, we demonstrated that Ru compounds, in special PMC79 and LCR220, present promising anticancer activity in CRC cells and potential to be used as new metallodrugs for CRC therapy.

2023-07-20 | PXD041324 | Pride

Quantitative proteome analysis of LAP1-deficient human fibroblasts reveals key signaling pathways deregulated in LAP1-associated diseases

Project description:Lamina-associated polypeptide 1 (LAP1), a ubiquitously expressed nuclear envelope protein, seems to be essential for the maintenance of cell homeostasis. Although rare, mutations in the human LAP1-encoding TOR1AIP1 gene have been associated to the development of many severe pathologies (e.g. dystonia, myasthenic syndrome, muscular dystrophy, cardiomyopathy and multisystemic syndrome), which can culminate in the premature death of affected individuals. Despite recent evidence of the pathogenicity of TOR1AIP1 genetic alterations, a knowledge gap still exists regarding the physiological roles of LAP1 and, therefore, additional investigation is required to fully understand its biological relevance. To this end, a quantitative proteome analysis of patient-derived skin fibroblasts carrying a pathological TOR1AIP1 mutation (LAP1 E482A), which had been linked to strongly reduced LAP1 protein levels, was carried out. Using the liquid chromatography with tandem mass spectrometry (LC–MS/MS) technology, 386 differentially expressed proteins were found in LAP1 E482A fibroblasts relative to control fibroblasts. A bioinformatic analysis of the LC–MS/MS-identified differentially expressed proteins revealed several biological processes misregulated as a result of human LAP1 deficiency, such as DNA repair, messenger RNA degradation, proteostasis, glutathione metabolism/response to oxidative stress, neuronal development and muscle contraction, among others. Besides shedding light on potential new LAP1’s functions, this work also provides valuable clues about key signaling pathways that may be targeted in disease-modifying therapies for LAP1-associated disorders.

2024-06-27 | PXD035200 | Pride

Proteomic profile of human breast cancer cells expressing normal levels or absent of the long non-coding RNA NORAD.

Project description:We describe here the proteome of the human breast cancer cell line MDA-MB-231 expressing normal levels of the lncRNA NORAD, or after knock-down NORAD with siRNA and LNA gapmers.

2023-08-28 | PXD039920 | Pride

Mycoplasma pneuminiae and Mycoplasma agalactiae Proteomics

Project description:During evolution, each bacterial strain shapes its metabolism in order to colonise a diversity of niches. Unraveling the biochemical reactions underlying bacteria metabolism is important for biotechnological purposes and for understanding relationships within a complex microbiome as well as the microbiome’s connection with its host. Here we propose a new approach to identifying active metabolic pathways, by integrating essentiality analysis and protein abundance. As an example, we used two bacterial species (Mycoplasma pneumoniae and Mycoplasma agalactiae) that share a high gene similarity yet show significant metabolic differences. After integrating all available metabolic knowledge about their enzymes, metabolites and reactions, we built detailed metabolic maps of their carbon metabolism. We determined the carbon sources that allow growth in M. agalactiae (as known for M. pneumoniae) and introduced glucose-dependent growth in M. agalactiae. By analyzing gene essentiality and performing quantitative proteomics, we could predict the active metabolic pathways and directionalities for the sugar, phospholipids, DNA/RNA precursors, glycoproteins, and glycolipids metabolism of these two bacteria. Comparison between predicted and experimentally determined active pathways shows an excellent agreement. Thus, protein essentiality profiling using transposon sequencing analysis combined with quantitative proteomics and metabolic maps could be used to determine and engineer metabolic fluxes.

2020-06-08 | PXD015800 | Pride

LAP1 interactome profiling provides new insights into LAP1’s physiological functions

Project description:The nuclear envelope (NE), a protective membrane bordering the nucleus, is composed of highly specialized proteins that are indispensable for normal cellular activity. Lamina-associated polypeptide 1 (LAP1) is a NE protein whose functions are just beginning to be unveiled. The fact that mutations causing LAP1 deficiency are extremely rare and pathogenic is indicative of its paramount importance to preserve human health, anticipating that LAP1 might have a multifaceted role in the cell. Mapping the LAP1 protein interactome is, thus, imperative to achieve an integrated view of its potential biological properties. To this end, we employed in silico- and mass spectrometry-based approaches to identify candidate LAP1-interacting proteins, whose functional attributes were subsequently characterized using bioinformatics tools. Our results suggest that LAP1 may participate in cellular processes as diverse as chromatin and cytoskeleton organization, DNA repair, RNA processing, translation as well as protein biogenesis and turnover. Novel interactions between LAP1 and DNA repair proteins were additionally validated, strengthening the previously proposed involvement of LAP1 in the maintenance of genomic stability. Overall, the data presented in this study reaffirm the biological relevance of LAP1 and the need to deepen our knowledge about this NE protein, providing new insights that will help guiding future research towards a mechanistic understanding of LAP1’s functioning.

2025-01-13 | PXD056445 | Pride

Transcriptome and Micronome analysis of OPLL

Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. MicroRNAs are small nucleatides that function as regulators of gene expression in almost any biological process. However, few microRNAs are reported to have a role in the pathological process of OPLL. Therefore, we performed high-throughput microRNA sequencing and transcriptome sequencing of primary OPLL and PLL cells in order to decipher the interacting network of microRNAs in OPLL. MRNA and microRNA profiles were done using primary culture cells of human ossification of the posterior longitudinal ligament (OPLL) tissue and normal posterior longitudinal ligament (PLL) tissue.

2016-04-04 | E-GEOD-69787 | biostudies-arrayexpress

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

Project description:Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde crosslinking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organisation, but this has not been tested extensively. We investigate the murine HoxD locus with 5C and FISH in different developmental and activity states, and in the presence or absence of epigenetic regulators. We identify situations where the two datasets are concordant, but find other conditions where chromatin topographies extrapolated from 5C or FISH data are not compatible. We conclude that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart – influenced by nuclear environment and chromatin composition. We conclude that results obtained at high-resolution with either 3C methods or by FISH alone must be interpreted with caution and that conclusions about genome organisation should be validated by independent methods. 5C oligonucleotides were designed around EcoRI restriction sites following an alternative scheme

2015-01-02 | E-GEOD-61814 | biostudies-arrayexpress

PRM of eGFP and mCherry in human cells

Project description:We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. In particular, we detect two clusters of tissues with an opposite pattern of codon preferences. We then use the identified patterns for the development of CUSTOM (https://custom.crg.eu), a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In a human cell model, we provide evidence that codon optimization should indeed take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles.

2023-02-24 | PXD037866 | Pride

Transcriptome analysis of Advanced glycation end products treated ligament cells

Project description:Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. Recently, disorders of metabolism are thought to be the center of many diseases such as OPLL. Advanced glycation end product (AGE) are accumulated in many extracellular matrixes such as ligament fibers, and it can functions as cellular signal through its receptor (RAGE), contributing to various events such as atherosclerosis or oxidative stress. However, its role in OPLL formation is not yet known. Therefore, we performed high-through-put RNA sequencing on primary posterior longitudinal ligament cells treated with different doses of AGEs (1ÂµM, 5ÂµM and negative control), with or without BMP2 (1ÂµM). mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1ÂµM AGE-BSA, 5ÂµM AGE-BSA, 1ÂµM AGE-BSA with BMP2, 5ÂµM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton

2016-02-16 | E-GEOD-65952 | biostudies-arrayexpress

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