Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stable Isotope Labeling by Amino acid in Vivo (SILAV)

ABSTRACT: Intravenous administration of stable isotope labeled amino acid ((13)C6-leucine) to humans recently made it possible to study the metabolism of specific biomarkers in plasma using High Resolution mass spectrometry (MS). This labeling approach could be of great interest for monitoring many leucine-containing peptides in parallel, using HRMS. This will make it possible to quantify the rates of synthesis and clearance of a large range of proteins in humans with a view to obtaining new insights into protein metabolism processes and the pathophysiology of diseases such as Alzheimer's disease.

ORGANISM(S): Homo Sapiens

SUBMITTER: Jerome VIALARET

PROVIDER: PXD046373 | panorama | Mon Nov 10 00:00:00 GMT 2025

REPOSITORIES: PanoramaPublic

ACCESS DATA

Json Xml

Publications

Enabling population protein dynamics through Bayesian modeling.

Lehmann Sylvain S Vialaret Jérôme J Gabelle Audrey A Bauchet Luc L Villemin Jean-Philippe JP Hirtz Christophe C Colinge Jacques J

Bioinformatics (Oxford, England) 20240801 8

<h4>Motivation</h4>The knowledge of protein dynamics, or turnover, in patients provides invaluable information related to certain diseases, drug efficacy, or biological processes. A great corpus of experimental and computational methods has been developed, including by us, in the case of human patients followed in vivo. Moving one step further, we propose a novel modeling approach to capture population protein dynamics using Bayesian methods.<h4>Results</h4>Using two datasets, we demonstrate tha ...[more]

PMID: 39078204

Similar Datasets

Stable Isotope Labeling by Amino acid in Vivo (SILAV)

Project description:Intravenous administration of stable isotope labeled amino acid ((13)C6-leucine) to humans recently made it possible to study the metabolism of specific biomarkers in cerebrospinal fluid (CSF) and in plasma using targeted mass spectrometry (MS). This labeling approach could be of great interest for monitoring many leucine-containing peptides in parallel, using Mass Spectrometry. This will make it possible to quantify the rates of synthesis and clearance of a large range of proteins in humans with a view to obtaining new insights into protein metabolism processes and the pathophysiology of diseases such as Alzheimer's disease.

2025-11-15 | PXD046142 | panorama

Impaired cardiac branched-chain amino acid metabolism in a novel model of diabetic cardiomyopathy

Project description:Metabolic alterations occur in the heart of patients with type 2 diabetes mellitus (T2DM). However, the relationships between branched-chain amino acid (BCAA) metabolism and the pathophysiology of diabetic cardiomyopathy (DbCM) remain unclear. Here, we sought to establish a novel model of DbCM and reveal its metabolic alterations, especially focusing on BCAA metabolism. Using adipocyte-specific 3′-phosphoinositide–dependent kinase 1 (PDK1)-deficient (A-PDK1KO) mice as a new model of DbCM, we demonstrated that cardiac BCAA catabolic enzymes were down-regulated in these mice, leading to the accumulation of BCAAs in the heart. Mechanistically, the accumulation of the BCAA leucine could cause cardiac hypertrophy via the activation of mammalian target of rapamycin complex 1 (mTORC1). A-PDK1KO mice mimic the cardiac phenotypes and metabolic alterations seen in human DbCM and exhibit impaired BCAA metabolism in the heart. This model may contribute to a better understanding of DbCM pathophysiology and the development of novel therapies for it.

2025-04-23 | GSE268260 | GEO

Project description:APOE genotype influences the gut microbiome structure and function in humans and animals: relevance for Alzheimer's disease pathophysiology

| PRJNA533610 | ENA

Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation

Project description:Background: Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essential nutrients. However, how their depletion affects translation remains largely unclear. Here, we investigate the immediate effects of single, double, and triple branched-chain amino acid deprivation on translational dynamics in NIH3T3 cells using RNA-seq and ribosome profiling. Results: All starvation conditions increased ribosome dwell times, with pronounced stalling at all valine codons during valine and triple starvation, whereas leucine and isoleucine starvation produced milder, codon-specific effects. Notably, stalling under isoleucine deprivation largely decreased under triple starvation. Positional enrichment of valine codons near the 5' end and downstream isoleucine codons potentially contributes to these patterns, suggesting a possible elongation bottleneck that influences translational responses under branched-chain amino acid starvation. The presence of multiple valine stalling sites was associated with decreased protein levels. Finally, codon-specific dwell time changes correlated strongly with patterns of tRNA isoacceptor charging. Conclusions: Together, these findings suggest that differential ribosome stalling under branched-chain amino acid starvation reflects a balance between amino acid supply, tRNA charging dynamics, codon position, and stress-response signaling.

2025-09-02 | GSE291652 | GEO

Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation

Project description:Background Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essential nutrients. However, how their depletion affects translation remains largely unclear. Here, we investigate the immediate effects of single, double, and triple branched-chain amino acid deprivation on translational dynamics in NIH3T3 cells using RNA-seq and ribosome profiling. Results All starvation conditions increased ribosome dwell times, with pronounced stalling at all valine codons during valine and triple starvation, whereas leucine and isoleucine starvation produced milder, codon-specific effects. Notably, stalling under isoleucine deprivation largely decreased under triple starvation. Positional enrichment of valine codons near the 5′ end and downstream isoleucine codons potentially contributes to these patterns, suggesting a possible elongation bottleneck that influences translational responses under branched-chain amino acid starvation. The presence of multiple valine stalling sites was associated with decreased protein levels. Finally, codon-specific dwell time changes correlated strongly with patterns of tRNA isoacceptor charging. Conclusions Together, these findings suggest that differential ribosome stalling under branched-chain amino acid starvation reflects a balance between amino acid supply, tRNA charging dynamics, codon position, and stress-response signaling.

2025-09-02 | GSE291653 | GEO

The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa

Project description:Filamentous fungi are one of the primary degraders of plant biomass because of their ability to produce enzymes that break down complex polysaccharides. The production of cellulolytic enzymes in fungi is dependent on transcription factors. In this article, we identified a N. crassa Zn2Cys6 transcription factor Clr5 that regulates the expression of cellulase on cellulose. N. crassa Δclr5 exhibited a significant decrease in secreted proteins (~46%), endo-glucanase (~55%), xylanase (~33%), β-glucosidase (~38%), and exocellulase (~40%) compared with the WT, while transcriptomic analysis revealed that clr5 was essential in cellulase expression. We also determined that clr5 is crucial in amino acid- Leucine and Histidine metabolism. When using Leucine or Histidine as solo nitrogen source, Δclr5 strain cannot grow as normally as WT, and the expression of most CAZyme genes were reduced obviously, which indicated nitrogen metabolism played an important role in cellulose degradation. Moreover, the function of Clr5 is conservative in M. thermophila, the other fungi with a capacity for biomass degradation.

2023-12-06 | GSE222372 | GEO

Excitatory Neuronal ErbB4 Drives Early Pathophysiology of Alzheimer's Disease

Project description:Excitatory Neuronal ErbB4 Drives Early Pathophysiology of Alzheimer's Disease

| PRJNA1237264 | ENA

Transcriptomics profiling of Alzheimer's disease reveal novel molecular targets

Project description:Our data provide a comprehensive list of transcriptomics alterations and warrant holistic approach including both coding and non-coding RNAs in functional studies aimed to understand the pathophysiology of LOAD We performed directional RNA sequencing on high quality RNA samples extracted from hippocampi of 4 late onset Alzheimer's diseas (LOAD) and 4 age-matched controls.

2015-04-01 | E-GEOD-67333 | biostudies-arrayexpress