Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of HDL isolates reveals method-driven variability between ultracentrifugation and immunoaffinity chromatography: an interlaboratory approach

ABSTRACT: Therefore, the aim of our study is to systematically compare the effect of two different methods of HDL isolation, namely UC and IAC, performed in two independent research laboratories. For this purpose, we used the same plasma pool and protocols optimized to evaluate the influence of those variables in HDL proteome composition.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Francielle Aguiar Gomes

LAB HEAD: Graziella Eliza Ronsein

PROVIDER: PXD066558 | Pride | 2026-01-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	241116_HDL_100ng_DIA_HolzerLab_IAC_Day1_A.raw	Raw
	241116_HDL_100ng_DIA_HolzerLab_IAC_Day1_B.raw	Raw
	241116_HDL_100ng_DIA_HolzerLab_IAC_Day1_C.raw	Raw
	241116_HDL_100ng_DIA_HolzerLab_IAC_Day2_A.raw	Raw
	241116_HDL_100ng_DIA_HolzerLab_IAC_Day2_B.raw	Raw

Items per page:

1 - 5 of 37

Publications

Proteomic analysis of HDL isolates reveals method-driven variability: An interlaboratory approach.

Gomes Francielle Aguiar FA Souza Junior Douglas Ricardo DR Holzer Michael M Ronsein Graziella Eliza GE

Journal of lipid research 20251205 1

The high-density lipoprotein (HDL) is the most heterogeneous and protein-rich lipoprotein, and its complex proteome has been correlated with many distinct properties. However, the lack of a standardized approach for HDL isolation, combined with the fact that different methods capture overlapping, but distinct HDL subspecies make the establishment of a composition-function relationship a challenge. Key factors influencing HDL proteomic profile are the isolation methodology and the technical varia ...[more]

PMID: 41354322

Similar Datasets

Proteomic dynamic changes in HDL subfractions from mouse plasma

Project description:HDL proteome dynamics may determine HDL cardioprotective functions. We aimed to characterize proteome and lipid profiles in small, medium and large (S/M/L) HDL fractions and analyze their functions. We characterized mouse HDL fractions by their high phospholipid (PL) content and collected S/M/L-HDLsubfractions by using fast protein liquid chromatography. The pooled S/L/M-HDL elution was subjected to mass spectrometry (MS) analysis using a Qstar XL-MS system, performing HDL subpopulation proteomic analysis. Fifty-one HDL proteins (39 in S-HDL, 27 in M-HDL and 29 in L-HDL) were identified and grouped into 4 functional categories (5 in lipid metabolism, 24 in immune response, 7 in coagulation, and 14 others). There were 16, 3 and 7 proteins present in only the S-HDL, M-HDL and L-HDL subfractions, respectively, and 11 proteins overlapped in all S/M/L-HDL subfractions. The dynamic changes in relative HDL protein levels were then characterized based on their functional groups by biological and bioinformatical methods.

2019-11-12 | PXD011185 | Pride

HDL Isolated by Immunoaffinity, Ultracentrifugation, or Precipitation is Compositionally and Functionally Distinct.

Project description: Not available

| S-EPMC9720336 | biostudies-literature

HDL proteome across 93 mouse strains

Project description:High-density lipoproteins (HDL) are nanoparticles with >80 associated proteins, phospholipids, cholesterol and cholesteryl esters. We have identified and quantified the ultracentrifugation isolated HDL proteome across 93 strains of mice, a diverse inbred strains of mice, Hybrid Mouse Diversity Panel (HMDP).

2019-04-24 | PXD009473 | Pride

Apolipoprotein A1 forms 5/5 and 5/4 antiparallel dimers in human high-density lipoprotein

Project description:We performed zero-order chemical cross-linking mass spectrometry experiments on reconstituted discoidal HDL and human HDL to determine the APOA1 orientations in these particles.

2019-04-09 | PXD009927 | Pride

Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux

Project description:Specific mutations in Apolipoprotein A-I (ApoA-I) of high-density lipoprotein (HDL) are responsible for a late-onset systemic amyloidosis. Carriers do not exhibit increased cardiovascular disease risk despite reduced levels of ApoA-I/ HDL-cholesterol. To explain this paradox, we show that the HDL particle profile of L75P and L174S patients presents a higher relative abundance of the 8.4 nm vs 9.6 nm particles, and that serum from patients, as well as reconstituted 8.4 and 9.6 nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4 nm rHDL have altered secondary structure composition and display a more flexible binding to lipids compared to their native counterpart. The reduced HDL-cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles and better cholesterol efflux due to altered, region-specific protein structure dynamics.

2020-11-20 | PXD021266 | Pride

sRNA sequencing of HDL from human donors

Project description:miRNAs and other small RNAs have been found associated with high-density lipoproteins (HDL). The aim of this study was to investigate the miRNA signature on human HDL from 10 donors.

2019-01-03 | GSE124559 | GEO

Molecular mechanisms vascular smooth muscle cell (VSMC) acquisition of macrophage features in response to cholesterol loading

Project description:In this study, murine primary aortic smooth muscle cells (SMCs) were transcriptionally profiled at baseline, after 3 d of cholesterol loading, and after 3 d of subsequent cholesterol unloading with HDL treatment, to identify vascular SMC genes that are transcripionally dysregulated in response to cholesterol loading and/or unloading. Mouse aortic SMCs were isolated from thoracic aortas of 8 week-old C57BL/6 mice (as described in Rong et al., Proc Nat Acad Sci USA, v100, pp13531M-bM-^@M-^S13536, 2003) and subconfluent cell preparations were harvested and transcriptionally profiled (baseline group) or treated with 10 M-NM-<g/mL cholesterol:methyl-M-NM-2-cyclodextrin complex (1:6 molar ratio) for 72 h for cholesterol loading. Of the cholesterol-loaded cells, samples were transcriptionally profiled (cholesterol samples) or treated for an additional 72 h with 100 M-NM-<g/mL human HDL and then transcriptionally profiled (HDL treatment). For all transcriptional profiling, RNA was isolated from cells using TRIzol, and labeled aRNA was prepared for hybridization to Affymetrix Mouse Genome 430 2.0 microarrays according to the manufacturer's protocol. Probe-level intensities were background-adjusted and normalized (in two separate analyses, one with baseline and cholesterol-treated samples, and the other analysis with all three sample groups) using Robust Multichip Average and combined into probesets using probe-to-probeset mappings from the University of Michigan CustomCDF project based on Ensembl Gene identifiers (release 59). Using the data from the analysis that combined the baseline and cholesterol-loaded samples, log2 probeset intensities were compared the between baseline and cholesterol sample groups using a one-way ANOVA with a P value cutoff determined by a Benjamini-Hochberg false discovery rate threshold of 0.05. Analysis (I): baseline and cholesterol-treated sample groups. Analysis (II): all three sample groups.

2015-02-06 | E-GEOD-47744 | biostudies-arrayexpress

Expression data from human coronary artery endothelial cells treated with HDL components

Project description:We quantified differential gene (mRNA) expression in human coronary artery cells treated with native HDL, reconstituted HDL, lipid-free apolipoprotein A-I, small unilamellar vesicles, or PBS control. These data were used to determine which genes are regulated by native HDL compared to components of HDL and categorize data based on shared sets of genes and distinct sets of genes regulated by each component.

2014-02-27 | GSE53201 | GEO

HDL suppresses the type I interferon response

Project description:Background: High density lipoprotein (HDL) protects the artery wall by removing cholesterol from lipid-laden macrophages. However, recent evidence suggests that it might also inhibit atherogenesis by combating inflammation. Methods and Results: To identify potential anti-inflammatory mechanisms, we challenged macrophages with lipopolysaccharide (LPS), an inflammatory microbial ligand for Toll-like receptor 4 (TLR4). HDL inhibited the expression of 33% (301 of 911) of the genes normally induced by LPS, microarray analysis revealed. One of its major targets was the type I interferon response pathway, a family of potent viral immunoregulators controlled by TLR4 and the TRAM/TRIF signaling pathway. Unexpectedly, HDL’s ability to inhibit gene expression was independent of cellular cholesterol stores. Moreover, it was unaffected by downregulation of two ATP-binding cassette transporters, ABCA1 and ABCG1, that promote cholesterol efflux. To examine the pathway’s potential in vivo relevance, we used mice deficient in apolipoprotein (apo) A-I, HDL’s major protein. After infection with Salmonella (a Gram-negative bacterium that expresses LPS), apoA-I–deficient mice had 6-fold higher plasma levels of interferon-beta-a key regulator of the type I interferon response than did wild-type mice. Conclusions: HDL inhibits a subset of LPS-stimulated macrophage genes that regulate the type I interferon response, and its action is independent of sterol metabolism. These findings raise the possibility that regulation of macrophage genes by HDL might link innate immunity and cardioprotection. 12 arrays, 3 experimental groups, mMncN (no treatment), mMncL (LPS treated, exposed for 4 h to serum-free medium or serum-free medium supplemented with 100 ng/mL of LPS), and mMwtL (HDL treated, Macrophages were treated for 4 h with serum-free medium or serum-free medium supplemented with 50 mg/mL of HDL, washed twice with PBS).

2010-10-01 | E-GEOD-19340 | biostudies-arrayexpress

sRNA sequencing of miRNAs exported to HDL from primary human islets

Project description:miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from primary islets to HDL in vitro.

2019-01-16 | GSE125136 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data