Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients

Fragnoud, Romain; Yugueros-Marcos, Javier; Pachot, Alexandre; Bedin, F.

doi:10.1186/1477-5956-10-60

Cited by 15 publications

(8 citation statements)

References 40 publications

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“…Consistent with this possibility, in our study DHF/DSS cases had lower VDBP than controls, even though this difference was not statistically significant. Circulating VDBP might decrease in patients with severe dengue through reduced protein expression but this was not the case in one study of 10 patients [31]. An anecdotal report of five cases with DF suggested that the administration of vitamin D and calcium during the acute episode shortened the duration of disease [32]; thus, the potential therapeutic value of enhancing vitamin D bioavailability during acute dengue infection requires careful consideration in future investigations.…”

Section: Discussionmentioning

confidence: 99%

Vitamin D serostatus and dengue fever progression to dengue hemorrhagic fever/dengue shock syndrome

et al. 2017

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Vitamin D could modulate pathways leading to dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). We examined the associations of serum total 25-hydroxy vitamin D [25(OH)D] and vitamin D binding protein (VDBP) concentrations in patients with uncomplicated dengue fever (DF) with risk of progression to DHF/DSS. In a case-control study nested in a cohort of DF patients who were followed during the acute episode in Bucaramanga, Colombia, we compared 25(OH)D and VDBP at onset of fever between 110 cases who progressed to DHF/DSS and 235 DF controls who did not progress. 25(OH)D concentrations were also compared between the acute sample and a sample collected >1 year post-convalescence in a subgroup. Compared with 25(OH)D ⩾75 nmol/l, adjusted odds ratios (95% CI) for progression were 0·44 (0·22-0·88) and 0·13 (0·02-1·05) for 50 to 75 nmol/l (vitamin D insufficiency) and <50 nmol/l (vitamin D deficiency), respectively (P, trend = 0·003). Mean 25(OH)D concentrations were much lower post-convalescence compared with the acute episode, regardless of case status. Compared with controls, mean VDBP was non-significantly lower in cases. We conclude that low serum 25(OH)D concentrations in DF patients predict decreased odds of progression to DHF/DSS.

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Section: Discussionmentioning

confidence: 99%

Vitamin D serostatus and dengue fever progression to dengue hemorrhagic fever/dengue shock syndrome

et al. 2017

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“…As shown in Table , regulation windows varied between +1.39 to +2.29, depending on the combination of ICPL tags used for comparison. This determination of exclusion criteria is similar to other studies that have adopted a normalized expression differences of one or two SD, used arbitrary assigned transformed intensity ratios, or experimentally determined ICPL Heavy/Light ratio values. , …”

Section: Resultsmentioning

confidence: 81%

“…This determination of exclusion criteria is similar to other studies that have adopted a normalized expression differences of one or 44 two SD, 45 used arbitrary assigned transformed intensity ratios, 46 or experimentally determined ICPL Heavy/Light ratio values. 34,47 Partial characterization of the urine proteome by in-solution fractionation and LC-MS/MS Reaction with ICPL reagents (containing a nicotinoyloxysuccinimide group with deuterium and/or 13C substitutions) and εamino groups results in the loss of a basic side chain and a shift in the isoelectric point of basic peptides toward a more acidic pI. 36 We therefore applied isoelectric focusing on a pH 3−10 gradient, followed by refocusing of the most acidic fractions on a pH 3−6 gradient to evaluate the labeled urine proteins present.…”

Section: Determination Of a Control Regulation Window For Icpl Labeli...mentioning

confidence: 99%

The utility of isotope-coded protein labeling for prioritization of proteins found in ovarian cancer patient urine

Rainczuk

Condina²,

Pelzing³

et al. 2013

J. Proteome Res.

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Urine offers a number of attractive features as a sample type for biomarker discovery, including noninvasive sampling, quantity and availability, stability, and a narrow dynamic range. In this study we report the first application of isotope coded protein labeling (ICPL), coupled with in-solution isoelectric fractionation and LC-MALDI-TOF/TOF, to examine and prioritize urinary proteins from ovarian cancer patients. Following the definition of stringent exclusion criteria a total of 579 proteins were identified with 43% providing quantitation data. Protein abundance changes were validated for selected proteins by ESI-Qq-TOF MS, following which Western blot and immunohistochemical analysis by tissue microarray was used to explore the biological relevance of the proteins identified. Several established markers (e.g., HE4, osteopontin) were identified at increased levels in ovarian cancer patient urine, validating the approach used; we also identified a number of potential marker candidates (e.g., phosphatidylethanolamine binding protein 1, cell-adhesion molecule 1) previously unreported in the context of ovarian cancer. We conclude that the ICPL strategy for identification and relative quantitation of urine proteins is an appropriate tool for biomarker discovery studies, and can be applied for the selection of potential biomarker candidates for further characterization.

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“…The peptides of bacteria may be directly detectable in human serum using mass spectrometry (Cheung et al, 2015). It may be possible to detect the presence of infectious agents either via the host response or from the presence of the pathogen's own proteins (Fragnoud, Yugueros-Marcos, Pachot, & Bedin, 2012;Haverland, Villeneuve, Ciborowski, & Fox, 2016;Kruh-Garcia et al, 2014). Blood-based protein biomarkers for diagnosis of Alzheimer disease including VCAM1, ILGFBP2, Carcinoembryonic antigen, CD40, and macrophage inflammatory protein alpha 1 and SOD were discovered by screening with a panel of immunoassays (Doecke et al, 2012).…”

Section: Discovery Of Biomarkers By Mass Spectrometrymentioning

confidence: 99%

The characterization of cell surface receptor complexes by affinity chromatography, liquid chromatography and tandem mass spectrometry

Dufresne¹

2021

Preprint

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Cell surface receptors are of critical importance to the treatment of disease but are difficult to isolate and identify by classical approaches. Here, a robust and general method for capturing a receptor complex from the surface of live cells with ligands presented on nanoscopic beads is demonstrated. Two forms of affinity chromatography: the presentation of a biotinylated ligand to the surface of live cells and recovered by classical affinity chromatography was compared to the presentation of the ligand on the surface of nanoscopic chromatography beads for the isolation of the IgG-FcR complex from the surface of live cells. The IgG ligand was first characterized by LC-ESI-MS/MS and compared to controls by classical statistical methods in order to minimize the total error rate of protein identification. The first strategy was to isolate the IgG-FcR complex using biotinylated IgG (IgG-B) compared to IgG with a DTT-cleavable biotin spacer arm (IgG-SS-B) to activate and capture the receptor associated supramolecular complex. In this method, live cells were incubated on ice with IgG, IgG-B or IgG-S-S-B, for 30 minutes, washed and disrupted by French press. After washing, the IgG-B and IgG-S-S-B ligands were eluted from a streptavidin-agarose column in DTT followed by mercaptoethanol, 2M NH4OH and then 50mM biotin in 2 M NH4OH and the ligand remaining on the columns was scrubbed with 2% SDS or digested with trypsin. The analysis of the eluted fractions and SDS scrub by dot blots or Western blots with streptavidin-HRP (SA-HRP) or donkey anti human IgG-HRP (Dk anti-hIgG-HRP) probes agreed with liquid chromatography and tandem mass spectrometry (LC-ESI-MS/MS) of the tryptic peptides that IgG-B or IgG-S-S-B was non-specifically eluted by ammonium hydroxide buffer. LC-ESI-MS/MS of the DTT eluted fraction from the charged streptavidin column (agarose-SA-B-S-S-IgG) to release the S-IgG ligand showed detectable amounts of the S-IgG complex and minimal amounts of Fc and Fcrl proteins. Some of the known components of the Fc mediated phagocytic pathway were enriched in DDT and BME in the Biotin-S-S-IgG-FCGR compared to Biotin-IgG controls. Many variations of the classical ligand affinity chromatography method for the isolation of cell surface receptors were investigated including the use of detergents, heat aggregated ligands, the use of cross linkers and the capture of IgG over streptavidin or protein G chromatography. None of these methods specifically captured Fc receptors however the identified proteins were different from background binding controls. In the second strategy, IgG coated PMMA and melamine micro and glass nano beads were presented to live cells, homogenized by French pressing, isolated by ultracentrifugation and then extracted by a salt and acetonitrile step gradient. Laser confocal scanning microscopy, dot blots with Coomassie staining or Western blot all confirm the three nano and micro bead surfaces: silica, melamine and PMMA were coated in IgG and were able to bind RAW 264.7 macrophages. Fc receptors were identified in significant numbers in the silica nano treatments compared to controls as well as members of the FcR mediated phagocytic pathway with very little background binding. In contrast to the strategy of classical affinity chromatography applied to integral membrane receptors, the use of ligand coated micro, and as shown here for the first time, silica nano beads, was effective at binding and capturing a receptor from the surface of a live cell and may serve as a general method for isolating receptor complexes on the nano scale.

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Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients

Cited by 15 publications

References 40 publications

Vitamin D serostatus and dengue fever progression to dengue hemorrhagic fever/dengue shock syndrome

Vitamin D serostatus and dengue fever progression to dengue hemorrhagic fever/dengue shock syndrome

The utility of isotope-coded protein labeling for prioritization of proteins found in ovarian cancer patient urine

The characterization of cell surface receptor complexes by affinity chromatography, liquid chromatography and tandem mass spectrometry

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