Investigation of urine proteome of preterm newborns with respiratory pathologies

Стародубцева, Н. Л.; Kononikhin, Alexey; Бугрова, А. Е.; Chagovets, Vitaliy; Indeykina, Maria I.; Krokhina, Ksenia N.; Nikitina, I. V.; Kostyukevich, Yury; Popov, Igor; Ларина, И. М.; Timofeeva, Leila A.; Frankevich, Vladimir; Ionov, Ionov O.V.; Degtyarev, D.N.; Nikolaev, Eugene; Сухих, Г. Т.

doi:10.1016/j.jprot.2016.06.012

Cited by 12 publications

(11 citation statements)

References 39 publications

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“…For MS analysis, in‐solution digestion was used. CVF proteins were reduced with 0.1М dithiothreitol (DTT) in 8M urea (pH 8.5), alkylated with 0.55M iodoacetamide, precipitated in acetone with trifluoroacetic acid (TFA), and digested with trypsin …”

Section: Methodsmentioning

confidence: 99%

Label‐free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

et al. 2019

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Cervicovaginal fluid (CVF) is a valuable source of clinical information about the female reproductive tract in both nonpregnant and pregnant women. The aim of this study is to specify the CVF proteome at different stages of cervix neoplastic transformation by label-free quantitation approach based on liquid chromatography tandem mass spectrometry (LC-MS/MS) method. The proteome composition of CVF from 40 women of reproductive age with human papillomavirus (HPV)-associated cervix neoplastic transformation (low-grade squamous intraepithelial lesion [LSIL], high-grade squamous intraepithelial lesion [HSIL], and CANCER) was investigated. Hierarchical clustering and principal component analysis (PCA) of the proteomic data obtained by a label-free quantitation approach show the distribution of the sample set between four major clusters (no intraepithelial lesion or malignancy [NILM], LSIL, HSIL and CANCER) depending on the form of cervical lesion. Multisample ANOVA with subsequentWelch's t test resulted in 117 that changed significantly across the four clinical stages, including 27 proteins significantly changed in cervical cancer. Some of them were indicated as promising biomarkers previously (ACTN4, VTN, ANXA1, CAP1, ANXA2, and MUC5B). CVF proteomic data from the discovery stage were analyzed by the partial least squares-discriminant analysis (PLS-DA) method to build a statistical model, allowing to differentiate severe dysplasia (HSIL and CANCER) from the mild/normal stage (NILM and LSIL), and receiver operating characteristic (ROC) area under the curve (AUC) were obtained on an independent set of 33 samples. The sensitivity of the model was 77%, and the specificity was 94%; AUC was equal to 0.87. CVF proteome proved to be reflect the stage of cervical epithelium neoplastic process.

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Section: Methodsmentioning

confidence: 99%

Label‐free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

et al. 2019

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“…Of note, the three proteome-based groups evidenced significantly different resistance, reactance and AX values measured by FOT, regardless of being LP or T. Specifically, we identified groups of children with different respiratory impedance based on the molecular stratification of fractionated urinary proteome. Unlike the entire urine sample used in previous studies by Becker et al and Starodubtseva et al [9,13], we utilized the extracellular vesicle fraction, which is considered the carrier of functional signals [14], making it possible to identify over 1100 proteins. Indeed, correct fractionation is confirmed by the level of typical free urinary proteins: we found that albumin and serotransferrin levels, free proteins in urine samples, were decreased 5-6 times with respect to the levels usually reported in the entire urine [13].…”

Section: Discussionmentioning

confidence: 99%

“…Unlike the entire urine sample used in previous studies by Becker et al and Starodubtseva et al [9,13], we utilized the extracellular vesicle fraction, which is considered the carrier of functional signals [14], making it possible to identify over 1100 proteins. Indeed, correct fractionation is confirmed by the level of typical free urinary proteins: we found that albumin and serotransferrin levels, free proteins in urine samples, were decreased 5-6 times with respect to the levels usually reported in the entire urine [13]. By contrast, typical exosomal proteins were detected at a higher level in urinary extracellular vesicle samples; for example, inter-alpha-trypsin inhibitors, such as ITIH4, increased 5-6 times compared to the level found in the entire urine [13].…”

Section: Discussionmentioning

confidence: 99%

Shotgun Proteomics of Isolated Urinary Extracellular Vesicles for Investigating Respiratory Impedance in Healthy Preschoolers

et al. 2021

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Urine proteomic applications in children suggested their potential in discriminating between healthy subjects from those with respiratory diseases. The aim of the current study was to combine protein fractionation, by urinary extracellular vesicle isolation, and proteomics analysis in order to establish whether different patterns of respiratory impedance in healthy preschoolers can be characterized from a protein fingerprint. Twenty-one 3–5-yr-old healthy children, representative of 66 recruited subjects, were selected: 12 late preterm (LP) and 9 full-term (T) born. Children underwent measurement of respiratory impedance through Forced Oscillation Technique (FOT) and no significant differences between LP and T were found. Unbiased clustering, based on proteomic signatures, stratified three groups of children (A, B, C) with significantly different patterns of respiratory impedance, which was slightly worse in group A than in groups B and C. Six proteins (Tripeptidyl peptidase I (TPP1), Cubilin (CUBN), SerpinA4, SerpinF1, Thy-1 membrane glycoprotein (THY1) and Angiopoietin-related protein 2 (ANGPTL2)) were identified in order to type the membership of subjects to the three groups. The differential levels of the six proteins in groups A, B and C suggest that proteomic-based profiles of urinary fractionated exosomes could represent a link between respiratory impedance and underlying biological profiles in healthy preschool children.

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“…Trypsinolysis was performed as described earlier. 17 Briefly, after reduction (dithiothreitol, 0.1 M, 4 h, 37℃), alkylation (iodoacetamide, 0.05 M, room temperature, 15 min in the dark), and consequent precipitation by 10 volumes of acetone with 0.1% (v/v) trifluoroacetic acid, the washed sediment was resuspended in 200 mM ammonium bicarbonate buffer (1 mg/mL, pH 8.0) and digested with modified porcine trypsin (Promega, USA) (enzyme/protein 1:100, 6 h, 37℃). As a control sample, the total protein from the same pooled sample was precipitated and trypsinized as follows.…”

Section: Methodsmentioning

confidence: 99%

The high-resolution mass spectrometry study of the protein composition of amyloid-like urine aggregates associated with preeclampsia

Sergeeva

Zakharova

Бугрова

et al. 2019

Eur J Mass Spectrom (Chichester)

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The study of protein misfolding and post-translational processing abnormalities is a promising diagnostic approach for socially significant pathologies associated with the accumulation of abnormal forms of proteins. Recently, it was shown that amyloid-like aggregates can be observed in the urine of pregnant women with preeclampsia, which is the most severe hypertensive complication that can lead to fateful outcomes. The protein composition of urine aggregates may clarify the molecular mechanisms underlying the pathology and has not yet been studied in detail. Using a proteomic approach based on high-resolution mass spectrometry, we studied the protein composition of amyloid-like structures that aggregate in the presence of Congo red azo-dye in the urine of pregnant women with preeclampsia. Fragments of β-sheets of α-1-antitrypsin, complement 3, haptoglobin, ceruloplasmin, and trypstatin were identified as most likely targets for Congo red binding.

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Investigation of urine proteome of preterm newborns with respiratory pathologies

Cited by 12 publications

References 39 publications

Label‐free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

Label‐free cervicovaginal fluid proteome profiling reflects the cervix neoplastic transformation

Shotgun Proteomics of Isolated Urinary Extracellular Vesicles for Investigating Respiratory Impedance in Healthy Preschoolers

The high-resolution mass spectrometry study of the protein composition of amyloid-like urine aggregates associated with preeclampsia

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