scholarly journals Proteomic Studies for the Investigation of γ-Globin Induction by Decitabine in Human Primary Erythroid Progenitor Cultures

2020 ◽  
Vol 9 (1) ◽  
pp. 134
Author(s):  
Andria Theodorou ◽  
Marios Phylactides ◽  
Eleni Katsantoni ◽  
Kostas Vougas ◽  
Spyros D. Garbis ◽  
...  
Keyword(s):  
Stress Proteins ◽  
Chromatin Modification ◽  
Protein Stabilization ◽  
Absolute Quantitation ◽  
Erythroid Progenitor ◽  
Itraq Analysis ◽  
Proteomic Approach ◽  
Pharmacological Targets ◽  
Liquid Chromatography Tandem Mass ◽  
Isobaric Tags

Reactivation of γ-globin is considered a promising approach for the treatment of β-thalassemia and sickle cell disease. Therapeutic induction of γ-globin expression, however, is fraught with lack of suitable therapeutic targets. The aim of this study was to investigate the effects that treatment with decitabine has on the proteome of human primary erythroid cells from healthy and thalassemic volunteers, as a means of identifying new potential pharmacological targets. Decitabine is a known γ-globin inducer, which is not, however, safe enough for clinical use. A proteomic approach utilizing isobaric tags for relative and absolute quantitation (iTRAQ) analysis, in combination with high-pH reverse phase peptide fractionation followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), was employed to investigate the effects of decitabine treatment. Bioinformatics analysis making use of the Database for Annotation, Visualization and Integrated Discovery (DAVID) was employed for functional annotation of the 192 differentially expressed proteins identified. The data are available via ProteomeXchange with identifier PXD006889. The proteins fall into various biological pathways, such as the NF-κB signaling pathway, and into many functional categories including regulation of cell proliferation, transcription factor and DNA binding, protein stabilization, chromatin modification and organization, and oxidative stress proteins.

scholarly journals Partial Proteome Map of Campylobacter Jejuni Strain Nctc11168 by Gel-Free Proteomics Analysis

2014 ◽  
Vol 2 (4) ◽  
pp. 464-477
Author(s):  
Zilun Shi ◽  
Chris Dawson ◽  
Stephen L.W. On ◽  
Malik Altaf Hussain
Keyword(s):  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
Brain Heart Infusion ◽  
Cell Protein ◽  
Absolute Quantitation ◽  
Whole Cell ◽  
Itraq Analysis ◽  
Proteomic Approach ◽  
Whole Cell Protein ◽  
Isobaric Tags

A proteome map of the foodborne pathogen Campylobacter jejuni NCTC11168 was analyzed using a state-of-the-art gel-free proteomic approach for the first time. A whole cell protein extract was prepared from the C. jejuni strain NCTC11168 grown in brain heart infusion (BHI) broth at 42°C under microaerobic conditions. A gel-free technique using isobaric tags for relative and absolute quantitation (iTRAQ) was employed to create a protein expression profile of the strain. Liquid chromatography-mass spectrometry (LC-MS/MS) was used to identify the proteins. Protein functionalities were searched to classify them. A total of 235 proteins were identified in the whole cell protein fraction of C. jejuni NCTC11168 cells using iTRAQ analysis. Functional grouping of the identified proteins showed that forty percent of these proteins were associated with energy metabolism, protein synthesis and genetic information processing. iTRAQ was faster, easier and proved more sensitive than two-dimensional gel-based proteomics approaches previously applied to C. jejuni, making it an attractive tool for further studies of cellular physiological response. DOI: http://dx.doi.org/10.3126/ijasbt.v2i4.11253  Int J Appl Sci Biotechnol, Vol. 2(4): 464-477 

Proteome Analysis of Testicular Tissue in Varicocele Rats Using iTRAQ Labeling Technology

2020 ◽  
Author(s):  
lu xian feng ◽  
zhao wei ◽  
liu jian rong ◽  
wang dan feng ◽  
yuan cai xia ◽  
...  
Keyword(s):  
Protein Transport ◽  
Proteome Analysis ◽  
Testicular Tissue ◽  
P Value ◽  
Absolute Quantitation ◽  
Tissue Samples ◽  
Itraq Analysis ◽  
Potential Biomarker ◽  
Liquid Chromatography Tandem Mass ◽  
Isobaric Tags

Abstract Purpose Varicocele (VC) is considered as the main cause of male infertility, clear and definite molecular markers of varicocele disease are helpful for early prevention and timely treatment. This study was in order to examine the effect of varicocele on protein expression in testicular tissue.Methods The testicular tissue samples of normal rats and varicocele rats were used for proteomic analysis and functional bioinformatics analysis. The proteins with a fold change of > 1.2 or < 1.2, and with a P-value < 0.05 were used to identify up- and downregulation proteins between the varicocele and control rats, and two target proteins were selected and verified with western blot.Results It was found that seminiferous epithelium was disordered and spermatogenic cells were injured seriously in varicocele group. A total of 65 differentially expressed proteins were identified compared with normal group by liquid chromatography tandem mass spectrometry (LC-MS/MS) and isobaric tags for relative and absolute quantitation (iTRAQ) analysis, including 31 up-regulated proteins and 34 down-regulated proteins, respectively. Functions of those proteins were mainly related to the following processes: signal transduction, protein cycle, transmembrane transport, protein transport, vesicular mediated transport, cell division, and membrane tissue. Two down regulated proteins of ATPase and Cu2+-transporting alpha (ATP7A) and Calcium and integrin-binding protein 1 (CIB1) in varicocele rats were selected and confirmed.Conclusion Protein spectrum of testicular tissue in varicocele rats was different from that in normal rats. Low expressions of ATP7A and CIB1 may be affect testicular spermatogenic function and can be used as a potential biomarker for testicular tissue to maintain normal spermatogenic function.

scholarly journals Quantitative proteomic profiling of Cervicovaginal fluid from pregnant women with term and preterm birth

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Young Eun Kim ◽  
Kwonseong Kim ◽  
Han Bin Oh ◽  
Sung Ki Lee ◽  
Dukjin Kang
Keyword(s):  
Preterm Birth ◽  
Pregnant Women ◽  
Neonatal Morbidity ◽  
Differentially Expressed ◽  
Proteomic Profiling ◽  
Absolute Quantitation ◽  
Term Birth ◽  
Liquid Chromatography Tandem Mass ◽  
Isobaric Tags ◽  
Cervicovaginal Fluid

Abstract Background Preterm birth (PTB) is one of major causes of perinatal mortality and neonatal morbidity, but knowledge of its complex etiology is still limited. Here we present cervicovaginal fluid (CVF) protein profiles of pregnant women who subsequently delivered at spontaneous preterm or term, aiming to identify differentially expressed CVF proteins in PTB and term birth. Methods The CVF proteome of women who sequentially delivered at preterm and term was analyzed using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional nanoflow liquid chromatography-tandem mass spectrometry (2D-nLC-MS/MS). We compared the CVF proteome of PTB (n = 5) and control subjects (term birth, n = 7) using pooled control CVF (term birth, n = 20) as spike-in standard. Results We identified 1294 CVF proteins, of which 605 were newly identified proteins. Of 990 proteins quantified in both PTB and term birth, 52 proteins were significantly up/down-regulated in PTB compared to term birth. The differentially expressed proteins were functionally associated to immune response, endopeptidase inhibitors and structural constituent of cytoskeleton. Finally, we confirm the down-regulation of SERPINB7 (a serine-type protease inhibitor) in PTB compared to control by Western blot. Conclusions Taken together, our study provide quantitative CVF proteome profiles of pregnant women who ultimately delivered at preterm and term. These promising results could help to improve the understanding of PTB etiology and to discover biomarkers for asymptomatic PTB.

Plasma-based proteomics reveals lipid metabolic and immunoregulatory dysregulation in post-stroke depression

2014 ◽  
Vol 29 (5) ◽  
pp. 307-315 ◽  
Author(s):  
Y. Zhan ◽  
Y.-T. Yang ◽  
H.-M. You ◽  
D. Cao ◽  
C.-Y. Liu ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Expression Profiles ◽  
Absolute Quantitation ◽  
Post Stroke ◽  
Reactive Protein ◽  
Proteomic Approach ◽  
Psychiatric Complication ◽  
Post Stroke Depression ◽  
Healthy Control ◽  
Isobaric Tags

AbstractBackground:Post-stroke depression (PSD) is the most common psychiatric complication facing stroke survivors and has been associated with increased distress, physical disability, poor rehabilitation, and suicidal ideation. However, the pathophysiological mechanisms underlying PSD remain unknown, and no objective laboratory-based test is available to aid PSD diagnosis or monitor progression.Methods:Here, an isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic approach was performed to identify differentially expressed proteins in plasma samples obtained from PSD, stroke, and healthy control subjects.Results:The significantly differentiated proteins were primarily involved in lipid metabolism and immunoregulation. Six proteins associated with these processes – apolipoprotein A-IV (ApoA-IV), apolipoprotein C-II (ApoC-II), C-reactive protein (CRP), gelsolin, haptoglobin, and leucine-rich alpha-2-glycoprotein (LRG) – were selected for Western blotting validation. ApoA-IV expression was significantly upregulated in PSD as compared to stroke subjects. ApoC-II, LRG, and CRP expression were significantly downregulated in both PSD and HC subjects relative to stroke subjects. Gelsolin and haptoglobin expression were significantly dysregulated across all three groups with the following expression profiles: gelsolin, healthy control > PSD > stroke subjects; haptoglobin, stroke > PSD > healthy control.Conclusions:Early perturbation of lipid metabolism and immunoregulation may be involved in the pathophysiology of PSD. The combination of increased gelsolin levels accompanied by decreased haptoglobin levels shows promise as a plasma-based diagnostic biomarker panel for detecting increased PSD risk in post-stroke patients.

scholarly journals Identification of Proteins Implicated in the Increased Heart Rate in ShenSongYangXin-Treated Bradycardia Rabbits by iTRAQ-Based Quantitative Proteomics

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Zhouying Liu ◽  
Jian Huang ◽  
Youping Huo ◽  
Jing Gong ◽  
Yinhui Zhang ◽  
...  
Keyword(s):  
Heart Rate ◽  
Quantitative Proteomics ◽  
Sinoatrial Node ◽  
Absolute Quantitation ◽  
Treatment Groups ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Isobaric Tags ◽  
Altered Proteins ◽  
Chinese Medicine Treatment

The present study tries to identify proteins implicated in bradycardia rabbits in hearts after ShenSongYangXin (SSYX, a traditional Chinese medicine) treatment. Eighteen adult rabbits were randomly assigned to three groups: sham, model, and SSYX treatment groups. Heart rate was recorded in rabbits and proteins were isolated from ventricular muscle. We used isobaric tags for elative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry to identify altered proteins after SSYX treatment. The heart rate decreased after six weeks due to the injury of the sinoatrial node in the model group. This effect was partially reversed by 4-week SSYX treatment. A total of a2988 proteins were quantified by performing the iTRAQ-based experiments. Of these, 86 proteins were differentially expressed according to our criteria (42 upregulated and 44 downregulated). The identification of key proteins implicated in the treatment of bradycardia could serve as a foundation to better understand and further explore the molecular mechanism of SSYX treatment.

scholarly journals Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques

2007 ◽  
Vol 189 (9) ◽  
pp. 3434-3444 ◽  
Author(s):  
M. Jiang ◽  
S. M. Sullivan ◽  
A. K. Walker ◽  
J. R. Strahler ◽  
P. C. Andrews ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Protein Identification ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Absolute Quantitation ◽  
Proteomic Approach ◽  
Assembly Factors ◽  
Associated Proteins ◽  
Isobaric Tags

ABSTRACT Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16°C and 37°C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.

scholarly journals Quantitative Proteomics Analysis by Isobaric Tags for Relative and Absolute Quantitation Identified Lumican as a Potential Marker for Acute Aortic Dissection

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Guorong Gu ◽  
Weizhong Cheng ◽  
Chenling Yao ◽  
Jun Yin ◽  
Chaoyang Tong ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Quantitative Proteomics ◽  
Acute Aortic Dissection ◽  
Serum Marker ◽  
Serum Biomarkers ◽  
Serum Samples ◽  
Absolute Quantitation ◽  
Itraq Analysis ◽  
Potential Marker ◽  
Isobaric Tags

Acute aortic dissection (AAD) is a serious vascular disease. Currently the diagnosis relies on clinical and radiological means whereas serum biomarkers are lacking. The purpose of this study was to identify potential serum biomarkers for AAD using isobaric tags for relative and absolute quantitation (iTRAQ) approach. A total of 120 serum samples were collected from three groups: AAD patients (n=60), patients with acute myocardial infarction (AMI,n=30), and healthy volunteers (n=30), whereas the first 10 samples from each group were used for iTRAQ analysis. Using iTRAQ approach, a total of 174 proteins were identified as significantly different between AAD patients and healthy subjects. Among them, forty-six proteins increased more than twofold, full-scale analysis using serum sample for the entire 120 subjects demonstrated that Lumican level was significantly increased relative to control and AMI samples. Further, Lumican level correlated with time from onset to admission in AAD but not AMI samples. Using iTRAQ approach, our study showed that Lumican may be a potential AAD-related serum marker that may assist the diagnosis of AAD.

scholarly journals Analysis of Chronic Mild Stress-Induced Hypothalamic Proteome: Identification of Protein Dysregulations Associated With Vulnerability and Resiliency to Depression or Anxiety

2021 ◽  
Vol 14 ◽  
Author(s):  
Weibo Gong ◽  
Wei Liao ◽  
Chui Fang ◽  
Yanchen Liu ◽  
Hong Xie ◽  
...  
Keyword(s):  
Hpa Axis ◽  
Chronic Mild Stress ◽  
Regulation System ◽  
Mild Stress ◽  
Absolute Quantitation ◽  
Protein Targets ◽  
Proteomic Approach ◽  
Parallel Reaction Monitoring ◽  
Independent Analysis ◽  
Isobaric Tags

Chronic stress as a known risk factor leads to hyperactivity of the hypothalamus-pituitary-adrenal (HPA) axis in both depression and anxiety. However, the stress-induced dysfunction of the HPA axis in these disorders especially the common and unique molecular dysregulations have not been well-explored. Previously, we utilized a chronic mild stress (CMS) paradigm to segregate and gain depression-susceptible, anxiety-susceptible, and insusceptible groups. In this study, we continue to examine the possible protein expression alterations of the hypothalamus as the center of the HPA axis in these three groups by using a proteomic approach. Though isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative analysis, a total of 593 dysregulated proteins were identified. These were potentially associated with vulnerability and adaptability of CMS-caused depression or anxiety and therefore might become novel investigative protein targets. Further independent analysis using parallel reaction monitoring (PRM) indicated that 5, 7, and 21 dysregulated proteins were specifically associated with depression-susceptible, anxiety-susceptible, and insusceptible groups, respectively, suggesting that the same CMS differently affected the regulation system of the rat hypothalamic proteome. In summary, the current proteomic research on the hypothalamus provided insights into the specific and common molecular basis for the HPA dysfunction mechanisms that underlie resiliency and vulnerability to stress-induced depression or anxiety.

scholarly journals The Oral Microbiome and Salivary Proteins Influence Caries in Preschool Children

2019 ◽  
Author(s):  
Wang Chen ◽  
Qian Jiang ◽  
GuoWei Yan ◽  
DeQin Yang
Keyword(s):  
Preschool Children ◽  
Free Group ◽  
Critical Role ◽  
Alpha Diversity ◽  
Oral Microbiome ◽  
Salivary Proteins ◽  
Absolute Quantitation ◽  
Core Microbiome ◽  
Liquid Chromatography Tandem Mass ◽  
Isobaric Tags

Abstract Background Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in preschool children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.Methods Children six to eight years old living in rural isolated areas with or without caries were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ)technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry(LC-MS/MS), respectively.Results We found the six most abundant phyla (Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria, and Candidate division TM7). The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P<0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P<0.05). The core microbiome was defined as 18 predominant genera in preschool children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups.Conclusions The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for preschool children with caries. In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.

scholarly journals Incomptine a Induces Apoptosis, ROS Production and a Differential Protein Expression on Non-Hodgkin′s Lymphoma Cells

2021 ◽  
Vol 22 (19) ◽  
pp. 10516
Author(s):  
Emmanuel Pina-Jiménez ◽  
Fernando Calzada ◽  
Elihú Bautista ◽  
Rosa María Ordoñez-Razo ◽  
Claudia Velázquez ◽  
...  
Keyword(s):  
Protein Expression ◽  
Sesquiterpene Lactones ◽  
Annexin V ◽  
Fold Change ◽  
Absolute Quantitation ◽  
Dapi Staining ◽  
Differential Protein Expression ◽  
Differential Protein ◽  
Proteomic Approach ◽  
Isobaric Tags

Sesquiterpene lactones are of pharmaceutical interest due their cytotoxic and antitumor properties, which are commonly found within plants of several genera from the Asteraceae family such as the Decachaeta genus. From Decachaeta incompta four heliangolide, namely incomptines A-D have been isolated. In this study, cytotoxic properties of incomptine A (IA) were evaluated on four lymphoma cancer cell lines: U-937, Farage, SU-DHL-2, and REC-1. The type of cell death induced by IA and its effects on U-937 cells were analyzed based on its capability to induce apoptosis and produce reactive oxygen species (ROS) through flow cytometry with 4′,6-diamidino-2-phenylindole staining, dual annexin V/DAPI staining, and dichlorofluorescein 2′,7′-diacetate, respectively. A differential protein expression analysis study was carried out by isobaric tags for relative and absolute quantitation (iTRAQ) through UPLC-MS/MS. Results reveal that IA exhibited cytotoxic activity against the cell line U-937 (CC50 of 0.12 ± 0.02 μM) and the incubation of these cells in presence of IA significantly increased apoptotic population and intracellular ROS levels. In the proteomic approach 1548 proteins were differentially expressed, out of which 587 exhibited a fold-change ≥ 1.5 and 961 a fold-change ≤ 0.67. Most of these differentially regulated proteins are involved in apoptosis, oxidative stress, glycolytic metabolism, or cytoskeleton structuration.

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