scholarly journals Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Suxiang Lu ◽  
Qian Xiong ◽  
Kang Du ◽  
Xiaoni Gan ◽  
Xuzhen Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Multiple Reaction Monitoring ◽  
Limb Regeneration ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Bioinformatics Analyses ◽  
Fin Regeneration ◽  
Early Stages

Abstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis. Results The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton. Conclusions To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.

Comparative iTRAQ Proteomics Identified Myocardium Proteins Associated with Hypoxia of Yak

2019 ◽  
Vol 16 (4) ◽  
pp. 314-329
Author(s):  
Asma Babar ◽  
Tserang Donko Mipam ◽  
Shixin Wu ◽  
Chuanfei Xu ◽  
Mujahid Ali Shah ◽  
...  
Keyword(s):  
Protein Expression ◽  
High Altitude ◽  
Molecular Mechanisms ◽  
Pressure Overload ◽  
Differentially Expressed ◽  
Matrix Remodeling ◽  
Cardiovascular Development ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Hypoxic Adaptation

<P>Background: Yaks inhabit high-altitude are well-adapted to the hypoxic environments. Though, the mechanisms involved in regulatory myocardial protein expression at high-altitude were not completely understood. </P><P> Objective: To revel the molecular mechanism of hypoxic adaptation in yak, here we have applied comparative myocardial proteomics in between yak and cattle by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) labelling. </P><P> Methods: To understand the systematic protein expression variations in myocardial tissues that explain the hypoxic adaptation in yak, we have performed iTRAQ analysis combined with Liquid Chromatography- Tandem Mass Spectrometry (LC-MS/MS). Bioinformatics analysis was performed to find the association of these Differentially Expressed Proteins (DEPs) in different functions and pathways. Protein to protein interaction was analyzed by using STRING database. </P><P> Results: 686 Differentially Expressed Proteins (DEPs) were identified in yak with respect to cattle. From which, 480 DEPs were up-regulated and 206 were down-regulated in yak. Upregulated expression of ASB4, STAT, HRG, RHO and TSP4 in yak may be associated with angiogenesis, cardiovascular development, response to pressure overload to heart and regulation of myocardial contraction in response to increased oxygen tension. The up-regulation of mitochondrial proteins, ACAD8, GPDH-M, PTPMT1, and ALDH2, may have contributed to oxidation within mitochondria, hypoxia-induced cell metabolism and protection of heart against cardiac ischemic injuries. Further, the upregulated expression of SAA1, PTX, HP and MBL2 involved in immune response potentially helpful in myocardial protection against ischemic injuries, extracellular matrix remodeling and free heme neutralization/ clearance in oxygen-deficient environment. </P><P> Conclusion: Therefore, the identification of these myocardial proteins in will be conducive to investigation of the molecular mechanisms involved in hypoxic adaptations of yaks at high-altitude condition.</P>

Identification of the Altered Proteins Related to Colon Carcinogenesis by iTRAQ-based Quantitative Proteomic Analysis

2019 ◽  
Vol 16 (4) ◽  
pp. 297-306
Author(s):  
Chunhua Luo ◽  
Defu Yao ◽  
Teck Kwang Lim ◽  
Qingsong Lin ◽  
Yingfu Liu
Keyword(s):  
Colorectal Cancer ◽  
Epithelial Cells ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Bacterial Invasion ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Proteomic Approach ◽  
Escherichia Coli Infection ◽  
Altered Proteins

Background:The molecular mechanisms or valuable biomarkers for early diagnosis of colorectal cancer (CRC) are not fully elucidated yet.Objective:To understand the proteomic changes at the global level in the carcinogenesis of CRC, differentially expressed proteins between normal intestinal epithelial cells CCD841 and colorectal cancer cells HCT116 were identified.Method:The isobaric tags for relative and absolute quantitation (iTRAQ) coupled with 2D LC-MS/MS proteomic approach were performed for screening the altered proteins between cells CCD841 and HCT116.Results:A total of 1947 proteins were identified after filtering and using a 1% false discovery rate. Based on a final cutoff (> 3.16 and < 0.32), 229 proteins were found to be significantly altered, among which 95 (41%) were up-regulated while 134 (59%) were down-regulated. Gene Ontology analysis revealed that the differentially expressed proteins were mainly cell part proteins involved in cellular process and binding in terms of subcellular distribution, biological process, and molecular function. KEGG analysis indicated that the differentially expressed proteins were significantly involved in the process of focal adhesion, pathogenic Escherichia coli infection, leukocyte transendothelial migration, bacterial invasion of epithelial cells, regulation of actin cytoskeleton, DNA replication and so on.Conclusion:Collectively, our data identified differentially expressed proteins in colon cancer carcinogenesis, which could provide the clues on unraveling the molecular mechanism of CRC.

scholarly journals Proteomic analysis of decidua in patients with recurrent pregnancy loss (RPL) reveals mitochondrial oxidative stress dysfunction

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Xiang-Jie Yin ◽  
Wei Hong ◽  
Fu-Ju Tian ◽  
Xiao-Cui Li
Keyword(s):  
Oxidative Stress ◽  
Western Blotting ◽  
Pregnancy Loss ◽  
Molecular Mechanisms ◽  
Recurrent Pregnancy Loss ◽  
Differentially Expressed ◽  
Decidual Cell ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Cox 2

Abstract Background Pregnancy is a complicated physiological process. The multifaceted regulation of maternal–fetal interface is of great importance for maintaining normal pregnancy and avoiding fetal rejection and secondary abortion. Previous studies have focused on the clinical features or pathological biomarkers of fetal rejection and abortion. However, no significant breakthrough has been made. Therefore, it is important to understand the molecular mechanisms of recurrent pregnancy loss (RPL) to identify potential therapeutic strategies. The aim of this study was to investigate the pathogenesis of RPL. Methods In this study, Relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis was used to identify differentially expressed proteins in decidual from RPL patients and matched normal controls. Further, Molecules NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (ndufb3) and cyclooxygenase-2 (COX-2) were validated by immunohistochemistry (IHC), Western blotting, CCK8 and mitochondrial red fluorescent probe (Mito-Tracker Red CMXRos). Results A total of 456 proteins reached the threshold of a 1.5-fold change were identified for further bioinformatics analysis. Upon mapping the differentially expressed proteins using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database, iTRAQ results were confirmed by assessing NDUFB3 and COX-2 protein levels in specimens of decidual tissue by Western blotting. Our study indicates that the level of COX-2 and NDUFB3 were significantly increased in decidual cell from RPL patients. Overexpression of NDUFB3 inhibited cell vitality and oxidative stress of decimal cell. Further, our found that overexpression NDUFBD3 in decidual cell decreased the mitochondrial membrane potential expression levels. These results suggest that NDUFB3 might play an important role in promote the pathological process of RPL. Conclusions This comprehensive analysis of RPL proteomics reveals novel candidate: NDUFB3, which could be further investigated for explanation of the pathological mechanism of RPL.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics

2020 ◽  
Vol 8 (1) ◽  
pp. 76
Author(s):  
Jian-Yu Meng ◽  
Mbuya Sylvain Ntambo ◽  
Philippe C. Rott ◽  
Hua-Ying Fu ◽  
Mei-Ting Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Vascular System ◽  
Lipid Transfer Protein ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Differentially Expressed Proteins ◽  
Lipid Transfer ◽  
Leaf Scald ◽  
Improvement Programs ◽  
Xanthomonas Albilineans

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.

scholarly journals iTRAQ Quantitative Analysis of Multidrug Resistance Mechanisms in Human Gastric Cancer Cells

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Huai-Dong Hu ◽  
Feng Ye ◽  
Da-Zhi Zhang ◽  
Peng Hu ◽  
Hong Ren ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Multidrug Resistance ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Human Gastric Cancer ◽  
Differentially Expressed Proteins ◽  
Gastric Cancer Cells ◽  
Proteomic Approach

Multidrug resistance (MDR) is a major obstacle towards a successful treatment of gastric cancer. However, the mechanisms of MDR are intricate and have not been fully understood. To elucidate the molecular mechanisms of MDR in gastric cancer, we employed the proteomic approach of isobaric tags for relative and absolute quantification (iTRAQ), followed by LC-MS/MS, using the vincristine-resistant SGC7901/VCR cell line and its parental SGC7901 cell line as a model. In total, 820 unique proteins were identified and 91 proteins showed to be differentially expressed in SGC7901/VCR compared with SGC7901. Several differentially expressed proteins were further validated by western blot analysis. Furthermore, the association of MVP, one of the highly expressed proteins in SGC7901/VCR, with MDR was verified. Our study is the first application of iTRAQ technology for MDR mechanisms analysis in gastric cancer, and many of the differentially expressed proteins identified have not been linked to MDR in gastric cancer before, which showed the value of this technology in identifying differentially expressed proteins in cancer.

scholarly journals Identification of differentially expressed proteins in fresh and frozen–thawed boar spermatozoa by iTRAQ-coupled 2D LC–MS/MS

Reproduction ◽  
2014 ◽  
Vol 147 (3) ◽  
pp. 321-330 ◽  
Author(s):  
Xiaoli Chen ◽  
Huabin Zhu ◽  
Chuanhuo Hu ◽  
Haisheng Hao ◽  
Junfang Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Bioinformatic Analysis ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Protein Levels ◽  
Boar Semen ◽  
Isobaric Tags ◽  
Boar Spermatozoa

Cryodamage is a major problem in semen cryopreservation, causing changes in the levels of proteins that influence the function and motility of spermatozoa. In this study, protein samples prepared from fresh and frozen–thawed boar spermatozoa were compared using the isobaric tags for relative and absolute quantification (iTRAQ) labeling technique coupled to 2D LC–MS/MS analysis. A total of 41 differentially expressed proteins were identified and quantified, including 35 proteins that were present at higher levels and six proteins that were present at lower levels in frozen–thawed spermatozoa by at least a mean of 1.79-fold (P<0.05). On classifying into ten distinct categories using bioinformatic analysis, most of the 41 differentially expressed proteins were found to be closely relevant to sperm premature capacitation, adhesions, energy supply, and sperm–oocyte binding and fusion. The expression of four of these proteins, SOD1, TPI1, ODF2, and AKAP3, was verified by western blot analysis. We propose that alterations in these identified proteins affect the quality of cryopreserved semen and ultimately lower its fertilizing capacity. This is the first study to compare protein levels in fresh and frozen–thawed spermatozoa using the iTRAQ technology. Our preliminary results provide an overview of the molecular mechanisms of cryodamage in frozen–thawed spermatozoa and theoretical guidance to improve the cryopreservation of boar semen.

scholarly journals Quantitative Proteomics Analysis to Study the Protective Effects of Nerve Growth Factor on Hippocampal Mitochondria in VD Rats

2021 ◽  
Author(s):  
Yanmei Zhang ◽  
yuan yao ◽  
Runxiu Zhu ◽  
Niyang Aida ◽  
Jun Yuan ◽  
...  
Keyword(s):  
Nerve Growth Factor ◽  
Growth Factor ◽  
Molecular Mechanism ◽  
Molecular Mechanisms ◽  
Clinical Syndrome ◽  
Differentially Expressed ◽  
Protective Effects ◽  
Differentially Expressed Proteins ◽  
Sprague Dawley ◽  
Nerve Growth

Abstract Background Vascular dementia (VD) is a kind of clinical syndrome characterized with the impairment cognitive function caused by cerebrovascular disease. Genetics, biochemical, and morphological analyses of cell and animal models, reveal that mitochondria could have roles in this neurodegeneration. Methods We used Sprague-Dawley rats to establish VD model, and used the proteomics method based on relative quantification (iTRAQ) to identify the differentially expressed proteins in hippocampus mitochondria. Results A total of 33 differentially expressed proteins were identified between the VD rats and the VD rats treated with nerve growth factor groups. And five differentially expressed proteins (Rgs14, Slc7a14, Ppm1l, Kcnj10 and Syngr1) were identified after completing the sham-operate control, VD rats and VD rats treated with nerve growth factor groups, then successfully confirmed by western blot. Bioinformatics analysis suggested that the mitochondrial molecular mechanism of VD and the protective effect of nerve growth factor on mitochondrial function of VD rats may be due to different molecular mechanisms. Conclusion We estimated that mitochondrial dysfunction may be the onset of VD and key role in the pathological process of VD. This study not only has a deeper understanding of the mitochondrial molecular mechanism of VD, but also is helpful for the screening of drug targets.

scholarly journals Isobaric Tags for Relative and Absolute Quantitation-Based Quantitative Serum Proteomics Analysis in Ischemic Stroke Patients With Hemorrhagic Transformation

2021 ◽  
Vol 15 ◽  
Author(s):  
Zhifeng Qi ◽  
Shuhua Yuan ◽  
Xixi Zhou ◽  
Xunming Ji ◽  
Ke Jian Liu
Keyword(s):  
Ischemic Stroke ◽  
Interaction Analysis ◽  
Hemorrhagic Transformation ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Stroke Patients ◽  
Absolute Quantitation ◽  
Metabolic Pathway Analysis ◽  
Serum Proteomics ◽  
Isobaric Tags

Hemorrhagic transformation (HT), which occurs with or without reperfusion treatments (thrombolysis and/or thrombectomy), deteriorates the outcomes of ischemic stroke patients. It is essential to find clinically reliable biomarkers that can predict HT. In this study, we screened for potential serum biomarkers from an existing blood bank and database with 243 suspected acute ischemic stroke (AIS) patients. A total of 37 patients were enrolled, who were diagnosed as AIS without receiving reperfusion treatment. They were divided into two groups based on whether they were accompanied with HT or not (five HT and 32 non-HT). Serum samples were labeled by isobaric tags for relative and absolute quantitation (iTRAQ) and analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and compared under NCBInr database. A total of 647 proteins in sera samples were captured, and the levels of 17 proteins (12 upregulated and five downregulated) were significantly different. These differentially expressed proteins were further categorized with Gene Ontology functional classification annotation and Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis into biological processes. Further protein–protein interaction analysis using String database discovered that, among the differentially expressed proteins, 10 pairs of proteins were found to have crosstalk connections, which may have direct (physical) and indirect (functional) interactions for the development of HT. Our findings suggest that these differentially expressed proteins could serve as potential biomarkers for predicting HT after ischemic stroke.

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