Genetic network and pathway analysis of differentially expressed proteins during critical cellular events in fracture repair

2007 ◽  
Vol 100 (2) ◽  
pp. 527-543 ◽  
Author(s):  
Xinmin Li ◽  
Hali Wang ◽  
Edward Touma ◽  
Emma Rousseau ◽  
Richard J. Quigg ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Genetic Network ◽  
Fracture Repair ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Cellular Events

scholarly journals Proteomics profiling and pathway analysis of hippocampal aging in rhesus monkeys

2019 ◽  
Author(s):  
Shu Meng ◽  
Wenchao Xia ◽  
Meng Pan ◽  
Yangjie Jia ◽  
Zhanlong He ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Rhesus Monkeys ◽  
Rhesus Macaques ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Marker Selection ◽  
Biological Pathway Analysis ◽  
Age Related ◽  
Tandem Mass Tag ◽  
High Level

Abstract Background: Aged rhesus monkeys exhibit deficits in memory mediated by the hippocampus. Although extensive research has been carried out on the characteristics of human hippocampal aging, there is still very little scientific understanding of the changes associated with hippocampal aging in rhesus monkeys. To explore the proteomics profiling and pathway-related changes in the rhesus hippocampus during the aging process, we conducted a high throughput quantitative proteomics analysis of hippocampal samples from two groups of rhesus macaques aged 6 years and 20 years, using 2-plex tandem mass tag (TMT) labeling. In addition, we used a comprehensive bioinformatics analysis approach to investigate the enriched signaling pathways of differentially expressed proteins (the ratios of 20-y vs. 6-y, ≥1.20 or ≤ 0.83). Results: In total, 3,260 proteins were identified with a high level of confidence in rhesus hippocampus. We found 367 differentially expressed proteins related to rhesus hippocampus aging. Based on biological pathway analysis, we found these aging-related proteins were predominantly enriched in the electron transport chain, NRF2 pathway, focal adhesion-PI3K-AKT-mTOR signaling pathway and cytoplasmic ribosome proteins. Data are available via ProteomeXchange with identifier PXD011398. Conclusion: This study provides a detail description of the proteomics profile related to rhesus hippocampal aging. These findings should make an important contribution to further mechanistic studies, marker selection and drug development for the prevention and treatment of aging or age-related neurodegeneration.

scholarly journals Differential Protein Abundance in Dark-Cutting and Normal-pH Beef

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
F. Kiyimba ◽  
S. Hartson ◽  
J. Rogers ◽  
G. Mafi ◽  
D. VanOverbeke ◽  
...  
Keyword(s):  
Protein Expression ◽  
Pathway Analysis ◽  
Solid Phase ◽  
Muscle Protein ◽  
Expression Profiles ◽  
Protein Profile ◽  
Differentially Expressed ◽  
Cutting Condition ◽  
Differentially Expressed Proteins ◽  
Differential Protein

ObjectivesDark-cutting beef is a meat quality defect in which meat does not display the marketable bright-red color. Although previous studies have indicated that the ultimate pH of dark-cutting beef is greater than normal, the mechanistic basis for the occurrence is not clear. Various mitochondrial and glycolytic enzymes/proteins are involved in muscle metabolism and lowering of pH. However, limited knowledge is currently available on the muscle protein profile differences between dark-cutting and normal-pH beef. The objective of the current study was to identify proteins related to the development of the dark-cutting condition by comparing the protein expression differences between dark-cutting and normal-pH beef.Materials and MethodsDark-cutting and normal-pH beef samples were collected from six (n = 6) different animals after slaughter. Tissue samples (0.5 g) were digested in 5 mL of lysis buffer. Tissue lysates were homogenized, boiled, sonicated using a bioruptor and centrifuged at 10,000 g for 10 min. Samples were digested with trypsin/Lys-C overnight at 37°C, after which additional 2 µg/mL of protease was added and digestion was continued for another 8h. The resulting trypsinolytic peptides were acidified to 1% trifluoroacetic acid and purified by solid phase extraction with C18 affinity media. Protein expression profiles of both dark-cutting and normal-pH beef samples were determined using LC-MS/MS mass spectrometry-based proteomics. Collected raw data instrument files were searched against a bovine proteome database of 23,968 bovine proteome sequences using MaxQuant (V.1.5.3.8). Differential protein expression analysis was done in Perseus (V.1.5.1.3). Ingenuity pathway analysis (IPA) was utilized to determine the significant pathways of the differentially expressed proteins in dark-cutting and normal-pH beef. Gene ontology enrichment pathway analysis was performed to determine the main functions of the differentially expressed proteins in dark-cutting and normal-pH beef identified in our samples.ResultsMass spectrometry analysis identified 1148 proteins, and 97 of these proteins were differentially expressed between normal-pH and dark-cutting beef (P < 0.05). Fold change of 1.5 was observed for 29 proteins. Dark-cutting beef had 19 abundant proteins, while normal-pH beef had 10 abundant proteins. The majority of the upregulated proteins in dark-cutting beef were involved in mitochondrial functioning and metabolism, while the majority of the downregulated proteins were important in glycogen degradation, calcium signaling, α-adrenergic signaling, n-NOS-signaling and the proteasome pathways.ConclusionThe results identify new protein biomarkers associated with dark-cutting and suggest new mechanistic explanations for the dark-cutting phenotype.

scholarly journals Proteomics profiling and pathway analysis of hippocampal aging in rhesus monkeys

2019 ◽  
Author(s):  
Shu Meng ◽  
Wenchao Xia ◽  
Meng Pan ◽  
Zhanlong He ◽  
Wei Ge
Keyword(s):  
Pathway Analysis ◽  
Rhesus Monkeys ◽  
Rhesus Macaques ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Marker Selection ◽  
Biological Pathway Analysis ◽  
Age Related ◽  
Tandem Mass Tag ◽  
High Level

Abstract Background Aged rhesus monkeys exhibit deficits in memory mediated by the hippocampus. Although extensive research has been carried out on the characteristics of human hippocampal aging, there is still very little scientific understanding of the changes associated with hippocampal aging in rhesus monkeys. To explore the proteomics profiling and pathway-related changes in the rhesus hippocampus during the aging process, we conducted a high throughput quantitative proteomics analysis of hippocampal samples from two groups of rhesus macaques aged 6 years and 20 years, using 2-plex tandem mass tag (TMT) labeling. In addition, we used a comprehensive bioinformatics analysis approach to investigate the enriched signaling pathways of differentially expressed proteins (20-y vs. 6-y ≥1.20 or ≤ 0.83). Results In total, 3,260 proteins were identified with a high level of confidence in rhesus hippocampus. We found 367 differentially expressed proteins related to rhesus hippocampus aging. Based on biological pathway analysis, we found these aging-related proteins were predominantly enriched in the electron transport chain, NRF2 pathway, focal adhesion-PI3K-AKT-mTOR signaling pathway and cytoplasmic ribosome proteins. Data are available via ProteomeXchange with identifier PXD011398. Conclusion This study provides a further understanding of the proteomics profile related to rhesus hippocampal aging, which will help to elucidate the differences between rhesus and human hippocampal aging. These findings should make an important contribution to further mechanistic studies, marker selection and drug development for the prevention and treatment of aging or age-related neurodegeneration.

scholarly journals Quantitative analysis of proteomic profiling in constipation colon biopsies

2020 ◽  
Author(s):  
Chen Ye ◽  
Qiyi Chen ◽  
Di Zhao ◽  
Hongliang Tian ◽  
Xueying Zhang ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Pathway Analysis ◽  
Expression Profiles ◽  
Human Colon ◽  
Quantitative Information ◽  
Differentially Expressed ◽  
Spectrometric Analysis ◽  
Common Disease ◽  
Differentially Expressed Proteins ◽  
Proteomic Profiling

Abstract Background Chronic constipation is a common disease and between 2% and 27% of people are suffering from it in the world. Rare studies explore the diversity of genetic polymorphisms and cell metabolisms in constipation. This study provided a first analysis of constipation-related proteomic data. Methods To help elucidate the potential mechanisms responsible for constipation, proteomic profiling of human colon biopsy specimens was performed. Dysregulated proteins in disease tissues compared with normal tissues were characterized from the expression profiles by Liquid chromatography–mass spectrometry and Tandem Mass Tag proteomic methodology and further subjected to pathway analysis to identify altered biological processes and signaling pathways. Results A total of 5,208 proteins were identified, of which 4,522 had quantitative information. All the differentially expressed proteins displayed fold change greater than 1.3 were considered as dysregulated. Specifically, 42 proteins were up-regulated and 23 proteins were down-regulated in constipation samples. Bioinformatics analysis showed that most of the differentially expressed proteins were involved in the cellular process, single-organism process, metabolic process, biological regulation and response to stimulus. Pathway analysis of dysregulated proteins in constipation showed that the up-regulated proteins mainly participated in drug metabolism-cytochrome P450. Conclusions The TMT method followed by mass spectrometric analysis was applied to study the biopsy proteomic profiling alterations in constipation patients. Our results clearly proved that different protein profiles and signaling pathways were involved in constipation patients.

scholarly journals Proteome Analysis in PAM Cells Reveals That African Swine Fever Virus Can Regulate the Level of Intracellular Polyamines to Facilitate Its Own Replication through ARG1

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1236
Author(s):  
Qiangyun Ai ◽  
Xiwei Lin ◽  
Hangao Xie ◽  
Bin Li ◽  
Ming Liao ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Host Cell ◽  
Pathway Analysis ◽  
High Performance ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Proteomics Data

In 2018, African swine fever broke out in China, and the death rate after infection was close to 100%. There is no effective and safe vaccine in the world. In order to better characterize and understand the virus–host-cell interaction, quantitative proteomics was performed on porcine alveolar macrophages (PAM) infected with ASFV through tandem mass spectrometry (TMT) technology, high-performance liquid chromatography (HPLC), and mass spectrometry (MS). The proteome difference between the simulated group and the ASFV-infected group was found at 24 h. A total of 4218 proteins were identified, including 306 up-regulated differentially expressed proteins and 238 down-regulated differentially expressed proteins. Western blot analysis confirmed changes in the expression level of the selected protein. Pathway analysis is used to reveal the regulation of protein and interaction pathways after ASFV infection. Functional network and pathway analysis can provide an insight into the complexity and dynamics of virus–host cell interactions. Further study combined with proteomics data found that ARG1 has a very important effect on ASFV replication. It should be noted that the host metabolic pathway of ARG1-polyamine is important for virus replication, revealing that the virus may facilitate its own replication by regulating the level of small molecules in the host cell.

Mass Spectrometry-based Label-free Quantitative Proteomic Analysis of CCl4-induced Acute Liver Injury in Mice Intervened by Total Glycosides from Ligustri Lucidi Fructus

2020 ◽  
Vol 17 ◽  
Author(s):  
Qian Lu ◽  
Hai-Zhu Xing ◽  
Nian-Yun Yang
Keyword(s):  
Insulin Resistance ◽  
Liver Injury ◽  
Protein Expression ◽  
Signaling Pathway ◽  
Proteomic Analysis ◽  
Acute Liver Injury ◽  
Liver Cells ◽  
Differentially Expressed ◽  
Liver Protein ◽  
Differentially Expressed Proteins

Background: CCl4 acute liver injury (ALI) is a classical model for experimental research. However, there are few reports involved in the fundamental research of CCl4-induced ALI Ligustri Lucidi Fructus (LLF) are and its prescription have been used to treat hepatitis illness clinically. LLF and its active ingredients displayed anti-hepatitis effects, but the mechanism of function has not been fully clarified Objective: To investigate the proteomic analysis of CCl4-induced ALI, and examine the effects of active total glycosides (TG) from LLF on ALI of mice4, including histopathological survey and proteomic changes of liver tissues, and delineate the possible underlying mechanism. Methods: CCl4 was used to produce ALI mice model. The model mice were intragastrically administrated with TG and the liver his-topathological changes of mice were examined. At the end of test, mice liver samples were collected, after protein denaturation, re-duction, desalination and enzymatic hydrolysis, identification was carried out by nano LC-ESI-OrbiTrap MS/MS technology. The data was processed by Maxquant software. The differentially-expressed proteins were screened and identified, and their biological information was also analyzed based on GO and KEGG analysis. Key protein expression was validated by Western blot analysis Results: A total of 705 differentially-expressed proteins were identified during the normal, model and administration group. 9 signifi-cant differential proteins were focused based on analysis. Liver protein expression changes of CCl4-induced ALI mice were mainly involved in several important signal channels, namely FoxO signaling pathway, autophagy-animal, insulin signaling pathway. TG has anti-liver damnification effect in ALI mice, the mechanism of which is related to FoxO1 and autophagy pathways Conclusion: CCl4 inhibited expression of insulin-Like growth factor 1 (Igf1) and 3-phosphoinositide-dependent protein kinase 1 (Pdpk1) in liver cells and induced insulin resistance, thus interfered with mitochondrial autophagy and regeneration of liver cells and the metabolism of glucose and lipid, and caused hepatic necrosis in mice. TG resisted liver injury in mice. TG adjusted the expression level of key proteins Igf1 and Pdpk1 after liver injury and improved insulin resistance, thus promoted autophagy and resisted the liver damage

scholarly journals Differentially expressed proteins in platelets derived from patients with hypertension

2021 ◽  
Author(s):  
Yobana Armenta-Medina ◽  
Ivette Martínez-Vieyra ◽  
Oscar Medina-Contreras ◽  
Claudia G. Benitez-Cardoza ◽  
Albertana Jiménez-Pineda ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Differentially Expressed Proteins

scholarly journals ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Rong Zhang ◽  
Weitao Jiang ◽  
Xin Liu ◽  
Yanan Duan ◽  
Li Xiang ◽  
...  
Keyword(s):  
Fusarium Moniliforme ◽  
Abiotic Factors ◽  
Fusarium Verticillioides ◽  
Protein Profile ◽  
Sugar Metabolism ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Differentially Expressed Proteins ◽  
Apple Replant Disease ◽  
Qrt Pcr

Abstract Background Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp. in ARD was further clarified. Methods In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis. Results A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P< 0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P< 0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. Conclusions This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

Sign in / Sign up

Export Citation Format

Share Document