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 Proteomic signatures of human visceral and subcutaneous adipocytes

2021 ◽  
Author(s):  
Pavel Hruska ◽  
Jan Kucera ◽  
Matej Pekar ◽  
Pavol Holeczy ◽  
Miloslav Mazur ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Protein Profile ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Obese Women ◽  
Biosynthetic Activity ◽  
Mitochondrial Energy Metabolism ◽  
Key Factor

Abstract Objective Adipose tissue distribution is a key factor influencing metabolic health and risk in obesity-associated comorbidities. Here we aim to compare the proteomic profiles of mature adipocytes from different depots. Methods Abdominal subcutaneous (SA) and omental visceral adipocytes (VA) were isolated from paired AT biopsies obtained during bariatric surgery of 19 severely obese women (BMI &gt; 30 kg/m 2) and analysed using state-of-the-art mass spectrometry. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to investigate proteome signature properties and to examine a possible association of the protein expression with the clinical data. Results We identified 3,686 protein groups and found 1,140 differentially expressed proteins (adj. p-value &lt; 0.05), of which 576 proteins were upregulated in SA and 564 in VA samples. We provide a global protein profile of abdominal SA and omental VA, present the most differentially expressed pathways and processes distinguishing SA from VA, and correlate them with clinical and body composition data. We show that SA are significantly more active in processes linked to vesicular transport and secretion, and to increased lipid metabolism activity. Conversely, the expression of proteins involved in the mitochondrial energy metabolism and translational or biosynthetic activity is higher in VA. Conclusion Our analysis represents a valuable resource of protein expression profiles in abdominal SA and omental VA, highlighting key differences in their role in obesity.

scholarly journals TMT-based proteomic and bioinformatic analyses of human granulosa cells from obese and normal-weight female subjects

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chenchen Si ◽  
Nan Wang ◽  
Mingjie Wang ◽  
Yue Liu ◽  
Zhihong Niu ◽  
...  
Keyword(s):  
Protein Expression ◽  
Granulosa Cells ◽  
Follicular Fluid ◽  
Expression Profiles ◽  
Normal Weight ◽  
Differentially Expressed ◽  
Tandem Mass ◽  
Differentially Expressed Proteins ◽  
Obese Subjects ◽  
Female Subjects

Abstract Background Increasing evidence supports a relationship between obesity and either infertility or subfertility in women. Most previous omics studies were focused on determining if the serum and follicular fluid expression profiles of subjects afflicted with both obesity-related infertility and polycystic ovary syndrome (PCOS) are different than those in normal healthy controls. As granulosa cells (GCs) are essential for oocyte development and fertility, we determined here if the protein expression profiles in the GCs from obese subjects are different than those in their normal-weight counterpart. Methods GC samples were collected from obese female subjects (n = 14) and normal-weight female subjects (n = 12) who were infertile and underwent in vitro fertilization (IVF) treatment due to tubal pathology. A quantitative approach including tandem mass tag labeling and liquid chromatography tandem mass spectrometry (TMT) was employed to identify differentially expressed proteins. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were then conducted to interrogate the functions and pathways of identified proteins. Clinical, hormonal, and biochemical parameters were also analyzed in both groups. Results A total of 228 differentially expressed proteins were noted, including 138 that were upregulated whereas 90 others were downregulated. Significant pathways and GO terms associated with protein expression changes were also identified, especially within the mitochondrial electron transport chain. The levels of free fatty acids in both the serum and follicular fluid of obese subjects were significantly higher than those in matched normal-weight subjects. Conclusions In GCs obtained from obese subjects, their mitochondria were damaged and the endoplasmic reticulum stress response was accompanied by dysregulated hormonal synthesis whereas none of these changes occurred in normal-weight subjects. These alterations may be related to the high FFA and TG levels detected in human follicular fluid.

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.

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 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 Cite-Seq Reveals Distinct Patterns and Potential Mechanisms of Relapse in Pediatric AML

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3458-3458
Author(s):  
Tsz-Kwong Man ◽  
Mohammad Javad Najaf Panah ◽  
Jessica L. Elswood ◽  
Pavel Sumazin ◽  
Michele S. Redell
Keyword(s):  
Protein Expression ◽  
Single Cell ◽  
Actin Polymerization ◽  
Conflicts Of Interest ◽  
Limit Of Detection ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cell Types ◽  
Differentially Expressed ◽  
Pediatric Aml

Abstract Introduction - Acute myeloid leukemia (AML) is an aggressive disease with a relapse rate of approximately 40% in children. Progress in improving cure rates has been slow, in part because AML is very heterogeneous. Molecular studies consistently show that most cases are comprised of distinct subclones that diminish or expand over the course of therapy. Single-cell profiling methods now allow parsing of the leukemic population into subsets based on gene and/or protein expression patterns. We hypothesized that comparing the features of the subsets that are dominant at relapse with those that are dominant at diagnosis would reveal mechanisms of treatment failure. Methods - We profiled diagnosis-relapse pairs from 6 pediatric AML patients by Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq). All patients were treated at Texas Children's Cancer Center and consented to banking of tissue for research. CITE-Seq was performed by Immunai (New York, NY) using a customized panel of 65 oligonucleotide-tagged antibodies, the 10x Genomics Chromium system for single-cell RNA library generation, and the Novaseq 6000 for sequencing. After data cleanup and normalization, clustering by scRNA-seq was done using the Seurat package. Cell-type identification of clusters was facilitated by published healthy bone marrow scRNA-seq datasets (van Galen et al, Cell 2019). Differentially expressed genes (DEGs) and proteins (DEPs) between diagnosis and relapse were determined using Wilcoxin ranked sum tests. Results - We generated single-cell transcriptomes for a total of 28,486 cells from 12 samples, with a mean of 2373 cells and 1416 genes per sample. Samples were integrated with batch effect correction, producing 30 distinct clusters (cell types) in total (Figure 1A). Cell types with expression profiles consistent with lymphocytes and erythroid precursors were identified in multiple patients, whereas AML cell types tended to be specific to individual patients (Figure 1B). For patients TCH1, TCH2 and TCH3, the most abundant cell types at diagnosis were rare at relapse, and cell types that were rare at diagnosis became dominant at relapse. For these 3 cases, we identified DEGs between the dominant diagnosis cell types and dominant relapse cell types. We found 18 genes that were upregulated at relapse in at least 2 of the cases. Several genes related to actin polymerization were enriched (ARPC1B, ACTB, PFN1), possibly reflecting an enhanced capacity for adhesion and migration. Also of note, macrophage migration inhibitory factor (MIF) and its receptor CD74 were upregulated at relapse, suggesting a role in chemoresistance. For patients TCH4, TCH5 and TCH6, the same cell types that were abundant at diagnosis were also abundant at relapse, and few genes were significantly altered between diagnosis and relapse in multiple cases. Only SRGN, which encodes the proteoglycan serglycin, and GAPDH were altered in 2 of these 3 cases, and both were downregulated at relapse. We performed similar comparisons to identify proteins that were differentially expressed between diagnosis and relapse pairs. The number of DEPs between the dominant diagnosis and relapse cell types ranged from 0 (TCH1 and TCH6) to 5 (TCH2). The only protein altered in more than one case was CD7, which was enriched at relapse in TCH2, TCH3 and TCH4. Conclusions - From CITE-Seq profiling of 6 pediatric AML cases we identified two distinct patterns of relapse. For 3 cases, relapse occurred by expansion of a subset that was small but present at diagnosis. Enrichment of genes associated with adhesion and survival signaling suggests that these cells survived because they were well-equipped to take advantage of interactions with the microenvironment. For 3 other cases, the population that was dominant at diagnosis persisted and expanded at relapse with few substantial changes in gene or protein expression profiles. This pattern suggests that these AML cells were a priori equipped to survive chemotherapy, even though bulk disease levels were transiently reduced below the limit of detection. Most profiled proteins did not change substantially between diagnosis and relapse. An exception is CD7, which was enriched at relapse in 50% of our cases and represents a potential therapeutic target. Analysis of more cases will refine these relapse patterns, reveal potential mechanisms of chemoresistance and inform the development of novel therapies. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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.

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>

Sign in / Sign up

Export Citation Format

Share Document