differential proteins
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PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261488
Author(s):  
Wenshu Meng ◽  
Chenyang Zhao ◽  
Youhe Gao

Purpose To explore and compare urine proteome changes among rat models by intraperitoneal injection with single bacteria and co-injection with two bacteria. Method Escherichia coli and Staphylococcus aureus are two common human pathogens. Three rat models were established: (i) the intraperitoneal co-injection of E. coli and S. aureus model (ES model), (ii) intraperitoneal injection of E. coli model (E model), and (iii) intraperitoneal injection of S. aureus model (S model). Urinary proteomes on days 0, 1 and 2 of the three models were analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results A total of 111, 34 and 94 differential proteins were identified in the ES model, E model and S model, respectively. Among them, some differential proteins were reported to be associated with bacterial infection. Approximately 47% differential proteins in the E model overlapped with ES model, and 37% differential proteins in the S model overlapped with ES model. Compared with the E model and S model, a total of 71 unique differential proteins were identified in the ES model. Conclusion Our results indicated that (1) the urine proteome could distinguish different bacterial intraperitoneal injections models and (2) the effects of co-injection with two bacteria on the urine proteome were not simple superposition of single injection.


2021 ◽  
Author(s):  
Ruohui LIN ◽  
Bingying XIE ◽  
Lihua XIE ◽  
Jirong GE ◽  
Shengqiang Li

Abstract Background Gushukang (GSK) capsule is a Chinese patent medicine for the treatment of osteoporosis (OP). It has been widely used in clinics. However, the specific mechanism and target of GSK in the treatment of osteoporosis is not clear, which needs further study. Methods Metabolomics (GC/MS) and proteomics (TMT-LC-MC/MC) together with bioinformatics (KEGG pathway enrichment), correlation analysis (pearson correlation matrix) and joint pathway analysis (Metabo Analyst) were employed to discover the underlying mechanisms of GSK. Results The regulations of differential proteins Cant1, Gstz1, Aldh3b1, Bid and Slc1a3 in the common metabolic pathway of differential proteins and metabolites between GSK/OP and OP/SHAM were corrected in GSK group. The regulations of 12 metabolites (Tyramine、Thymidine、Deoxycytidine、Cytosine、L-Aspartate and so on) were differential in the common enrichment metabolic pathway between GSK /OVX and OVX/SHAM. Differential proteins and metabolites jointly regulate 11 metabolic pathways, such as purine metabolism, pyrimidine metabolism, histidine metabolism, beta-Alanine metabolism and so on. Conclusion GSK may protect bone metabolism in osteoporosis rats by affecting nucleotide metabolism, amino acid metabolism and immune system.


2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Kang Zhao ◽  
Jucun Huang ◽  
Hongmei Xia ◽  
Jianjun Zhang ◽  
Liming Liu

Background. Hepatic fibrosis is a severe liver disease that has threatened human health for a long time. In order to undergo timely and adequate therapy, it is important for patients to obtain an accurate diagnosis of fibrosis. Laboratory inspection methods have been efficient in distinguishing between advanced hepatic fibrosis stages (F3, F4), but the identification of early stages of fibrosis has not been achieved. The development of proteomics may provide us with a new direction to identify the stages of fibrosis. Methods. We established serum proteomic maps for patients with hepatic fibrosis at different stages and identified differential expression of proteins between fibrosis stages through ultra-high-performance liquid chromatography tandem mass spectrometry proteomic analysis. Results. From the proteomic profiles of the serum of patients with different stages of liver fibrosis, a total of 1,338 proteins were identified. Among three early fibrosis stages (control, F1, and F2), 55 differential proteins were identified, but no proteins simultaneously exhibited differential expression between control, F1, and F2. Differential proteins were detected in the comparison between different fibrosis stages. Significant differences were found between advanced fibrosis stages (F2-vs.-F3 and F3-vs.-F4) through a series of statistical analysis, including hierarchical clustering, Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes pathway, and protein-protein interaction network analysis. The differential proteins identified by GO annotation were associated with biological processes (mainly platelet degranulation and cell adhesion), molecular functions, and cellular components. Conclusions. All potential biomarkers identified between the stages of fibrosis could be key points in determining the fibrosis staging. The differences between early stages may provide a useful reference in addressing the challenge of early fibrosis staging.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weiwei Qin ◽  
Xiao Zhang ◽  
Lingnan Chen ◽  
Qiujie Li ◽  
Benwang Zhang ◽  
...  

AbstractUrine is a promising resource for biomarker research. Therefore, the purpose of this study was to investigate potential urinary biomarkers to monitor the disease activity of ventilator-induced lung injury (VILI). In the discovery phase, a label-free data-dependent acquisition (DDA) quantitative proteomics method was used to profile the urinary proteomes of VILI rats. For further validation, the differential proteins were verified by parallel reaction monitoring (PRM)-targeted quantitative proteomics. In total, 727 high-confidence proteins were identified with at least 1 unique peptide (FDR ≤ 1%). Compared to the control group, 110 proteins (65 upregulated, 45 downregulated) were significantly changed in the VILI group (1.5-fold change, P < 0.05). The canonical pathways and protein–protein interaction analyses revealed that the differentially expressed proteins were enriched in multiple functions, including oxidative stress and inflammatory responses. Finally, thirteen proteins were identified as candidate biomarkers for VILI by PRM validation. Among these PRM-validated proteins, AMPN, MEP1B, LYSC1, DPP4 and CYC were previously reported as lung-associated disease biomarkers. SLC31, MEP1A, S15A2, NHRF1, XPP2, GGT1, HEXA, and ATPB were newly discovered in this study. Our results suggest that the urinary proteome might reflect the pathophysiological changes associated with VILI. These differential proteins are potential urinary biomarkers for the activity of VILI.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12406
Author(s):  
Wenshu Meng ◽  
Dan Xu ◽  
Yunchen Meng ◽  
Weinan Zhang ◽  
Yaqi Xue ◽  
...  

Purpose Urine can sensitively reflect early pathophysiological changes in the body. The purpose of this study was to explore the changes of urine proteome in rats with regular swimming exercise. Methods In this study, experimental rats were subjected to daily moderate-intensity swimming exercise for 7 weeks. Urine samples were collected at weeks 2, 5, and 7 and were analyzed by using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Results Unsupervised clustering analysis of all urinary proteins identified at week 2 showed that the swimming group was distinctively different from the control group. Compared to the control group, a total of 112, 61 and 44 differential proteins were identified in the swimming group at weeks 2, 5 and 7, respectively. Randomized grouping statistical analysis showed that more than 85% of the differential proteins identified in this study were caused by swimming exercise rather than random allocation. According to the Human Protein Atlas, the differential proteins that have human orthologs were strongly expressed in the liver, kidney and intestine. Functional annotation analysis revealed that these differential proteins were involved in glucose metabolism and immunity-related pathways. Conclusion Our results revealed that the urinary proteome could reflect significant changes after regular swimming exercise. These findings may provide an approach to monitor the effects of exercise of the body.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yuhang Huan ◽  
Jing Wei ◽  
Jingjing Zhou ◽  
Min Liu ◽  
Jian Yang ◽  
...  

Major depressive disorder (MDD) is a common mental disorder that can cause substantial impairments in quality of life. Clinical treatment is usually built on a trial-and-error method, which lasts ~12 weeks to evaluate whether the treatment is efficient, thereby leading to some inefficient treatment measures. Therefore, we intended to identify early candidate urine biomarkers to predict efficient treatment response in MDD patients. In this study, urine samples were collected twice from 19 respondent and 10 non-respondent MDD patients receiving 0-, 2-, and 12-week treatments with escitalopram. Differential urinary proteins were subsequently analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Our two pilot tests suggested that the urine proteome reflects changes associated with major depressive disorder at the early stage of treatment measures. On week 2, 20 differential proteins were identified in the response group compared with week 0, with 14 of these proteins being associated with the mechanisms of MDD. In the non-response group, 60 differential proteins were identified at week 2, with 28 of these proteins being associated with the mechanisms of MDD. In addition, differential urinary proteins at week 2 between the response and non-response groups can be clearly distinguished by using orthogonal projection on latent structure-discriminant analysis (OPLS-DA). Our small pilot tests indicated that the urine proteome can reflect early effects of escitalopram therapy between the response and non-response groups since at week 2, which may provide potential early candidate urine biomarkers to predict efficient treatment measures in MDD patients.


2021 ◽  
Author(s):  
Chenyang Zhao ◽  
Lilong Wei ◽  
Jing Wei ◽  
Youhe Gao

AbstractObjectiveTo provide diagnostic evidence and clues for patients with fever of unknown origin (FUO) through urine proteomics analysis.MethodsUrine samples of FUO were one–to–many analysed by using liquid chromatography tandem mass spectrometry(LC–MS/MS) to identify differential proteins and related biological pathways. One–to–many analysis means a comparative analysis of one sample to many controls.ResultsWe observed biological pathways related to fever, such as LXR/RXR activation, FXR/RXR activation and acute phase response signaling, etc., which indicates that urine can obviously distinguish disease from health status. In addition, we found that the results of each sample were different, which highlight the necessity of one–to–many analysis.ConclusionsThe combined method of urine proteomics and one–to–many analysis can provide clues for FUO, and might also be applied to the exploration of any unknown disease.


2021 ◽  
Author(s):  
lin fang li ◽  
Yao liu ◽  
mu hu chen ◽  
ying chun hu

Abstract Objective This study applies the data independent acquisition (DIA) technique combined with bioinformatics to identify differential proteins in sepsis patients and performed ELISA method to validate the candidate protein of clinical value, in an attempt to find new biomarkers for the diagnosis and prognosis of sepsis. Methods Blood samples from sepsis patients (Sepsis group, n = 50) and healthy individuals (NC group, n = 10) were collected from Affiliated Hospital of Southwest Medical University. Mass spectrometry analysis was designed for 22 sepsis samples (randomly selected) and 10 healthy controls by DIA method, and the obtained differential proteins were subjected to GO annotation, meta-analysis and survival analysis to identify the candidate biomarker protein. ELISA was applied to validate the protein expression in original cohorts. ROC curves based on ELISA data were plotted to discuss the diagnostic and prognostic performance of the candidate protein and several clinical indexes, including C-reactive protein (CRP), procalcitonin (PCT) and lactate (Lac). Results DIA data showed that there were 142 differential proteins in the Sepsis group versus the NC group, comprising 36 down-regulated and 106 up-regulated. GO annotation revealed that the differential proteins were significantly enriched in the biological functions involved in immune response, response to stress, inflammatory response, and cell activation. The top 11 proteins with the greatest difference were found according to the p-values in DIA (FUCO2, MGAT1, OAF, AACT, TFRC, CCL14, EXTL2, KLKB1, TETN,CRP,SAA1). Meta-analysis identified significant differential expression of TFRC in the NC versus Sepsis and in the Survival versus Non-survival groups based on GEO database. Survival analysis revealed that the low expression of TFRC indicated a higher survival rate in sepsis patients. ELISA found TFRC concentration in collected clinical samples were significant differential in the NC versus Sepsis and in the Survival versus Nonsurvival groups (p < 0.05). ROC curves gave an AUC of 0.790 for TFRC in distinguishing the normal individuals and sepsis patients, showing good diagnostic performance. Besides, the AUC for TFRC in distinguishing the survivors and deaths was 0.744, indicating good prognostic performance, which was superior to PCT, CRP and Lac. Conclusion This study identified TFRC through DIA, bioinformatics and ELISA analyses, which showed differential expression in sepsis patients as well as good diagnostic and prognostic value. TFRC is expected to be a potential biomarker for sepsis.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Quan Li ◽  
Xiangyang Li ◽  
Hui Lin

The extracts of decay-resistant tree species are important research objects for the future development of wood preservatives. To understand the antifungal mechanisms of Coriolus versicolor inhibition with methanol extracts of C. camphora xylem, the protein profiles of C. versicolor were analyzed using 2-DE followed by MALDI-TOF/MS and bioinformatic analyses. The results showed that 41 protein spots were obviously changed among the 366-385 protein spots of C. versicolor treated with methanol extracts of C. camphora xylem. Twenty-one protein spots were upregulated, and 20 protein spots were downregulated. Cellular localization was performed to identify these differential proteins, and biological process and functional analysis found that 9 of these proteins were in the cytoplasm, 6 were intracellular, and 5 were in the mitochondrion. A total of 18.8% were mapped to small-molecule metabolic processes, 12.5% to cellular amino acid metabolic processes, and 10.9% to cellular nitrogen compound metabolic processes. Twenty-five percent of the differential proteins were associated with ion bonding, 15% with oxidoreductase activity, and 15% with ATPase activity and transmembrane transport activity. Downregulated expression of aspartate aminotransferase, ATP synthase alpha chain, DEAD/DEAH-box helicase, and phosphoglycerate kinase showed that the methanol extracts of C. camphora xylem disrupted functional aspects such as nitrogen and carbon metabolism, energy metabolism, hormone signal response, and glucose metabolism, eventually leading to C. versicolor inhibition.


2021 ◽  
Author(s):  
Juan Wang ◽  
Jianping Mao ◽  
Gang Chen ◽  
Yuanmei Huang ◽  
Jinjin Zhou ◽  
...  

Abstract This study aimed to explore the proteins in cord blood that could regulate the development of neonatal bronchi and lungs, and to find a new target for the prevention and treatment of bronchopulmonary dysplasia (BPD). In this study, proteomic analysis was used to analyze the proteins in cord blood of preterm and term infants. A total of 100 differentially expressed (57 up-regulated and 43 down-regulated) proteins were identified from preterm with BPD and term infants cord blood (fold change ≥ 1.5, P value < 0.05). GO analysis revealed that the major enrichment functions of these differential proteins were multi-organism process, stimulus, immune system process growth, reproductive process, development process and antioxidant activity. The signaling pathways involved included insulin resistance, insulin signaling pathway, IL−17 signaling pathway, PI3K−Akt signaling pathway, NF−kappa B signaling pathway, glucagon signaling pathway, apoptosis, MAPK signaling pathway, as well as glycolysis/gluconeogenesis. Further protein and protein interact (PPI) analysis revealed that the interacting proteins involved were PGAM1, CNN2, HSP90AA and DAG1, which were all crucial in the development of BPD. We found that these differential proteins in cord blood might regulate bronchopulmonary development through the abovementioned signaling pathways or their interaction proteins, which may provide a new research direction for the intervention of BPD.


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