Common Differentially Expressed Proteins Research Articles

ITRAQ-based protein profiling and functional identification of four genes involved in rice basal resistance against Magnaporthe oryzae in two contrasting rice genotypes

Rice blast, caused by Magnaporthe oryzae, is one of the most destructive rice diseases. Developing blast-resistant rice cultivars represents the most economical and environmentally friend strategy for managing the disease. In our previous study, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative protein quantification was carried out to investigate the resistance gene Piz-t gene-mediated resistance response to infection in two contrasting rice genotypes of the Piz-t transgenic Nipponbare line (NPB-Piz-t) and its wild-type Nipponbare (NPB). Here, from the comparisons of differentially expressed proteins (DEPs) of NPB-Piz-t to the avirulent isolate KJ201 (KJ201-Piz-t)and the virulent isolate RB22 (RB22-Piz-t) with mock-treated NPB-Piz-t (Mock-Piz-t), NPB to the virulent isolate KJ201(KJ201-NPB) and RB22 (RB22-NPB) with mock-treated NPB (Mock-NPB), 1, 1, and 6 common DEPs were, respectively, identified at 24, 48 and 72 h post-inoculation (hpi) in the susceptible comparisons of RB22-Pizt/Mock-Piz-t, KJ201-NPB/Mock-NPB, and RB22-NPB/Mock-NPB, involving in gi|54,290,836 and gi|59,800,021 were identified in the resistance comparison KJ201-Piz-t/Mock-Piz-t at 48 and 72 hpi respectively. Moreover, four genes of Os01g0138900 (gi|54,290,836), Os04g0659300 (gi|59,800,021), Os09g0315700 (gi|125,563,186) or Os04g0394200 (gi|21,740,743) were knocked out or overexpressed in NPB using gene over-expression and CRISPR/Cas9 technology, and results verified that the Os01g0138900 obviously affected the rice blast resistance. Further, expression and targeted metabolomics analysis illuminated the resistance response of cysteine-containing substances as gi|59,800,021 under blast infection. These results provide new targets for basal resistance gene identification and open avenues for developing novel rice blast resistant materials.

Integrative proteomic profiling of lung tissues and blood in acute respiratory distress syndrome.

Acute respiratory distress syndrome and acute lung injury (ARDS/ALI) still lack a recognized diagnostic test and pharmacologic treatments that target the underlying pathology. To explore the sensitive non-invasive biomarkers associated with pathological changes in the lung of direct ARDS/ALI, we performed an integrative proteomic analysis of lung and blood samples from lipopolysaccharide (LPS)-induced ARDS mice and COVID-19-related ARDS patients. The common differentially expressed proteins (DEPs) were identified based on combined proteomic analysis of serum and lung samples in direct ARDS mice model. The clinical value of the common DEPs was validated in lung and plasma proteomics in cases of COVID-19-related ARDS. We identified 368 DEPs in serum and 504 in lung samples from LPS-induced ARDS mice. Gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEPs in lung tissues were primarily enriched in pathways, including IL-17 and B cell receptor signaling pathways, and the response to stimuli. In contrast, DEPs in the serum were mostly involved in metabolic pathways and cellular processes. Through network analysis of protein-protein interactions (PPI), we identified diverse clusters of DEPs in the lung and serum samples. We further identified 50 commonly upregulated and 10 commonly downregulated DEPs in the lung and serum samples. Internal validation with a parallel-reacted monitor (PRM) and external validation in the Gene Expression Omnibus (GEO) datasets further showed these confirmed DEPs. We then validated these proteins in the proteomics of patients with ARDS and identified six proteins (HP, LTA4H, S100A9, SAA1, SAA2, and SERPINA3) with good clinical diagnostic and prognostic value. These proteins can be viewed as sensitive and non-invasive biomarkers associated with lung pathological changes in the blood and could potentially serve as targets for the early detection and treatment of direct ARDS especially in hyperinflammatory subphenotype.

Effects of High-Fat Diet on Cardiovascular Protein Expression in Mice Based on Proteomics.

To investigate the effect of high-fat diet on protein expression in mouse heart and aorta using proteomic techniques. A high-fat diet was used to construct an obese mouse model, and body weight was checked regularly. After the experiment, serum lipid and oxidative stress levels were measured. Proteomic detection of cardiac and aortic protein expression. Cardiac and aortic common differentially expressed proteins (Co-DEPs) were screened based on proteomic results. Subsequently, functional enrichment analysis and screening of key proteins were performed. A high-fat diet significantly increased body weight in mice. Obese mice had considerably higher levels of TC, TG, LDL-C, ROS, and MDA. In the heart and aorta, 17 Co-DEPs were discovered. The results of functional analysis of these proteins indicated that they were mainly related to lipid metabolism. Ech1, Decr1, Hsd17b4, Hsdl2 and Acadvl were screened as key proteins. In mice, a high-fat diet causes lipid metabolism to become disrupted, resulting in higher levels of oxidative stress and lipid peroxidation products. Ech1, Decr1, Hsd17b4, Hsdl2 and Acadvl as cardiac and aortic Co-DEPs are closely related to lipid metabolism and may serve as potential diagnostic and therapeutic targets for obesity-induced cardiovascular disease.

ODP034 Circulating Protein Biomarkers for Discriminating Malignant from Benign Adrenal Tumors Using Mass Spectrometry-Based Proteomic Analysis

Abstract Backgrounds Adrenal cortical carcinoma (ACC) is a rare malignant tumor derived from the adrenal gland with a poor prognosis. Since there is no effective medical treatment, early diagnosis and surgical resection are the only way to cure ACC completely. However, early diagnosis of ACC is sometimes tricky because there are no useful diagnostic biomarkers to differentiate ACC from benign adrenal tumors. Therefore, we aimed to identify circulating protein biomarkers to distinguish malignant from benign adrenal tumors using mass spectrometry-based proteomic analysis. Methods Plasma samples were obtained from 27 patients with ACC and 69 age- and sex-matched patients with adrenal adenoma. We performed the liquid chromatography-tandem mass spectrometry (LC-MS/MS) with a data-independent acquisition (DIA) method in plasma samples. Among the quantified 381 proteins, differentially expressed proteins (DEPs) were selected using Student's t-tests for pairwise comparison with a false discovery rate < 0. 05 and |fold-change|> 1.5. In addition, we performed machine learning algorithms such as random forest and XGBoost to select featured DEPs to discriminate ACC. Results The mean age of patients was 52 years, and 38 (39.6%) patients were male. Among 19 DEPs, 8 proteins were overexpressed and 11 were underexpressed in ACC patients. In a further analysis using machine learning algorithms, random forest identified 4 proteins as important features for establishing the classifier. The panels with these four proteins showed a good discrimination performance with an area under the curve (AUC) of 0.94 and an accuracy of 0.96. Eight proteins were identified in the XGBoost algorithm. Four proteins in plasma samples were common DEPs from the traditional methods and machine learning algorithms. Conclusions High plasma levels of two proteins (One is involved in the migration, attachment and organization of cells into tissues. The other is V region of the variable domain of immunoglobulin light chains), and low plasma levels of two proteins (One is involved in cell-cell adhesion and recognition. The other is V region of the variable domain of immunoglobulin heavy chain) might be circulating protein biomarkers of ACCs compared with benign adrenal adenomas. Presentation: No date and time listed

Effects of Electron Beam Irradiation on Portunus trituberculatus Based on Tandem-Mass Tag-Based Quantitative Proteomic Analysis

ABSTRACT The short shelf life of Portunus trituberculatus is an important factor limiting the progress of this industry. Electron beam irradiation (EBI) can effectively kill the microorganisms, but the effect of EBI on crab muscle tissue remains unknown. In this study, a proteomics method based on labeling with the tandem-mass tag (TMT) was used to study the protein changes occurring in crabs under different doses of EBI at 0, 2, 4, 6, 8, and 10 kGy. A total of 6123 proteins were identified, of which 1490 were significantly differentially expressed proteins (DEPs), and 91 were common DEPs. An in-depth data analysis showed that the DEPs were involved in various cellular processes, particularly metabolic processes. We combined gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, and our results focused on oxidative phosphorylation, tight junction, and oxytocin signaling pathways. Key proteins responsible for the effects of EBI on crabs were also found.

Proteomics analysis reveals suppression of IL-17 signaling pathways contributed to the therapeutic effects of Jia-Wei Bu-Shen-Yi-Qi formula in a murine asthma model

BackgroundJia-Wei Bu-Shen-Yi-Qi formula (JWBSYQF), a Chinese herbal formula, is a commonly used prescription for treating asthma patients. However, the targeted proteins associated with JWBSYQF treatment remain unknown. PurposePresent study aims to evaluate the therapeutic efficacy of JWBSYQF and identify the targeted proteins in addition to functional pathways. Study designThe ovalbumin (OVA)-induced murine asthma model was established to explore the therapeutic effect of JWBSYQF treatment. Proteomic profiling and quantifications were performed using data-independent acquisition (DIA) methods. Differentially expressed proteins (DEPs) were validated via western blot (WB) and immunohistochemistry (IHC). MethodsA murine asthma model was made by OVA sensitization and challenge, and JWBSYQF (2.25, 4.50, 9,00 g/kg body weight) or dexamethasone (1 mg/ kg body weight) were administered orally. Airway hyperresponsiveness (AHR) to methacholine (Mch), inflammatory cell counts and classification in bronchoalveolar lavage fluid (BALF), lung histopathology, and cytokine levels were measured. Furthermore, DIA proteomic analyses were performed to explore the DEPs targeted by JWBSYQF and were further validated by WB and IHC. ResultsOur results exhibited that JWBSYQF attenuated AHR which was mirrored by decreased airway resistance and increased lung compliance. In addition, JWBSYQF-treated mice showed reduced inflammatory score, mucus hypersecretion, as well as reduced the number of BALF leukocytes along with decreased content of BALF Th2 inflammatory cytokines (IL-4, IL-5, IL-13) and serum IgE. Proteomics analysis identified 704 DEPs between the asthmatic mice and control group (MOD vs CON), and 120 DEPs between the JWBSYQF-treatment and the asthmatic mice (JWB-M vs MOD). A total of 33 overlapped DEPs were identified among the three groups. Pathway enrichment analysis showed that DEPs were significantly enriched in IL-17 signaling pathway, in which DEPs, Lcn2, TGF-β1, Gngt2, and Ppp2r5e were common DEPs between three experimental groups. WB and IHC results further validated expressional levels and tendency of these proteins. Our results also showed that JWBSYQF affects mitogen activated protein kinase (MAPK) and nuclear factor-κB (NF-κB) signaling pathways, that are activated by IL-17 signaling. ConclusionThe present study suggested that JWBSYQF could attenuate AHR and airway inflammation in OVA-induced asthmatic mice. In addition, proteomics analysis revealed that suppression of IL-17 signaling pathways contributes to the therapeutic effects of JWBSYQF.

The Effect of Prenatal Food Restriction on Brain Proteome in Appropriately Grown and Growth Restricted Male Wistar Rats.

BackgroundFetal growth restriction (FGR) has been associated with a higher risk of developing adverse perinatal outcomes and distinct neurodevelopmental and neurobehavioral disorders. The aim of the present study was to investigate the impact of prenatal food restriction on the brain proteome in both FGR and appropriately grown rats and to identify potential pathways connecting maternal malnutrition with altered brain development.MethodsTen time-dated pregnant Wistar rats were housed individually at their 12th day of gestation. On the 15th day of gestation, the rats were randomly divided into two groups, namely the food restricted one (n = 6) and the control group (n = 4). From days 15 to 21 the control group had unlimited access to food and the food restricted group was given half the amount of food that was on average consumed by the control group, based on measurements taken place the day before. On the 21st day of gestation, all rats delivered spontaneously and after birth all newborn pups of the food restricted group were weighed and matched as appropriately grown (non-FGR) or growth restricted (FGR) and brain tissues were immediately collected. A multiplex experiment was performed analyzing brain tissues from 4 FGR, 4 non-FGR, and 3 control male offspring. Differentially expressed proteins (DEPs) were subjected to bioinformatics analysis in order to identify over-represented processes.ResultsProteomic analysis resulted in the profiling of 3,964 proteins. Gene ontology analysis of the common DEPs using DAVID (https://david.ncifcrf.gov/) showed significant enrichment for terms related to cellular morphology, learning, memory and positive regulation of NF-kappaB signaling. Ingenuity Pathway Analysis showed significant induction of inflammation in FGR pups, whereas significant induction of cell migration and cell spreading were observed in non-FGR pups.ConclusionThis study demonstrated that in both FGR and non-FGR neonates, a range of adaptive neurodevelopmental processes takes place, which may result in altered cellular morphology, chronic stress, poor memory and learning outcomes. Furthermore, this study highlighted that not only FGR, but also appropriately grown pups, which have been exposed to prenatal food deprivation may be at increased risk for impaired cognitive and developmental outcomes.

Comparative Proteomic Analyses of the Liver in D-Galactosamine-Sensitized Mice Treated with Different Toll-Like Receptor Agonists.

Acute liver failure (ALF) is a severe consequence of abrupt hepatocyte injury and has lethal outcomes. Three toll-like receptor agonists, including polyinosinic-polycytidylic acid (poly(I:C)), lipopolysaccharide (LPS), and cytosine-phosphate-guanine (CpG) DNA, cause acute and severe hepatitis, respectively, in D-galactosamine (D-GalN)-sensitized mice. However, the molecular differences among three ALF models (LPS/D-GalN, poly(I:C)/D-GalN, and CpG DNA/D-GalN), are unclear. Here, tandem mass tag based quantitative proteomic analyses of three ALF mouse models are performed. 52 common differentially expressed proteins (DEPs) are identified, in three ALF groups, compared to the control. Gene ontology analyses show that among the common DEPs, ten proteins are involved in immune system process, and 39 proteins in metabolic process. Among 80,195, and 23 specifically-expressed proteins in poly(I:C)/D-GalN, LPS/D-GalN, and CpG DNA/D-GalN groups, LPS/D-GalN-specific proteins are mostly distributed in the endoplasmic reticulum and more enriched in metabolic pathways, whereas poly (I:C)/D-GalN-specific proteins are mainly in the membrane and CpG DNA/D-GalN-specific proteins are related to the ribosome structural composition. In conclusion, the common and specific DEPs in three ALF mouse models at molecular level are identified; and determined a close-to-complete reference map of mouse liver proteins which will be useful for clinical diagnosis and treatment of liver failure in humans.

ITRAQ-based quantitative tissue proteomic analysis of differentially expressed proteins (DEPs) in non-transgenic and transgenic soybean seeds

The unintended effects of transgenesis have increased food safety concerns, meriting comprehensive evaluation. Proteomic profiling provides an approach to directly assess the unintended effects. Herein, the isobaric tags for relative and absolute quantitation (iTRAQ) comparative proteomic approach was employed to evaluate proteomic profile differences in seed cotyledons from 4 genetically modified (GM) and 3 natural genotypic soybean lines. Compared with their non-GM parents, there were 67, 61, 13 and 22 differentially expressed proteins (DEPs) in MON87705, MON87701 × MON89788, MON87708, and FG72. Overall, 170 DEPs were identified in the 3 GM soybean lines with the same parents, but 232 DEPs were identified in the 3 natural soybean lines. Thus, the differences in protein expression among the genotypic varieties were greater than those caused by GM. When considering ≥2 replicates, 4 common DEPs (cDEPs) were identified in the 3 different GM soybean lines with the same parents and 6 cDEPs were identified in the 3 natural varieties. However, when considering 3 replicates, no cDEPs were identified. Regardless of whether ≥2 or 3 replicates were considered, no cDEPs were identified among the 4 GM soybean lines. Therefore, no feedback due to GM was observed at the common protein level in this study.

Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

BackgroundRice blast (caused by Magnaporthe oryzae) is one of the most destructive diseases of rice. While many blast resistance (R) genes have been identified and deployed in rice cultivars, little is known about the R gene-mediated defense mechanism. We used a rice transgenic line harboring the resistance gene Piz-t to investigate the R gene-mediated resistance response to infection.ResultsWe conducted comparative proteome profiling of the Piz-t transgenic Nipponbare line (NPB-Piz-t) and wild-type Nipponbare (NPB) inoculated with M. oryzae at 24, 48, 72 h post-inoculation (hpi) using isobaric tags for relative and absolute quantification (iTRAQ) analysis. Comparative analysis of the response of NPB-Piz-t to the avirulent isolate KJ201 and the virulent isolate RB22 identified 114 differentially expressed proteins (DEPs) between KJ201-inoculated NPB-Piz-t (KJ201-Piz-t) and mock-treated NPB-Piz-t (Mock-Piz-t), and 118 DEPs between RB22-inoculated NPB-Piz-t (RB22-Piz-t) and Mock-Piz-t. Among the DEPs, 56 occurred commonly in comparisons KJ201-Piz-t/Mock-Piz-t and RB22-Piz-t/Mock-Piz-t. In a comparison of the responses of NPB and NPB-Piz-t to isolate KJ201, 93 DEPs between KJ201-Piz-t and KJ201-NPB were identified. DEPs in comparisons KJ201-Piz-t/Mock-Piz-t, RB22-Piz-t/Mock-Piz-t and KJ201-Piz-t/KJ201-NPB contained a number of proteins that may be involved in rice response to pathogens, including pathogenesis-related (PR) proteins, hormonal regulation-related proteins, defense and stress response-related proteins, receptor-like kinase, and cytochrome P450. Comparative analysis further identified 7 common DEPs between the comparisons KJ201-Piz-t/KJ201-NPB and KJ201-Piz-t/RB22-Piz-t, including alcohol dehydrogenase I, receptor-like protein kinase, endochitinase, similar to rubisco large subunit, NADP-dependent malic enzyme, and two hypothetical proteins.ConclusionsOur results provide a valuable resource for discovery of complex protein networks involved in the resistance response of rice to blast fungus.