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Pharmacological perturbation studies based on protein-level signatures are fundamental for drug dis-covery.In the present study,we used a mass spectrometry(MS)-based proteomic platform to profile the whole proteome of the breast cancer MCF7 cell line under stress induced by 78 bioactive compounds.The integrated analysis of perturbed signal abundance revealed the connectivity between phenotypic behaviors and molecular features in cancer cells.Our data showed functional relevance in exploring the novel pharmacological activity of phenolic xanthohumol,as well as the noncanonical targets of clinically approved tamoxifen,lovastatin,and their derivatives.Furthermore,the rational design of synergistic inhibition using a combination of histone methyltransferase and topoisomerase was identified based on their complementary drug fingerprints.This study provides rich resources for the proteomic landscape of drug responses for precision therapeutic medicine.
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Diabetic foot(DF)is one of the most severe chronic complications of diabetes mellitus(DM),and it is an important cause of disability and mortality inpatients with DM.Changes in proteins in the tissues,organs and circulation of organisms can serve as microscopic reflections of the disease development process.Proteomics is an important technologyto explore the pathogenesis and treatment mechanism of dis-ease,and to find potential therapeutic targets and prognostic biomarkers of diseases.This article reviews the progress of proteomics research in DF.
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Objective:To investigate the CLEC3B protein of differentially expressed proteins(DEPs)in serum of normal persons and patients with sepsis,and explore the possibility that target C-type lectin domain family 3 member B(CLEC3B)protein was used as molecular markers of sepsis.Methods:Peripheral bloods of 10 healthy persons and 18 patients with sepsis were collected,and the data of peripheral serum proteins were collected by data independent acquisition(DIA)method.The data were uploaded to iDEP online platform to analyze the DEPs in peripheral blood of patients with sepsis.Bioinformatics analysis of these DEPs was conducted to screen out the key proteins of sepsis.Enzyme linked immunosorbent assay(ELISA)was used to verify and plot the receiver operating characteristic(ROC)curves of key proteins.Results:A total of 138 differentially expressed proteins(DEPs)were screened out by using proteomics analysis,of which 34 kinds of proteins were significantly down-regulated and 104 kinds of proteins were significantly up-regulated.DEPs mostly concentrated in cellular processes,biological regulation,biological process regulation,participating binding,catalytic activation,molecular function regulation,immune system,signal transduction and so on.A protein-protein interaction network was constructed by DEPs,which screened out the key protein CLEC3B.ELISA results showed that the CLEC3B protein concentration[(297.73±22.00)ng/mL]of patients in the sepsis group was significantly lower than that[(452.42±191.72)ng/mL]in the healthy group,and the difference was statistically significant(t=13.13,P=0.000).The area under curve(AUC)value of ROC curve,sensitivity and specificity of CLEC38 protein were respectively 0.998,97.73%and 100.0%.Conclusion:CLEC3B is significantly decreased in sepsis group,which sensitivity and specificity are high.It can be used as a potentially biological diagnostic biomarker of sepsis.
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Objective:Transcriptomics combined with proteomics was used to analyze the potential signaling pathways of epidermal growth factor-like domain 9 (EGFL9) affecting the proliferation, invasion and migration of hepatocellular carcinoma.Methods:RNA interference technique was used to build hepatocellular carcinoma cell line with EGFL9 Huh-7 gene knockdown, the control group (NC group) and experimental group (KD group), each group of three samples, were performed the transcriptome and proteomics analysis, screening differences genes and proteins, to express the correlation analysis, cluster analysis, and subsequently gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were used for gene function and pathway annotation enrichment analysis, respectively.Results:Based on omics analysis, there were 8 335 different genes in KD group compared with NC group, among which 4 207 were up-regulated and 4 128 were down-regulated. There were 298 different proteins, of which 188 were up-regulated and 110 down-regulated. Based on the combined analysis of the two omics, 213 differentially expressed genes were found. Among them, the top three common differentially expressed genes at the level of transcription and translation were transferrin receptor 2 (TFR2), annexin A1 (ANXA1) and solute carrier family 38 member 2(SLC38A2). The common differentially expressed genes were significantly enriched in cell cycle signaling pathway, amino acid biosynthesis pathway, p53 signaling pathway and glycolysis/gluconeogenesis signaling pathway.Conclusion:EGFL9 may participate in the regulation of cell function of hepatocellular carcinoma cells by regulating the expression of TFR2, ANXA1, LC38A2 and other genes, and may play a role through the regulation of cell cycle and other molecular signaling pathways.
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Objective:To evaluate the effect of Lactobacillus-derived extracellular vesicles (Lac-EVs) on lipopolysaccharide (LPS)-induced activation of microglia and proteomic analysis.Methods:BV2 microglia obtained from mice with good growth status were divided into 3 groups ( n=12 each) using a random number table method: control group (group C), LPS group (group L) and LPS+ Lac-EVs group (group L+ E). Group C was commonly cultured. Group L was incubated for 24 h with LPS (final concentration 1 μg/ml). Group L+ E was incubated for 24 h with Lac-EVs (final concentration 2.5 μg/ml) after being treated with LPS for 24 h. The expression of CD86 and CD206 was detected using immunofluorescence staining. Cell precipitates were taken from L and L+ E groups, and proteomics were used to screen for differentially expressed proteins between the two groups. The differentially expressed proteins were analyzed by the bioinformatics analysis, and two differentially expressed proteins, apolipoprotein A1 and G protein-coupled receptor kinase 2, were verified by quantitative real-time polymerase chain reaction and Western blot. Results:Compared with group C, the expression of CD86 was significantly up-regulated, and the expression of CD206 was down-regulated in group L ( P<0.05). Compared with group L, the expression of CD86 was significantly down-regulated, and the expression of CD206 was up-regulated in L+ E group ( P<0.05). One hundred and twenty-five differentially expressed proteins were identified using proteomics (FC=2.0, P<0.05), of which the expression of 66 proteins was up-regulated and the expression of 59 proteins was down-regulated. The results of GO analysis indicated that these differentially expressed proteins were mainly involved in biological processes such as endothelial cell proliferation, SDNA damage detection, and lipoprotein transport. The results of KEGG analysis indicated that there were differences in PPAR signaling pathway, endocytosis, metabolic pathway, MAPK signaling pathway, etc. The expression trends of the differentially expressed proteins determined by Western blot and quantitative real-time polymerase chain reaction were consistent with the results of proteomics. Conclusions:Lac-EVs can inhibit LPS-induced microglial polarization toward M1 phenotype, and the mechanism may be related to the up-regulated differential proteins apolipoprotein A1 and G protein-coupled receptor kinase 2.
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AIM To study the amino acids and proteins in 16 batches of commercial fish swim-bladders with different origins.METHODS A high performance liquid chromatography method based on pre-column derivatization using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate(AQC)was developed for the determination of contents and components of 17 amino acids in fish swim-bladders.Sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE)was performed to analyze the molecular weight distribution of proteins from different fish swim-bladders,and proteins in fish swim-bladders were identified by proteomics method.RESULTS The result showed that the determination of 17 amino acids had a good linear relationship(R2≥0.998 0).The average recovery rate was 85.62%-109.60%and the relative standard deviations of precision,stability and repeatability were less than 3.5%.The total content of the 17 amino acids in 16 batches of fish swim-bladders ranged from 468.31 mg/g to 620.05 mg/g.A total of 688 proteins including 11 collagens were identified from 16 batches of fish swim-bladder samples and a plenty of low-abundance proteins at 52-95 kDa were also detected in fish swim-bladders by SDS-PAGE.CONCLUSION This study provides a good reference for the quality evaluation and further utilization of fish swim-bladders.
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With the maturation of proteomics technologies in recent years, proteomics has made significant achievements in early detection of major diseases, disease classification, drug target discovery, and other fields. To explore the important role of proteomics, especially proteomics-based cutting-edge lifeomics technologies, in promoting the development of precision laboratory medicine and to discuss the opportunities and challenges faced during the clinical translation of innovative outcomes, the National Center for Protein Sciences-Beijing invited renowned experts and scholars in laboratory medicine, lifeomics, and precision medicine. The discussions revolved around the collaborative development of laboratory medicine and lifeomics, the future trends of new technologies in clinical laboratory testing, the innovation and development of lifeomics in laboratory medicine, the translational application of proteomics technologies in laboratory medicine, and the opportunities and challenges in the industrialization of proteomics achievements. All participants agreed that proteomics provides new directions and opportunities for precision diagnosis and treatment of diseases. However, close collaboration between academia, hospitals and industry is required. Additionally, challenges such as clinical applicability of equipment, standardization of detection methods and data, cost and quality control, talent cultivation, and the industrialization pathway need to be addressed.
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Stroke is an acute cerebrovascular disease, and a group of diseases that cause brain tissue damage due to sudden rupture of brain blood vessels or blockage of blood vessels, mainly including ischemic stroke and hemorrhagic stroke. In recent years, although some progresses have been achieved, there are still few biomarkers that can be used for effective warning and monitoring for people at high risk of stroke. Omics research is an important research strategy for discovering differential genes, molecules, and epigenetic markers in the process of disease occurrence and development. A systematic summary of progress made in recent years, in stroke genomics, transcriptomics, proteomics, and metabolomics in recent years, as well as their potential applications in stroke warning, diagnosis, and monitoring, was systematically discussed in the presence review, in order to provide reference for future research on stroke biomarkers.
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Objective A serum proteomic approach was used to explore the targets of action of Peitu Qingxin Granules(composed of Rhizoma Atractylodis Macrocephalae,Forsythiae Fructus,Imperatae Rhizoma,Pseudostellariae Radix,etc.)in the treatment of atopic dermatitis.Methods Five patients with atopic dermatitis were selected and treated with Peitu Qingxin Granules for 12 weeks,and five healthy volunteers were used as controls.The clinical core evaluation indexes of atopic dermatitis patients after treatment,including Eczema Area and Severity Index/Scoring Atopic Dermatitis(EASI/SCORAD),Pruritus Score,Patient-Oriented Eczema Measure(POEM),and quality of life index,were assessed.Serum samples were examined using data-independent acquisition-mass spectrometry(DIA-MS)technology,and serum differential proteins between atopic dermatitis patients and healthy people,as well as serum differential proteins in atopic dermatitis patients before and after treatment with Peitu Qingxin Granules were screened according to P＜0.05 and Fold Change>1.2.GO function enrichment analysis and KEGG pathway enrichment analysis were performed on the differential proteins.Results(1)Compared with the pre-treatment period,the clinical core evaluation indexes of patients with atopic dermatitis,including the EASI/SCORAD,Pruritus Score,POEM,and quality-of-life index,were significantly improved after treatment,and the differences were all statistically significant(P＜0.05,P＜0.01).(2)A total of 28 differential proteins were analyzed in the healthy control group and atopic dermatitis group,of which 12 proteins expressions were increased and 16 proteins were decreased,including ALAD(δ-aminolevulinic acid dehydrogenase),LTA4H(leukotriene A-4 hydrolase),CA1(carbonic anhydrase 1),F11(coagulation factor XI),and LCP1(lymphocyte cytoplasmic protein 1),etc..The main signaling pathways involved are PI3K-AKT signaling pathway,lipids and atherosclerosis,ECM-receptor interaction,platelet activation,NF-κB signaling pathway,and neutrophil extracellular trap formation.(3)A total of 12 different proteins were analyzed in atopic dermatitis patients before and after treatment with Peitu Qingxin Granules,of which 8 proteins were increased and 4 proteins were decreased,including ALAD,FGA(fibrinogen α-chain),IGHV3-64D,and IGHV3-38.They were mainly involved in signaling pathways such as lipids and atherosclerosis,complement pathway,Staphylococcus aureus infection,NF-κB signaling pathway,fluid shear stress and atherosclerosis.(4)The expressions of three protein targets including ALAD,FGA and IGHV3-64D,were significantly down-regulated in patients with atopic dermatitis and significantly up-regulated after treatment with Peitu Qingxin Granules.Conclusion The differentially expressed proteins ALAD,FGA and IGHV3-64D may be the action targets of Peitu Qingxin Granules in the treatment of atopic dermatitis,which lays the foundation for further experimental validation.
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ObjectiveTo observe the therapeutic effect of BD-77 by nebulized inhalation on animal models of various respiratory viral infections and investigate the mechanism of broad-spectrum antiviral action of BD-77 using proteomics. MethodThe influenza virus H1N1/FM1 experiment used ICR mice and divided them into a normal group， model group， Tamiflu group， and BD-77 groups of 75 and 37.5 g·L-1 for inhalation of 20 min and 25 min. Human coronavirus 229E and OC43 experiment divided the BALB/c mice into a normal group， model group， chloroquine phosphate group， and BD-77 groups of 75， 37.5， 18.75， and 9.375 g·L-1， with 10 mice in each group. Influenza virus H1N1/FM1 and human coronaviruses 229E and OC43 infection-induced pneumonia models were used to detect mouse lung index， and real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the viral load in lung tissue. Enzyme-linked immunosorbent assay （ELISA） was used to detect related inflammatory factors in lung tissue， and proteomics analysis was performed on the lung tissue of OC43-infected mice. ResultCompared with that in the normal group， the lung index of mice in each infection group was significantly increased （P<0.01）， and viral nucleic acid could be detected in the lung tissue of mice infected with human coronaviruses 229E and OC43. The levels of interleukin-6 （IL-6）， IL-10， and tumor necrosis factor-α （TNF-α） in the lung tissue of mice infected with human coronavirus 229E were all significantly increased （P<0.01）. BD-77 could significantly reduce the lung index of mice infected with influenza virus H1N1/FM1 and human coronaviruses 229E and OC43 （P<0.05， P<0.01）， cut down the viral load in the lungs of mice infected with human coronaviruses 229E and OC43 （P<0.01）， and lower the contents of IL-6， IL-10， and TNF-α in the lung tissue of mice infected with human coronavirus 229E （P<0.01）. Proteomics analysis of the lung tissue of OC43-infected mice showed that BD-77 regulated the AMPK signaling pathway， TNF signaling pathway， NOD-like signaling pathway， IL-17 signaling pathway， Forkhead box protein O （FoxO） signaling pathway， transforming growth factor-β （TGF-β） signaling pathway， and other signaling pathways. ConclusionNebulized inhalation of BD-77 is effective in treating pneumonia caused by influenza virus H1N1/FM1 and human coronaviruses 229E and OC43 infection in mice and may exert its antiviral effects by regulating the balance of cellular metabolism， enhancing the immune function of the host， and attenuating inflammatory responses.
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The prevalence rate of nonalcoholic fatty liver disease （NAFLD） reaches up to 30% around the world， and the disease has a serious impact on human health and constitutes a public health burden. Due to difficulties in the diagnosis and monitoring of NAFLD， it is important to identify potential drug targets and biomarkers， and multi-omics techniques hold great promise in the search for early diagnostic markers， therapeutic targets， and outcome and prognostic assessment of NAFLD. This article reviews the research advances in multi-omics techniques in the field of NAFLD in recent years， in order to provide a richer theoretical basis and new strategies for the prevention and treatment of NAFLD.
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OBJECTIVE To explore the regulatory mechanism of Danshen decoction on dyslipidemia in hyperlipidemia model rats. METHODS The experimental rats were divided into blank group （n＝9， no modeling）， model group （n＝8， modeling）， and Danshen decoction group （n＝9， modeling）. Starting from the 9th week of feeding with the high-fat diet， rats in the Danshen decoction group were given the corresponding medication solution （3.6 g/kg） intragastrically， while blank group and model group were given equal volume of normal saline， once a day， for 4 consecutive weeks. After 4 weeks of administration， the plasma levels of triglycerides （TG）， total cholesterol （TC）， low-density lipoprotein cholesterol （LDL-C）， and high-density lipoprotein cholesterol （HDL-C） were measured in each group of rats； the pathological and morphological changes of liver tissue were observed； the differential proteins between samples were screened out by TMT quantitative proteomic analysis； the expression levels of the key differentially expressed proteins in the liver， including epoxide hydrolase 2 （EPHX2）， perilipin 2 （PLIN2）， peroxisome proliferator activated receptor γ （PPAR γ） and glycogen synthase kinase-3β （GSK-3β）were detected. RESULTS Compared with the model group， the plasma levels of TC， TG and LDL-C in the Danshen decoction group were significantly reduced （P＜0.05）， while the level of HDL-C was significantly increased （P＜0.05）. The liver tissue of rats inmodel group showed uneven staining， disordered arrangement of liver plates， disappearance of liver sinusoids， nuclearcondensation or disappearance of some cells， swelling and fusion of cytoplasm， proliferation of connective tissue， and diffuse vacuolar-like fat droplet changes. The liver tissue of Danshen decoction group showed varying degrees of improvement in the above pathological and morphological. The results of differential protein analysis showed that the total number of differential proteins was 298 between the model group and the blank group； the total number of differential proteins was 139 between the model group and Danshen decoction group. Compared with the model group， the expression levels of EPHX2 and PLIN2 proteins in the liver tissue of rats in the Danshen decoction group were significantly reduced （P＜0.01）， while the expression levels of GSK-3β and PPARγ were significantly increased （P＜0.01）. CONCLUSIONS Danshen decoction has a significant improvement effect on the plasma lipid levels and the pathological and morphological of the liver tissue in hyperlipidemia model rats. Its regulatory mechanism may be related to the up-regulation of PPARγ and GSK-3β expression and down-regulation of EPHX2 and PLIN2 expression， and the signaling pathways involved may include PPAR-γ signal pathway.
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Objective To determine the acetylation level of nucleophosmin(NPM)in female breast cancer and to discuss its function through mutation of modified lysine sites.To construct positive and negative NPM mutants on its acetylated lysine sites and to express them in breast cancer cells.Methods Acetylation level and acetylated lysine sites of NPM in three breast cancer tissues and para-carcinoma tissues were detected by acetylome technology;NPM mutants were constructed by site-directed mutagenesis PCR,specific PCR products were digested by DpnI and transformed into Escherichia coli(E.coli)to obtain specific plasmids for mutants;The accuracy of mutants were verified by double restriction enzyme digestion and sequencing;The mutants were expressed in BT-549 cells by transient transfection and verified by RT-PCR method.Protein expression and acetylation level of NPM were validated by Western blotting;Function of NPM acetylation was analyzed by proteomic detection and bioinformatic analysis.Results The 27th and 32nd lysine of NPM were highly acetylated in breast cancer tissues,which were 2.76 and 2.22 times higher than those in adjacent normal tissues,respectively;The NPM mutants showed the same molecular weight as that of wild type NPM and contained expected mutation sites;Corresponding NPM mRNA levels of BT-549 cells transfected with NPM mutants were significantly increased.With the increase of wild type NPM expression level,NPM acetylation level increased,while decreased after 27th lysine underwent negative mutation.NPM acetylation can significantly change the expression levels of 101 proteins in BT-549 cells,which are enriched in regulation of cellular macromolecule biosynthesis,DNA-template transcription,RNA biosynthesis and RNA metabolism process.Conclusion NPM is highly acetylated in breast cancer and can play a key role in cellular macromolecule biosynthesis,DNA-templated transcription,RNA biosynthesis and RNA metabolism process.
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ObjectiveExosomes are microvesicles which could be secreted by all cell types with diameters between 30 and 150 nm. It was widely distributed in body fluids including blood, urine, and breast milk. Exosomes are considered as potential biomarkers and drug carriers by reason of containing nucleic acids, lipids, proteins and other bioactive molecules. Milk-derived exosomes have been widely used as drug delivery carriers to treat targeted diseases with a lower cost, higher biocompatibility and lower immunogenicity. Until now, there is no research about the milk-derived exosomes phosphorylation to reveal the difference of protein phosphorylation in different species of milk. To investigate the pathways and proteins with specific functions, phosphorylated proteomic analysis of milk-derived exosomes from different species is performed, and provide new ideas for exploring diversified treatments of disease. MethodsWhey and exosomes derived from bovine, porcine and caprine milk were performed for proteomics and phosphoproteomics analysis. The relationship between milk exosome proteins from different species and signaling pathways were analyzed using bioinformatics tools. ResultsA total of 4 191 global proteins, 1 640 phosphoproteins and 4 064 phosphosites were identified from 3 species of milk-derived exosomes, and the exosome proteins and phosphoproteins from different species were significantly higher than those of whey. Meanwhile, some special pathways were enriched like Fcγ-mediated phagocytosis from bovine exosomes, pathways related with neural and immune system from caprine exosomes, positive and negative regulation of multiple activities from porcine exosomes. ConclusionIn this study, the proteomic and phosphoproteomic analyses of exosomes and whey from bovine, porcine and caprine milk were carried out to reveal the difference of composition and related signaling pathways of milk exosome from different species. These results provided powerful support for the application of exosomes from different milk sources in the field of disease treatment.
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ObjectiveHair is an essential skin appendage, primarily composed of keratins and keratin-associated proteins. The protein composition and proportion of hair samples vary among different races and sexes. Currently, there is a lack of efficient methods to extract hair proteins. This study aims to explore the application of quantitative hair proteomics in distinguishing individual hair characteristics. MethodsBased on the exploration of sample processing and lysis buffer using three hair samples, we developed a stable and efficient hair protein extraction method, named PLEE (PTM lab for protein extraction from hair with high efficiency). We used the PLEE method to extract seven human hair samples and performed proteomic experiments on them using in-gel digestion method to produce data for analyzing hair protein composition and proportion among individuals. ResultsA total of 274 proteins were identified, among which 107 proteins were commonly present, and the number of non-common proteins ranged from 57-119, with some samples having unique identification proteins. Using the 107 commonly identified proteins for quantitative protein fractionation analysis, various samples were distinguished by clustering and principal component analysis, and technical repeated samples were merged, indicating the stability of the process. In addition, 10 key proteins (KRT33A, KRTAP9-6, KRT83, KRTAP7-1, KRT32, BLMH, KRT38, KRTAP11-1, NPAS1, KRTAP4-3) with large differences between individuals and stable protein identification within the same individual were screened. ConclusionThe protein composition of hair varies among different individuals, and the 10 selected proteins are expected to be key proteins for distinguishing individual hair characteristics and have significant potential applications in individual identification and criminal investigation.
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BACKGROUND:Previous studies have found that qi deficiency and blood stasis syndrome is the main syndrome among various TCM syndromes of cervical spondylotic myelopathy.However,there is no report on proteomic markers as early diagnosis indicators for the transformation of developmental cervical spinal stenosis with qi deficiency and blood stasis syndrome to cervical spondylotic myelopathy. OBJECTIVE:To explore serum proteomics difference between developmental cervical spinal stenosis and cervical spondylotic myelopathy and to find and identify the potential serum biomarkers between them. METHODS:Serum samples of nine patients with cervical spondylotic myelopathy of qi deficiency and blood stasis syndrome(experimental group)and nine patients with developmental cervical spinal stenosis of qi deficiency and blood stasis syndrome(control group)were collected.The proteomic analysis was carried out by Tandem Mass Tag combined with liquid chromatography tandem mass spectrometry,so as to find and identify differentially expressed proteins. RESULTS AND CONCLUSION:A total of 1027 significantly differential proteins were initially screened by TMT technology and 89 significantly differential proteins were finally identified(P<0.05).Compared with the control group,there were 45 up-regulated proteins in the experimental group,such as α-actinin-4,α-actinin-1,cell division control protein 42 homolog,integrin-linked protein kinase and B-actin.Conversely,there were 44 down-regulated proteins in the experimental group compared with the control group,such as fibronectin,fibrinogen γ chain,fibrinogen α chain,fibrinogen β chain.Gene ontology enrichment analysis indicated that these differential proteins were involved in signal receptor binding,kinase binding,protein kinase activity,integrin binding,actin filament binding and other molecular functions.Based on the Kyoto Encyclopedia of Genes and Genomes pathway analysis,20 common differential signal/metabolic pathways were identified,including Rap1 signaling pathway,adherens junction,tight junction,platelet activation,and regulation of actin cytoskeleton.Protein-protein interaction analysis showed that ILK,FGA,FGB,FGG,FN1,Cdc42,ACTN1,ACTN4 and ACTB were located at the nodes of protein-protein interaction network and were closely related to bone formation and destruction system,nervous system,coagulation system,cellular inflammation and other systems.To conclude,the serum differentially expressed proteins between developmental cervical spinal stenosis and cervical spondylotic myelopathy can be successfully screened by Tandem Mass Tag combined with liquid chromatography tandem mass spectrometry.ILK,FN1,CDC42 and ACTN 4 are identified as specific markers for the transformation of developmental cervical spinal stenosis with qi deficiency and blood stasis syndrome into cervical spondylotic myelopathy.These findings provide a basis for further clarifying the transformation mechanism.
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BACKGROUND:The mechanisms and targets of alendronate in the treatment of osteoporosis still need to be investigated in depth. OBJECTIVE:To investigate the mechanism by which alendronate regulates bone metabolism in rats with osteoporosis and to perform a bioinformatics analysis of differentially expressed proteins. METHODS:Female Sprague-Dawley rats were randomly divided into three groups(n=12 per group):model group,alendronate group and sham-operated group.Animal models of osteoporosis were prepared using ovariectomy in the model and alendronate groups.At 4 weeks after modeling,rats in the alendronate group were gavaged with alendronate;the other two groups were given the equal volume of normal saline.After 12 weeks of continuous gavage,the bone mineral density of the tibia was measured and the lumbar spine of the rats was taken for proteomic analysis using Tandem mass tag-liquid chromatography-tandem mass spectrometry technique to identify differentially expressed proteins for gene ontology,Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction analysis. RESULTS AND CONCLUSION:There were 32 up-regulated proteins and 51 down-regulated proteins identified between the alendronate group and model group.Gene ontology enrichment analysis showed that the differentially expressed proteins were mainly involved in molecular functions,such as binding and catalytic activity,and in biological processes,such as cellular process and metabolic process.Kyoto Encylopedia of Genes and Genomes enrichment analysis showed that the differentially expressed proteins in the alendronate group and model group were mainly involved in the biosynthesis of pantothenate and coenzyme A.Protein-protein interaction analysis indicated that among the differentially expressed proteins in the alendronate group and model group,Hspa1l,Enpp3,Unc45a,Myh9 and Cant1 were located at the nodes of the protein-protein interaction network and were closely related to bone metabolism.Overall,these findings indicate that alendronate may regulate bone metabolism in the rat model of osteoporosis by regulating the expression of differentially expressed proteins and biosynthesis of pantothenate and coenzyme A.
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BACKGROUND:As a common clinical digestive disorder,irritable bowel syndrome becomes an advantageous disease of acupuncture treatment.However,the therapeutic mechanisms remain unclear.The methodological characteristics of omics coincide with the multi-target and multi-level characteristics of acupuncture,providing the possibility of revealing the principle of acupuncture in the treatment of the disease. OBJECTIVE:To investigate the pathogenesis of irritable bowel syndrome with diarrhea(IBS-D)and the effect of acupuncture at the combined points(selected based on etiologies and symptoms)on IBS-D based on proteomics. METHODS:Twelve 3-month-old male Sprague-Dawley rats were randomly divided into three groups:a control group,an IBS-D model group and an acupuncture group.The IBS-D rat models were prepared using the CAS method.After successful modeling,bilateral Zusanli points,bilateral Neiguan points and Guanyuan points were selected for acupuncture treatment in the acupuncture group,with a frequency of 120 times/minute,1 minute of acupuncture every 4 minutes,and 15 minutes of needle retention,at an interval of 1 day every 6 days,for 28 days in total.Rats in the normal control group and the model group were not given any intervention.The pressure threshold of rat abdominal retraction reflex was measured to evaluate the visceral hypersensitivity of rats.Proteomics analysis was performed using the liquid chromatography-tandem mass spectrometry-based platform.MaxQuant software,Perseus software and DAVID,KOBAS,VENNY,STRING online tools were used for the bioinformatics analysis of proteomic data.Visualization analysis was done using Cytoscape 3.7.1 software. RESULTS AND CONCLUSION:There were 47 differentially expressed proteins between the IBS-D model and control groups.Function analysis of differentially expressed proteins revealed that the pathogenic mechanism of IBS-D was associated with abnormal energy metabolism,the imbalance of colon motor function and increased visceral sensitivity.Important proteins related to IBS-D pathogenesis included Atp5a1,Atp5c1,Idh3b,Atp2a3,Pdhb,Ppp1ca and Mapk3.Sixty-one differentially expressed proteins were identified between the acupuncture group and IBS-D model group.Acupuncture at the combined points reversed the up-regulation of nine differentially expressed proteins and the down-regulation of nine differentially expressed proteins.Bioinformatics analysis revealed that acupuncture at the combined points for IBS-D could function via multi-targets and multi-pathways,reverse the damage of energy metabolism caused by IBS-D,and play a role against oxidative stress and inflammation,thereby relieving pain and regulating the imbalance of intestinal function.Important proteins related to acupuncture effects included Atp5a1,Atp5c1,Pdhb,Sars,Uqcrc2,Prdx2,Prdx4,Ppp1ca,Manf and Tmsb4x3.All these findings preliminarily illustrate the potential molecular mechanisms of IBS-D and the effect of acupuncture at the combined points in the treatment of IBS-D at the protein level,which provide a basis for the clinical application of acupuncture at the combined points.
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BACKGROUND:Serum-specific biomarkers between normal healthy individuals and populations with developmental cervical canal stenosis(Qi deficiency and blood stasis syndrome)have not been fully defined. OBJECTIVE:To screen and identify the potential biomarkers of developmental cervical canal stenosis with Qi deficiency and blood stasis. METHODS:Serum samples were collected from nine patients with developmental cervical canal stenosis with Qi deficiency and blood stasis and eight healthy people.Differentially expressed proteins in serum were screened and identified using isotope relative labeling and absolute quantification combined with liquid chromatography tandem mass spectrometry.Western blot was used to verify some significant differentially expressed proteins. RESULTS AND CONCLUSION:A total of 61 differentially expressed proteins(P<0.05)were identified using tandem mass spectrometry techniques.Compared with the healthy normal population group,14 differentially expressed proteins such as complement component C1q receptor,apolipoprotein A4,and C-C motif chemokine ligand 18 were significantly upregulated,while 47 differentially expressed proteins such as myosin light chain 3,mitochondrial translation elongation factor,and nucleolar phosphoprotein 1 were significantly downregulated.The results of gene ontology enrichment analysis indicated that these differentially expressed proteins might participate in molecular functions such as regulation of chromosomal tissue,mitochondrial membrane tissue,and muscle system processes.Protein-protein interaction network analysis showed that 38 common differential proteins,including complement component C1q receptor,apolipoprotein A4,C-C motif chemokine ligand 18,myosin light chain 3,mitochondrial translation elongation factor,and nucleolar phosphoprotein 1,were located at functional network nodes between healthy normal individuals and those with developmental cervical canal stenosis(Qi deficiency and blood stasis syndrome),and were closely related to the local energy metabolism of the cervical spine,the production of cervical vertebral osteocytes,and the formation of osteoclasts.The main differentially expressed protein myosin light chain 3 was validated using western blot assay,and the validation results were consistent with the proteomic results.To conclude,the preliminary discovery of differentially expressed proteins in serum between healthy normal individuals and those with developmental cervical canal stenosis(Qi deficiency and blood stasis syndrome)through absolute quantitative technology combined with liquid chromatography tandem mass spectrometry technology suggests that myosin light chain 3 may be a specific serum marker for developmental cervical canal stenosis(Qi deficiency and blood stasis syndrome).
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Acute hypobaric hypoxic brain damage is a potentially fatal high-altitude sickness. Autophagy plays a critical role in ischemic brain injury, but its role in hypobaric hypoxia (HH) remains unknown. Here we used an HH chamber to demonstrate that acute HH exposure impairs autophagic activity in both the early and late stages of the mouse brain, and is partially responsible for HH-induced oxidative stress, neuronal loss, and brain damage. The autophagic agonist rapamycin only promotes the initiation of autophagy. By proteome analysis, a screen showed that protein dynamin2 (DNM2) potentially regulates autophagic flux. Overexpression of DNM2 significantly increased the formation of autolysosomes, thus maintaining autophagic flux in combination with rapamycin. Furthermore, the enhancement of autophagic activity attenuated oxidative stress and neurological deficits after HH exposure. These results contribute to evidence supporting the conclusion that DNM2-mediated autophagic flux represents a new therapeutic target in HH-induced brain damage.