Quantitative Proteomic Technology Research Articles

Study on the Relationship between Guanling Cattle Muscle Proteomics and Meat Quality within One Hour after Slaughter Based on Tmt-Labeled Quantitative Proteomic Technology

Study on the Relationship between Guanling Cattle Muscle Proteomics and Meat Quality within One Hour after Slaughter Based on Tmt-Labeled Quantitative Proteomic Technology

The Attenuating Effect of Low-Intensity Pulsed Ultrasound on Hypoxia-Induced Rat Chondrocyte Damage in TMJ Osteoarthritis Based on TMT Labeling Quantitative Proteomic Analysis.

Temporomandibular joint osteoarthritis (TMJOA) is a degenerative disease with a complex and multifactorial etiology. An increased intrajoint pressure or weakened penetration can exacerbate the hypoxic state of the condylar cartilage microenvironment. Our group previously simulated the hypoxic environment of TMJOA in vitro. Low-intensity pulsed ultrasound (LIPUS) stimulation attenuates chondrocyte matrix degradation via a hypoxia-inducible factor (HIF) pathway-associated mechanism, but the mode of action of LIPUS is currently poorly understood. Moreover, most recent studies investigated the pathological mechanisms of osteoarthritis, but no biomarkers have been established for assessing the therapeutic effect of LIPUS on TMJOA with high specificity, which results in a lack of guidance regarding clinical application. Here, tandem mass tag (TMT)-based quantitative proteomic technology was used to comprehensively screen the molecular targets and pathways affected by the action of LIPUS on chondrocytes under hypoxic conditions. A bioinformatic analysis identified 902 and 131 differentially expressed proteins (DEPs) in the <1% oxygen treatment group compared with the control group and in the <1% oxygen + LIPUS stimulation group compared with the <1% oxygen treatment group, respectively. The DEPs were analyzed by gene ontology (GO), KEGG pathway and protein-protein interaction (PPI) network analyses. By acting on extracellular matrix (ECM)-associated proteins, LIPUS increases energy production and activates the FAK signaling pathway to regulate cell biological behaviors. DEPs of interest were selected to verify the reliability of the proteomic results. In addition, this experiment demonstrated that LIPUS could upregulate chondrogenic factors (such as Sox9, Collagen Ⅱ and Aggrecan) and increase the mucin sulfate content. Moreover, LIPUS reduced the hydrolytic degradation of the ECM by decreasing the MMP3/TIMP1 ratio and vascularization by downregulating VEGF. Interestingly, LIPUS improved the migration ability of chondrocytes. In summary, LIPUS can regulate complex biological processes in chondrocytes under hypoxic conditions and alter the expression of many functional proteins, which results in reductions in hypoxia-induced chondrocyte damage. ECM proteins such as thrombospondin4, thrombospondin1, IL1RL1, and tissue inhibitors of metalloproteinase 1 play a central role and can be used as specific biomarkers determining the efficacy of LIPUS and viable clinical therapeutic targets of TMJOA.

Quantitative proteomic analysis of cervical cancer based on TMT-labeled quantitative proteomics

Cervical cancer is the second most common gynecological malignancy, which immensely threatens the well-being of women. However, the pathogenesis of cervical cancer is still unclear. Using tandem mass tags-labeled quantitative proteomic technology and bioinformatics tools, we analyzed the exfoliated cervical cells from the normal and cervical cancer groups to establish a cancer-specific protein profile, thereby identifying key proteins related to cervical oncogenesis. When compared with the normal group, a total of 351 differentially expressed proteins were identified in the cervical cancer group, including 247 up-regulated and 104 down-regulated proteins. Gene ontology function annotation revealed that the differentially expressed proteins were mainly involved in the single-multicellular organism process, multicellular organismal process, and negative regulation of biological process. These proteins were discerned to play a role in the extracellular membrane-bounded organelle, exosome of cell components, protein binding, structural molecule activity, and enzyme binding of molecular functions. The results of Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment proved that these differentially expressed proteins were mainly involved in PI3K − Akt, ECM-receptor interaction, complement and coagulation cascades, and other signaling pathways. Particularly, peroxiredoxin-2 may be involved in cervical tumor oncogenesis through inhibition of apoptosis signaling. SignificanceIn this study, we determined that the proteins of the cervical cancer group exhibited qualitative and quantitative changes, and a total of 351 differentially expressed proteins were identified. The functions and signaling pathways of these differentially expressed proteins have laid a theoretical foundation for elucidating the molecular mechanism of cervical cancer.

Analysis on tissue-related biomarkers in patients with acute aortic dissection

Objective: To explore the clinical implication of tissue-related biomarkers in patients with acute aortic dissection (AAD). Methods: It was a cross-sectional study. Ten Stanford Type A AAD patients, who were diagnosed and surgically treated in the Department of Cardiology, First Affiliated Hospital of Xinjiang Medical University, from December 2018 to August 2019, were selected as the case group. Meanwhile, 10 patients with atherosclerotic heart disease, who underwent coronary artery bypass grafting (CABG), were selected as control group. The ascending aorta tissue specimens from patients of the two groups were collected during the operation. Four-dimensional non-standard quantitative proteomics technology (4D-LFQ) was used to detect the protein profile of ascending aorta tissue specimens of the two groups and to screen out differentially expressed proteins and analyze their biological functions. Precise quantification of the selected target proteins was achieved by parallel response monitoring (PRM). Results: A total of 3 985 proteins were identified by 4D-LFQ technology, among which 3 350 proteins could be quantified. There were 39 proteins were significantly upregulated and 47 proteins were significantly downregulated in AAD group. The results of biological function analysis showed that most of the differentially expressed proteins were located in the extracellular, and their functions were mainly involved in cell migration and proliferation, inflammatory cell activation, cell contraction, and muscle organ development. The 15 selected proteins underwent precise quantification by PRM, and the results showed that integrin α-Ⅱb (ITGA2B), integrin α-M (ITGAM), integrin β-2 (ITGB2), integrin β-3 (ITGB3) were significantly upregulated in the ascending aorta tissue of AAD patients. Conclusion: ITGA2B, ITGAM, ITGB2, and ITGB3 are highly expressed in aortic tissues of patients with AAD, which may be used as biomarkers for the diagnosis of AAD patients.

Abstract 10505: S100a12 Aggravates Acute Myocardial Infarction Injury Through Excessive Neutrophil Extracellular Trap Formation

Introduction: S100A12 represents a novel biomarker and therapeutic target that regulates cardiovascular disease after its release from myeloid cells. However, the role of S100A12 in the etiology of Acute Myocardial Infarction (AMI) is not well understood. Neutrophil extracellular traps (NETs) are implicated in the pathogenesis of AMI and in the externalization of some S100 family members. Here, we investigated the effect of S100A12 on neutrophils’ function and myocardial injury after AMI. Methods and Results: Since S100A12 is a human specific molecule and not expressed in mice, we constructed transgenic (TG) mice expressing S100A12 in myeloid cells. By left anterior descending artery ligation and flow cytometry, we found that S100A12 markedly increased neutrophil infiltration and myocardial injury in TG mice compared to WT mice. Within the infarct zone, more neutrophil extracellular traps (NETs) were observed in TG mice, whereas intraperitoneal injection of DNase I decreased the damage effect of NETs. We used the overexpressing plasmid of S100A12 and observed that S100A12 enhanced the level of NETosis. Whereas, siRNA-mediated S100A12 silencing reduced the production of NETs. By ChIP and dual-luciferase reporter assay we found that Hypoxia-inducible factor-1α (HIF1α) directly bound to the promoter of the S100A12 gene and regulated S100A12 expression. We next used tandem mass tag (TMT) labeling quantitative proteomic technology and discovered that annexin a5 (ANXA5) was a receptor with significantly different expression level in TG compared with WT mice. Finally, we demonstrated that S100A12 increased NETs formation via receptor RAGE and ANXA5. Conclusions: Our findings reveal a critical role of S100A12 in regulating neutrophil activation and NETs formation, resulting in aggravated myocardial injury after AMI. In such a process, S100A12 regulates NETosis via the Hif1α-S100A12-ANXA5/RAGE pathway. S100A12 is a useful molecular marker and possible target for treatment for AMI.

Proteomic Response to Environmental Stresses in the Stolon of a Highly Invasive Fouling Ascidian

Ascidians, particularly those highly invasive ones, are typical fouling organisms to cause significantly negative ecological and economic influence in coastal ecosystems. Stolon, which is the unique structure of some solitary ascidians to complete the essential process of adhesion, possesses extremely high tolerance to environmental stresses during biofouling and invasions. However, the mechanisms underlying environmental tolerance remain largely unknown. Here, we used the quantitative proteomics technology, isobaric tags for relative and absolute quantitation (iTRAQ), to investigate the molecular response to environmental challenges (temperature and salinity) in the stolon of a highly invasive fouling ascidian, Ciona robusta. When compared with the control, a total of 75, 86, 123, and 83 differential abundance proteins were identified under low salinity, high salinity, low temperature, and high temperature stress, respectively. Bioinformatic analyses uncovered the key pathways under both temperature and salinity stresses, including “cytoskeleton,” “signal transduction,” and “posttranslational modification,” which were involved in stolon structure stability, protein synthesis, and stress response activation. Under the low salinity stress, the “extracellular matrix” pathway was identified to play a crucial role by regulating cell signal transduction and protein synthesis. To deal with the high salinity stress, stolon could store more energy by activating “carbohydrate/lipid transport” and “catabolism” pathways. The energy generated by “lipid metabolism” pathway might be beneficial to resist the low temperature stress. The upregulation of “cell cycle” pathway could inhibit cell growth, thus helping stolon conserve more energy against the high temperature stress. Our results here provide valuable references of candidate pathways and associated genes for studying mechanisms of harsh environmental adaptation and developing antifouling strategies in marine and coastal ecosystems.

ITRAQ-based quantitative proteomic analysis of the improved effects of total flavones of Dracocephalum Moldavica L. in chronic mountain sickness

To use isobaric tags for relative and absolute quantification (iTRAQ) technology to study the pathogenesis of chronic mountain sickness (CMS), identify biomarkers for CMS, and investigate the effect of total flavones of Dracocephalum moldavica L. (TFDM) on a rat model of CMS. We simulated high altitude hypobaric hypoxia conditions and generated a rat model of CMS. Following the administration of TFDM, we measured the pulmonary artery pressure and serum levels of hemoglobin (Hb), the hematocrit (Hct), and observed the structure of the pulmonary artery in experimental rats. Furthermore, we applied iTRAQ-labeled quantitative proteomics technology to identify differentially expressed proteins (DEPs) in the serum, performed bioinformatics analysis, and verified the DEPs by immunohistochemistry. Analysis showed that the pulmonary artery pressure, serum levels of Hb, and the Hct, were significantly increased in a rat model of CMS (P < 0.05). Pathological analysis of lung tissue and pulmonary artery tissue showed that the alveolar compartment had obvious hyperplasia and the pulmonary artery degree of muscularization was enhanced. Both pulmonary artery pressure and tissue morphology were improved following the administration of TFDM. We identified 532 DEPs by quantitative proteomics; gene ontology (GO)and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that metabolic pathways associated with coagulation and complement play crucial roles in the occurrence of CMS. Immunohistochemistry verified that several DEPs (α-1-acid glycoprotein, collagen, fibulin, haptoglobin, PLTP, and TAGLN2) are important biological markers for CMS. Our analyses demonstrated that TFDM can improve CMS and exert action by influencing the metabolic pathways associated with coagulation and complement. This process relieves pulmonary artery pressure and improves lung function. We also identified that α-1-acid glycoprotein, collagen, fibulin, haptoglobin, PLTP, and TAGLN2 may represent potential biomarkers for CMS.

Growth, Stoichiometry, and Palatability of Suaeda salsa From Different Habitats Are Demonstrated by Differentially Expressed Proteins and Their Enriched Pathways.

Suaeda salsa (L.) Pall., a medicinal and edible plant, has green and red-violet ecotypes that exhibit different phenotypes, tastes, and growth characteristics. However, few studies have focused on these differences from the aspect of differentially expressed proteins under the conditions of different habitats in the field. In this study, two ecotypes of S. salsa from the intertidal (control) and supratidal (treatment) habitats of the Yellow River Delta were selected. A total of 30 individual leaves were mixed into six samples (three biological replicates for each) and subjected to protein extraction by using tandem mass tag-labeled quantitative proteomic technology. A total of 4771 proteins were quantitated. They included 317 differentially expressed proteins (2.0-fold change, p < 0.05), among which 143 were upregulated and the remaining 174 were downregulated. These differentially expressed proteins mainly participated in biological processes, such as response to stimulus, stress, and biotic stimulus; in molecular functions, such as methyltransferase activity, transferase activity, one-C group transfer, and tetrapyrrole binding; and in cell components, such as non-membrane-bound organelles, intracellular non-membrane-bound organelles, chromosomes, and photosystems. The differentially expressed proteins were mainly enriched in eight pathways, among which the ribosome, phenylpropanoid biosynthesis, and photosynthesis pathways had higher protein numbers than the other pathways. The upregulation of differentially expressed proteins related to the ribosome and photosynthesis increased the relative growth rate and reduced the N:P ratio of S. salsa from the supratidal habitat, thereby improving its palatability. By contrast, most of the differentially expressed proteins involved in phenylpropanoid biosynthesis were downregulated in S. salsa from the intertidal habitat. This result indicated that S. salsa from the intertidal habitat might accumulate flavonoids, lignin, and other secondary metabolites in its leaves that confer a bitter taste. However, these secondary metabolites might increase the medicinal value of S. salsa from the intertidal habitat. This work could provide a theoretical basis and data support for the sustainable and high-value utilization of medicinal and edible plants from coastal wetlands.

Study on the mechanism of Salvia miltiorrhiza polysaccharides in relieving liver injury of broilers induced by florfenicol.

In order to explore the transcriptomics and proteomics targets and pathways of Salvia miltiorrhiza polysaccharides (SMPs) alleviating florfenicol (FFC)-induced liver injury in broilers, 60 1-day-old broilers were randomly divided into 3 groups: control group ( GP1) was fed tap water, FFC model (GP2) was given tap water containing FFC 0.15 g/L, and SMPs treatment group (GP3) was given tap water containing FFC 0.15 g/L and SMPs 5 g/L. Starting from 1 day of age, the drug was administered continuously for 5 days. On the 6th day, blood was collected from the heart and the liver was taken. Then 3 chickens were randomly taken from each group, and their liver tissues were aseptically removed and placed in an enzyme-free tube. Using high-throughput mRNA sequencing and TMT-labeled quantitative proteomics technology, the transcriptome and proteome of the three groups of broiler liver were analyzed, respectively. The results of the study showed that the liver tissue morphology of the chicks in the GP1 and GP3 groups was complete and there were no obvious necrotic cells in the liver cells. The liver tissue cells in the GP2 group showed obvious damage, the intercellular space increased, and the liver cells showed extensive vacuolation and steatosis. Compared with the GP1 group, the daily gain of chicks in the GP2 group was significantly reduced (P < 0.0 5 or P < 0.01). Compared with the GP2 group, the GP3 group significantly increased the daily gain of chicks (P <0.0 5 or P <0.01). Compared with the GP1 group, the serum levels of ALT, AST, liver LPO, ROS, and IL-6 in the GP2 group were significantly increased (P < 0.0 5 or P < 0.01), and the contents of T-AOC, GSH-PX, IL-4, and IL-10 in the liver were significantly decreased (P < 0.0 5 or P < 0.01). After SMPs treatment, the serum levels of ALT, AST, liver LPO, ROS, and IL-6 were significantly reduced (P < 0.0 5 or P < 0.01), and the contents of T-AOC, GSH-PX, IL-4, and IL-10 in the liver were significantly increased (P < 0.0 5 or P < 0.01). There were 380 mRNA and 178 protein differentially expressed between GP2 group and GP3 group. Part of DEGs was randomly selected for QPCR verification, and the expression results of randomly selected FABP1, SLC16A1, GPT2, AACS, and other genes were verified by QPCR to be consistent with the sequencing results, which demonstrated the accuracy of transcriptation-associated proteomics sequencing. The results showed that SMPs could alleviate the oxidative stress and inflammatory damage caused by FFC in the liver of chicken and restore the normal function of the liver. SMPs may alleviate the liver damage caused by FFC by regulating the drug metabolism-cytochrome P450, PPAR signaling pathway, MAPK signaling pathway, glutathione metabolism, and other pathways.

DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera.

The sacred lotus (Nelumbo nucifera) can maintain a stable floral chamber temperature between 30 and 35 °C when blooming despite fluctuations in ambient temperatures between about 8 and 45 °C, but the regulatory mechanism of floral thermogenesis remains unclear. Here, we obtained comprehensive protein profiles from receptacle tissue at five developmental stages using data-independent acquisition (DIA)-based quantitative proteomics technology to reveal the molecular basis of floral thermogenesis of N. nucifera. A total of 6913 proteins were identified and quantified, of which 3513 differentially abundant proteins (DAPs) were screened. Among them, 640 highly abundant proteins during the thermogenic stages were mainly involved in carbon metabolism processes such as the tricarboxylic acid (TCA) cycle. Citrate synthase was identified as the most connected protein in the protein-protein interaction (PPI) network. Next, the content of alternative oxidase (AOX) and plant uncoupling protein (pUCP) in different tissues indicated that AOX was specifically abundant in the receptacles. Subsequently, a protein module highly related to the thermogenic phenotype was identified by the weighted gene co-expression network analysis (WGCNA). In summary, the regulation mechanism of floral thermogenesis in N. nucifera involves complex regulatory networks, including TCA cycle metabolism, starch and sucrose metabolism, fatty acid degradation, and ubiquinone synthesis, etc.

Characterization of Novel Progression Factors in Castration-Resistant Prostate Cancer Based on Global Comparative Proteome Analysis.

Simple SummaryHere, we investigated prostate cancer (PCa) tissues at each stage of progression, from benign prostatic hyperplasia to castration-resistant prostate cancer (CRPC), based on quantitative proteomic technology, including tissues after androgen deprivation therapy (ADT). In total, we identified 4768 proteins, and 4069 of them were quantified. We performed a systematic bioinformatics analysis of 865 differentially expressed proteins (DEPs) in the combined PCa tissues. We found 15 DEPs, including FOXA1 and HMGN1–3, as novel factors were significantly involved in the progression to CRPC after ADT in T3G3. All targets were verified to have increased levels of FOXA1 and HMGN1–3 in CRPC by immunoblotting and indirect enzyme-linked immunosorbent assay. The FOXA1 and HMGN1–3 proteins could be used as CRPC-related factors in clinical therapeutic agents.Identifying the biological change from hormone-naïve prostate cancer to castration-resistant prostate cancer (CRPC) is a major clinical challenge for developing therapeutic agents. Although the pathways that lead to CRPC are not fully completely understood, recent evidence demonstrates that androgen signaling is often maintained through varied mechanisms. Androgen deprivation therapy (ADT) is used as a primary treatment for preventing the progression of prostate cancer (PCa). Here we investigated PCa tissues at each stage of progression, from benign prostatic hyperplasia (BPH) to CRPC, based on quantitative proteomic technology, including tissues after ADT. In total, 4768 proteins were identified in this study, of which 4069 were quantified in the combined PCa tissues. Among the quantified proteins, 865 were differentially expressed proteins (21.2%). Based on the quantitative protein results, we performed systematic bioinformatics analysis and found that the levels of 15 proteins, including FOXA1 and HMGN1–3, increased among T3G3, T3GX, and CRPC, despite the ADT. Among all targets, we verified the increased levels of FOXA1 and HMGN1–3 in CRPC by immunoblotting and indirect enzyme-linked immunosorbent assay. In summary, we discuss the changes in intracellular factors involved in the progression of CRPC PCa despite ADT. Moreover, we suggest that FOXA1 and HMGN1–3 proteins could be used as potential CRPC-related factors in clinical therapeutic agents.

Multi-omics analysis of brain tissue metabolome and proteome reveals the protective effect of gross saponins of Tribulus terrestris L. fruit against ischemic stroke in rat

Ethnopharmacological relevanceGross Saponins of Tribulus terrestris L. Fruit (GSTTF) has been reported to have a protective effect against ischemic stroke, but the related mechanism is complex and still not fully investigated. Aim of the studyThe combination of metabolomics and proteomics approach was applied to reveal the mechanisms of GSTTF in treating ischemic stroke. Materials and methodsThe metabolite and protein changes in brain tissue were analyzed by the LC-MS-based untargeted metabolomics method and tandem mass tags (TMT)-based quantitative proteomics technology. The multivariate statistical analysis and protein-protein interaction (PPI) analysis were conducted to screen out the biomarkers, and their related pathway was further investigated by the joint pathway analysis. ResultsA total of 110 metabolites and 359 differential proteins, which were mainly associated with complement and coagulation cascades, sphingolipid metabolism, glycerophospholipid metabolism, glutathione metabolism, and platelet activation, etc. were screened out from the rat brain tissue. The PPI network exhibited that the protein F2, Fga, Fgb, Fgg, Plg, and C3, which are greatly involved in the complement and coagulation cascades, have a relatively high connectivity degree, indicating their importance in the process of middle cerebral artery occlusion (MCAO). The GSTTF exerted a protective effect against MCAO via modulating multiple proteins on this pathway. Moreover, F2 played a key role during the protective process and worth to be further investigated due to it has been reported as one of the therapeutic targets of ischemic stroke. ConclusionThe present study could improve the understanding of the potential therapeutic mechanism of GSTTF against ischemic stroke.

ITRAQ-based quantitative proteomics and network pharmacology revealing hemostatic mechanism mediated by Zingiberis Rhizome Carbonisata in deficiency-cold and Hemorrhagic Syndrome rat models

Zingiberis Rhizome Carbonisata (ZRC) has been used as a hemostatic agent in traditional Chinese medicine (TCM). However, the underlying molecular mechanism remains unclear. In this study, network pharmacology method was used to predict the potential mechanism of ZRC on hemostasis, based on the structures of the main compounds. Then, iTRAQ-based quantitative proteomics analysis was used for verification of the candidate target proteins and pathways to illustrate the underlying mechanisms. Furthermore, the differentially expressed proteins (DEPs) in the enriched pathways were validated by Enzyme-linked immunosorbent assay. The results showed that the hemostasis mechanism of ZRC may be related to Platelet activation, Rap1 signaling pathway and Complement and coagulation cascades. And 10 proteins (Fermt3, ACTB, Talin, αIIbβ3, Fga, Fgb, Fgg, FXIIIb, Kng and PLC-β were identified as the target DEPs) are considered as the key factors related to hemostatic efficacy of ZRC. Thus, integrated network pharmacology and quantitative proteomics technology were applied for the effective illuminating the molecular mechanisms of Chinese material medica.

Liver proteomics analysis reveals abnormal metabolism of bile acid and arachidonic acid in Chinese hamsters with type 2 diabetes mellitus

Non-obese, spontaneous, and genetically predisposed type 2 diabetic Chinese hamsters exhibit metabolic abnormalities similar to those observed in human T2DM. Here, tandem mass tag (TMT)-based quantitative proteomics technology was used to screen and identify differentially abundant proteins in the liver that are associated with diabetes in Chinese hamsters. GO and KEGG pathway enrichment analysis were conducted to validate the findings, as well as qRT-PCR and western blotting. In total, 103 proteins were identified in the livers of diabetic hamsters, of which 48 were up-regulated and 55 were down-regulated. KEGG pathway enrichment analysis further demonstrated that linoleic acid metabolism, arachidonic acid metabolism, bile secretion, and other pathways were affected. Moreover, AQP9 and EPHX1 were significantly down-regulated in the bile secretion pathway, whereas PTGES2, Cyp2c27, and Cyp2c70 were associated with the arachidonic acid metabolic pathway. Serum levels of bile acid (BA) and arachidonic acid (AA) in diabetic Chinese hamsters were significantly higher than those in control hamsters. Cumulatively, our findings indicate that the five candidate proteins may be associated with abnormal BA and AA metabolism, suggesting their involvement in pathological changes in the livers of Chinese hamsters with T2DM. SignificanceThe liver proteomics of Chinese hamsters describes differentially abundant proteins associated with T2DM, while promoting this animal model as an appropriate and ideal platform for investigating underlying molecular mechanisms of T2DM. This study reveals abnormal bile acid and arachidonic acid metabolism in T2DM hamsters, which may provide insights for studying the relationship between candidate proteins and KEGG pathways to elucidate the underlying molecular mechanism associated with T2DM.

Comprehensive dynamic analysis of proteins in the spermatheca of female Haemaphysalis longicornis after copulation.

Ticks are obligate blood-sucking parasitic arthropods. When sucking the blood of hosts, they can also transmit a variety of pathogens to hosts that severely endanger the health of humans and animals. The spermatheca is an organ for the storage and protection of sperm and an important component of the reproductive system of female ticks. The spermatheca content changes dramatically over time after copulation. In particular, some proteins and polypeptide substances can influence the physiological functions of female ticks and promote blood feeding and egg laying by female ticks. To investigate the molecular mechanisms underlying the productive process of Haemaphysalis longicornis, data-independent acquisition (DIA) quantitative proteomics technology was used to perform in-depth research of the dynamic changes in all proteins in the spermatheca of ticks within a short time after copulation to look for key proteins in the spermatheca contents after copulation that affect the reproduction of female ticks in order to provide meaningful information for the comprehensive prevention and control of ticks.

Proteomics Analysis of Serum from COVID-19 Patients.

Coronavirus disease 2019 (COVID-19) is a worldwide pandemic. To understand the changes in plasma proteomics upon SARS-CoV-2 infection, we analyzed the protein profiles of plasma samples from 10 COVID-19 patients and 10 healthy volunteers by using the DIA quantitative proteomics technology. We compared and identified differential proteins whose abundance changed upon SARS-CoV-2 infection. Bioinformatic analyses were then conducted for these identified differential proteins. The GO/KEEG database was used for functional annotation and enrichment analysis. The interaction relationship of differential proteins was evaluated with the STRING database, and Cytoscape software was used to conduct network analysis of the obtained data. A total of 323 proteins were detected in all samples. Difference between patients and healthy donors was found in 44 plasma proteins, among which 36 proteins were up-regulated and 8 proteins were down-regulated. GO functional annotation showed that these proteins mostly composed of cellular anatomical entities and proteins involved in biological regulation, cellular processes, transport, and other processes. KEEG functional annotation further showed that these proteins were mainly involved in complement system activation and infectious disease processes. Importantly, a KEEG pathway (natural killer cell-mediated cytotoxicity) was enriched, with three important activators of this pathway, ICAM1/2 and IgG, being up-regulated. Protein–protein interaction (PPI) statistics indicated that, among these 44 proteins, 6 were the most significantly up-regulated (DBH, SHGB, TF, ICAM2, THBS1, and C1RL) while 2 were the most significantly down-regulated (APCS and ORM1). Results from this study showed that a few proteins associated with immune activation were up-regulated in patient plasma. In addition, this study established a method for extraction and quantitative determination of plasma components in convalescent plasma from COVID-19 patients.

Ubiquitin-Modified Proteome of SARS-CoV-2-Infected Host Cells Reveals Insights into Virus-Host Interaction and Pathogenesis.

The outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed a serious threat to global public health. The mechanism of pathogenesis and the host immune response to SARS-CoV-2 infection are largely unknown. In the present study, we applied a quantitative proteomic technology to identify and quantify the ubiquitination changes that occur in both the virus and the Vero E6 cells during SARS-CoV-2 infection. By applying label-free, quantitative liquid chromatography with tandem mass spectrometry proteomics, 8943 lysine ubiquitination sites on 3086 proteins were identified, of which 138 sites on 104 proteins were quantified as significantly upregulated, while 828 sites on 447 proteins were downregulated at 72 h post-infection. Bioinformatics analysis suggested that SARS-CoV-2 infection might modulate host immune responses through the ubiquitination of important proteins, including USP5, IQGAP1, TRIM28, and Hsp90. Ubiquitination modification was also observed on 11 SAR-CoV-2 proteins, including proteins involved in virus replication and inhibition of the host innate immune response. Our study provides new insights into the interaction between SARS-CoV-2 and the host as well as potential targets for the prevention and treatment of COVID-19.

The molecular regulatory mechanisms of the bacteria involved in serpentine weathering coupled with carbonation

Development of an effective biotechnological method of reducing the continuous emission of CO2 has caused wide public concern. Research on serpentine bio-weathering coupled with carbonation is a current focus of interest. To investigate the molecular mechanisms, Bacillus subtilis was cultured in the Mg2+-free medium with the addition of serpentine. Based on the composition of organic matter and the characterization of the weathered serpentine, quantitative proteomics technology was adopted to elucidate the roles of proteins played in the coupled process. Electrochemical analysis and vapor diffusion crystallization experiments were also performed to reveal the molecular mechanisms. The results demonstrated that more oxidoreductases were secreted to facilitate the transformation of serpentine, and drive the synthesis of organic acids to accelerate the weathering of serpentine. In the late stage of serpentine weathering, that is, the serpentine carbonation stage, the characterization of the secondary minerals showed that struvite and amorphous carbonate had been formed with some organic matter. In serpentine carbonation stage, excessive Ni in the microenvironment drove N metabolism to facilitate the elevation of pH, resulting in the serpentine carbonation. This study enriched our understanding of the molecular mechanisms at protein-level in serpentine bio-weathering coupled with carbonation.

Proteomic Analysis of Perihematoma Tissue from Patients with Intracerebral Hemorrhage Using iTRAQ-Based Quantitative Proteomics.

Intracerebral hemorrhage is a complicated disorder with limited proven prognostic and therapeutic targets and elusive mechanisms. With proteomic methods, we aimed to explore the global protein expression profile of perihematomal tissue from ICH patients and identify potential pathophysiological pathways and protein markers. Using iTRAQ-labeling quantitative proteomics technology, four ICH brain sample and four non-ICH brain samples were analyzed. Among the 3740 quantifiable proteins, 884 were dysregulated in the patients compared to those in the controls (p < 0.05). After bioinformatics analysis, the differentially expressed proteins were found to be mostly involved in hemostatic processes, nutrient metabolism signaling pathways, and antioxidation pathways. Moreover, fibronectin 1 was revealed to be at the center of the protein-protein interaction networks. In summary, the potential pathways and brain protein markers that could potentially be used to predict the prognosis of ICH were obtained from the altered proteomic profile of perihematomal tissue. Thus, these data may yield novel insights into the mechanisms of ICH-induced secondary brain injury.

Screening differentially expressed proteins of coronary heart disease with congenital cold syndrome based on tandem mass tag (TMT) technology

ABSTRACT In our previous studies, we discovered the congenital cold syndrome (CCS), which is characterized by ‘qi deficiency and qi stagnation, mixed cold and heat.’ And there is a type of syndrome with special incidence characteristic. However, the diagnosis of CCS still lacks an objective basis. In this study, we performed Tandem Mass Tag (TMT) based on quantitative proteomics technology to screen the significantly differentially expressed proteins (DEPs) in serum of patients with coronary heart disease (CHD) patients with CCS, patients with heart and kidney yang deficiency, and healthy people. A total of 22 DEPs (nine upregulated and 13 downregulated) were identified between patients with CCS and healthy subjects. Next, we performed GO and KEGG pathway enrichment analysis, we found the primary functions of DEPs of CCS were binding, catalytic activity, and molecular function regulator. These DEPs were mainly involved in important biological processes, such as cellular process, response to stimulus, localization, metabolic process, and biological regulation. The KEGG analysis revealed that the DEPs showed significant changes in fructose and mannose metabolism, Pentose phosphate pathway, and Arrhythmogenic right ventricular cardiomyopathy. After parallel reaction monitoring (PRM) verification, four upregulated target proteins (ALDOA, PCYOX1, Crisp3 and IGLV4-69) and three downregulated proteins (ALDOC, ADAMTSL-2 and C3) were accurately identified. These proteins were mainly related to immune response and glucose metabolism. These DEPs could be the marker proteins of coronary heart disease with CCS. This findings help to reveal the pathogenesis of CHD with CCS and provide potential therapeutic targets.