TMT-based Quantitative Proteomics Research Articles

Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

BackgroundThe identification of differentially expressed tumor-associated proteins and genomic alterations driving neoplasia is critical in the development of clinical assays to detect cancers and forms the foundation for understanding cancer biology. One of the challenges in the analysis of pancreatic ductal adenocarcinoma (PDAC) is the low neoplastic cellularity and heterogeneous composition of bulk tumors. To enrich neoplastic cells from bulk tumor tissue, coring, and laser microdissection (LMD) sampling techniques have been employed. In this study, we assessed the protein and KRAS mutation changes associated with samples obtained by these enrichment techniques and evaluated the fraction of neoplastic cells in PDAC for proteomic and genomic analyses.MethodsThree fresh frozen PDAC tumors and their tumor-matched normal adjacent tissues (NATs) were obtained from three sampling techniques using bulk, coring, and LMD; and analyzed by TMT-based quantitative proteomics. The protein profiles and characterizations of differentially expressed proteins in three sampling groups were determined. These three PDACs and samples of five additional PDACs obtained by the same three sampling techniques were also subjected to genomic analysis to characterize KRAS mutations.ResultsThe neoplastic cellularity of eight PDACs ranged from less than 10% to over 80% based on morphological review. Distinctive proteomic patterns and abundances of certain tumor-associated proteins were revealed when comparing the tumors and NATs by different sampling techniques. Coring and bulk tissues had comparable proteome profiles, while LMD samples had the most distinct proteome composition compared to bulk tissues. Further genomic analysis of bulk, cored, or LMD samples demonstrated that KRAS mutations were significantly enriched in LMD samples while coring was less effective in enriching for KRAS mutations when bulk tissues contained a relatively low neoplastic cellularity.ConclusionsIn addition to bulk tissues, samples from LMD and coring techniques can be used for proteogenomic studies. The greatest enrichment of neoplastic cellularity is obtained with the LMD technique.

Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed. Part I: Serum proteomes

This study examines whether maternal low ω6:ω3 ratio diet and offspring SW supplementation can improve offspring immunity and performance by elucidating the effects on piglet serum proteome. A total of 16 sows were given either a standard (CR, 13:1) or low ω6:ω3 ratio diet (LR, 4:1) during pregnancy and lactation and their male weaned piglets were supplemented with SW powder (4 g/kg, SW) or not (CT) in a 21-day post-weaning (PW) diet. Four PW piglet groups were then identified based on dam and piglet treatment, namely CRCT, CRSW, LRCT, and LRSW (n = 10 each). Piglet serum collected at weaning and d21 PW were analysed (n = 5 each) using TMT-based quantitative proteomics and validated by appropriate assays. The differentially abundant proteins (n = 122) displayed positive effects of maternal LR diet on anti-inflammatory properties and innate immune stimulation. Progeny SW diet activated the innate immunity and enhance the host defence during inflammation. These data demonstrate the value of decreasing ω6:ω3 ratio in maternal diet and SW supplementation in PW piglet's diet to boost their immunity and anti-inflammation properties. SignificanceThis novel proteomic study in post-weaned piglets addresses the interplay between maternal and offspring nutritional interventions in a context of rapid and dynamic alterations in piglet metabolic status around weaning. Decreasing ω6:ω3 ratio in maternal diet and SW supplementation in PW piglet's diet can boost their immunity and anti-inflammation properties. This study also provides new insights into piglet serum proteome regulation during post-weaning, a critical development period in swine.

Proteomic changes associated with maternal dietary low ω6:ω3 ratio in piglets supplemented with seaweed Part II: Ileum proteomes

This study evaluates how long-term dietary low ω6:ω3 ratio in sows and offspring's seaweed (SW) intake affects piglet intestinal function and growth through modifying ileum proteome. Sows were assigned to either control diet (CR, ω6:ω3 ratio = 13:1) or treatment diet (LR, ω6:ω3 = 4:1) during gestation and lactation (n = 8 each). The male weaned offspring were received a basal diet with or without SW powder supplementation (4 g/kg) for 21 days, denoted as SW and CT groups, respectively. In total, four groups of weaned piglets were formed following maternal and offspring's diets combination, represented by CRCT, CRSW, LRCT, and LRSW (n = 10 each). Piglet ileum tissue was collected on day 22 post-weaning and analysed using TMT-based quantitative proteomics. The differentially abundant proteins (n = 300) showed the influence of maternal LR diet on protein synthesis, cell proliferation, and cell cycle regulation. In contrast, the SW diet lowered the inflammation severity and promoted ileal tissue development in CRSW piglets but reduced the fat absorption capacity in LRSW piglets. These results uncovered the mechanism behind the anti-inflammation and intestinal-boosting effects of maternal LR diet in piglets supplemented with SW.

TMT-based quantitative proteomics analysis reveals the role of Notch signaling in FAdV-4-infected LMH cell.

Fowl adenovirus serotype 4 (FAdV-4) is recognized as a pathogen that causes hydropericardium syndrome. Irrespective of the pathway used by the virus to invade the chicken, the pathological characteristics of the disease include degeneration and necrosis of hepatocytes, formation of intranuclear inclusions, as well as inflammatory cell infiltration. Liver dysfunction constitutes one of the critical factors leading to death. Therefore, it is vital to investigate the virus-mediated severe pathological liver damage to further understand the pathogenesis of FAdV-4. Here, proteomics, a tandem mass tag (TMT)-based approach to directly analyze protein expression, was used to determine the protein expression during FAdV-4 proliferation in leghorn male hepatoma (LMH) cells. We identified 177 differentially expressed proteins associated with various biological processes and pathways. The functional enrichment analysis revealed that FAdV-4 could downregulate some signaling pathways in LMH cells, including NOD-like receptor signaling, RIG-I-like receptor signaling, NF-κB signaling, TNF signaling pathway, and Notch signaling, FoxO signaling, PI3K-Akt signaling, and autophagy. The results of proteomics screening suggested an association between FAdV-4 infection and Notch signaling in LMH in vitro, indicating that Notch signaling regulated the expression of inflammatory cytokines and interferons but not viral replication in LMH cells. These data contributed to the understanding of the immunopathogenesis and inflammopathogenesis of FAdV-4 infection and also provided valuable information for the further analysis of the molecular mechanisms underlying viral pathogenesis.

Evaluation of biological mechanisms of artemisinin on bovine mammary epithelial cells by integration of network pharmacology and TMT-based quantitative proteomics.

The sesquiterpene lactone, artemisinin, is a primary component of the medicinal plant Artemisia annua L., which has anti-inflammatory, antibacterial and antioxidant activities. However, the potential effects of artemisinin on the mammary gland of dairy cows and the underlying molecular mechanisms remain unclear. Here, we utilized systematic network pharmacology and proteomics to elucidate the mechanism by which artemisinin affects milk production and the proliferation of bovine mammary epithelial cells (BMECs). Nineteen bioactive compounds and 56 key targets were identified through database mining. To delineate the mechanism of artemisia’s activity, a protein-protein interaction network and integrated visual display were generated from bioinformatics assays to explore the relationships and interactions among the bioactive molecules and their targets. The gene ontology (GO) terms and kyoto encyclopedia of genes and genomes annotation suggested that the apoptotic process, cell division, p53 pathway, prolactin and PI3K-Akt pathways played vital roles in mammary gland development. Using proteomics analysis, we identified 122 up-regulated and 96 down-regulated differentially significant expressed proteins (DSEPs). The differentially significant expressed proteins had multiple biological functions associated with cell division, apoptosis, differentiation, and migration. Gene ontology enrichment analysis suggested that differentially significant expressed proteins may promote cell proliferation and regulate apoptosis in bovine mammary epithelial cells. Kyoto encyclopedia of genes and genomes pathway analysis indicated that several biological pathways, such as those involved in antigen processing and presentation, cell adhesion molecules and ribosomes, played significant roles in the effects of artemisinin on bovine mammary epithelial cells. These findings contribute to a comprehensive understanding of the mechanism by which artemisinin affects bovine mammary epithelial cells to improve mammary gland turnover by inducing cell proliferation and mammary gland development.

Proteomic Analysis of the Sphincter in a Neurogenic Bladder Caused by T10 Spinal Cord Injury.

This study aimed to conduct proteomic analysis of the sphincter in a neurogenic bladder caused by T10 spinal cord injury. The differentially expressed proteins (DEPs) of the sphincters (internal urethral sphincter) in the neurogenic bladders (NBs) of rats after complete transection of the T10 spinal cord segment were screened using tandem mass tag (TMT)-based quantitative labeling, and their biological information was analyzed. Twelve adult Sprague Dawley rats out of 40 were randomly assigned to the blank group (n = 12), while the remaining 28 were placed in the T10 spinal cord injury model via modified Hassan Shaker spinal cord transection; 12 of these rats were then randomly selected as the model group. The rats in both groups underwent urodynamics detection and hematoxylin and eosin (H&E) staining. The proteins expressed in the bladder sphincter were detected using TMT-based quantitative proteomics. DEPs were defined as proteins with fold change >1.5 or <1/1.5, p < 0.05, and unique peptide ≥2. The DEPs were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis using KOBAS 3.0., and gene ontology functional annotation analysis was performed using the Cytoscape 3.7.1. BiNGO plug-in. The protein-protein interaction network was then constructed using the interactive gene-retrieval tool STRING and Cytoscape software. The leak-point pressure and maximum cystometric volume in the model group were significantly higher than those in the blank group (p < 0.01), and H&E staining showed continuous interruption of the bladder sphincter fibers in the model group. A total of 250 DEPs were screened in the bladder sphincter, 83 of which were up-regulated and 167 of which were down-regulated. KEGG analysis of the DEPs was used to screen 15 pathways, including metabolic pathways, extracellular matrix (ECM)-receptor interaction, adhesion spots, the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway, the cytochalasin signaling pathway, and the advanced glycation end-products (AGE)/receptor for AGEs (RAGE) signaling pathway in diabetic complications and vascular smooth muscle contraction. It is of great significance to explore the pathological mechanism of non-inhibitory contraction of the bladder sphincter caused by spinal cord injury above the T10 segment from the perspective of ECM-receptor interaction, focal adhesion-activated PI3K/Akt signaling pathway, and cell relaxation signaling pathways. Synaptic vesicle glycoprotein (Sv2A) involved in the release of neurotransmitters from synaptic vesicles, arrestin β2 inhibitory proteins involved in α-adrenergic receptors and G-protein-coupled receptor internalization, and calmodulin and calmodulin binding protein involved in calcium-sensitive signaling pathways may be potential targets for developing new ways to treat bladder sphincter overactivity caused by T10 spinal cord injury.

TMT-based quantitative membrane proteomics identified PRRs potentially involved in the perception of MSP1 in rice leaves

Pathogen-associated molecular patterns (PAMPs) play a key role in triggering PAMPs triggered immunity (PTI) in plants. In the case of the rice-Magnaporthe oryzae pathosystem, fewer PAMPs and their pattern recognition receptors (PRRs) have been characterized. Recently, a M. oryzae snodprot1 homolog protein (MSP1) has been identified that functions as PAMP and triggering the PTI responses in rice. However, the molecular mechanism underlying MSP1-induced PTI is currently elusive. Therefore, we generated MSP1 overexpressed transgenic lines of rice, and a tandem mass tag (TMT)-based quantitative membrane proteomic analysis was employed to decipher the potential MSP1-induced signaling in rice using total cytosolic as well as membrane protein fractions. This approach led to the identification of 8033 proteins of which 1826 were differentially modulated in response to overexpression of MSP1 and/or exogenous jasmonic acid treatment. Of these, 20 plasma membrane-localized receptor-like kinases (RLKs) showed increased abundance in MSP1 overexpression lines. Moreover, activation of proteins related to the protein degradation and modification, calcium signaling, redox, and MAPK signaling was observed in transgenic lines expressing MSP1 in the apoplast. Taken together, our results identified potential PRR candidates involved in MSP1 recognition and suggested the overview mechanism of the MSP1-induced PTI signaling in rice leaves. SignificanceIn plants, recognition of pathogen pathogen-derived molecules, such as PAMPs, by plant plant-derived PRRs has an essential role for in the activation of PTI against pathogen invasion. Typically, PAMPs are recognized by plasma membrane (PM) localized PRRs, however, identifying the PM-localized PRR proteins is challenging due to their low abundance. In this study, we performed an integrated membrane protein enrichment by microsomal membrane extraction (MME) method and subsequent TMT-labeling-based quantitative proteomic analysis using MSP1 overexpressed rice. Based on these results, we successfully identified various intracellular and membrane membrane-localized proteins that participated in the MSP1-induced immune response and characterized the potential PM-localized PRR candidates in rice.

Tandem Mass Tag-Based Quantitative Proteomics Analysis of Gonads Reveals New Insight into Sexual Reversal Mechanism in Chinese Soft-Shelled Turtles.

Simple SummaryThe Chinese soft-shelled turtle has obvious sex dimorphism, which is an important aquatic economic species in China. Exogenous hormones can cause the sexual reversal of P. sinensis, but the molecular mechanism remains unclear. Here, TMT-based quantitative proteomics analysis of four types of P. sinensis (i.e., female (F), male (M), pseudo-female (PF), pseudo-male (PM)) gonads were performed. We found that there were common pathways, such as focal adhesion, endocytosis, apoptosis, ribosome, and spliceosome, which both played crucial roles in two comparison groups, including F vs. PM and M vs. PF. Furthermore, these differentially expressed proteins were associated with various biological processes, such as embryonic development and catabolic process, which were closely related to the sexual reversal of P. sinensis.Chinese soft-shelled turtles display obvious sex dimorphism. The exogenous application of hormones (estradiol and methyltestosterone) can change the direction of gonadal differentiation of P. sinensis to produce sex reversed individuals. However, the molecular mechanism remains unclear. In this study, TMT-based quantitative proteomics analysis of four types of P. sinensis (female, male, pseudo-female, and pseudo-male) gonads were compared. Quantitative analysis of 6107 labeled proteins in the four types of P. sinensis gonads was performed. We identified 440 downregulated and 423 upregulated proteins between pseudo-females and males, as well as 394 downregulated and 959 upregulated proteins between pseudo-males and females. In the two comparisons, the differentially expressed proteins, including K7FKG1, K7GIQ2, COL4A6, K7F2U2, and K7FF80, were enriched in some important pathways, such as focal adhesion, endocytosis, apoptosis, extracellular matrix-receptor interaction, and the regulation of actin cytoskeleton, which were upregulated in pseudo-female vs. male and downregulated in pseudo-male vs. female. In pathways such as ribosome and spliceosome, the levels of RPL28, SRSF3, SNRNP40, and HNRNPK were increased from male to pseudo-female, while they decreased from female to pseudo-male. All differentially expressed proteins after sexual reversal were divided into six clusters, according to their altered levels in the four types of P. sinensis, and associated with cellular processes, such as embryonic development and catabolic process, that were closely related to sexual reversal. These data will provide clues for the sexual reversal mechanism in P. sinensis.

TMT-based quantitative proteomics analysis and potential serum protein biomarkers for systemic lupus erythematosus

Systemic lupus erythematosus (SLE) was not only a typical systemic autoimmune disease, but also one of the most challenging heterogeneous diseases for physicians. Currently, the pathogenesis of SLE was unclear, and there were no accurate, universal or easy-to-use diagnostic criteria for assessing SLE activity and predicting SLE severity. Proteins were direct effectors of biological mechanisms, and were closer to clinical phenotypes than the other discovered biomarkers. Moreover, proteins were widely used as biomarkers for clinical diagnosis and mechanism research of many diseases. Herein, we compared the proteins profiles of healthy individuals (HCs) and SLE patients to reveal the pathogenesis and provide evidence for diagnosis and management of persons with SLE. Serum samples were collected from 28 SLE patients and 30 HCs. Tandem mass tag (TMT)-based quantitative proteomics method was used to identify, screen and detect differentially expressed proteins (DEPs) in the collected serum samples. A total of 744 proteins were identified, and 84 of them were considered as DEPs with 71 upregulated and 13 downregulated. Bioinformatics analysis suggested that these DEPs were mainly involved in many biological processes, including immune response, signal transduction, inflammatory response, proteolysis, innate immune response and apoptosis, which were closely related to the pathogenesis of SLE. After comprehensive analysis, serum amyloid A1 (SAA1) and endothelin (CD248) were identified as specific biomarkers for the diagnosis of SLE, and were confirmed by subsequent enzyme-linked immunosorbent assays (ELISA), indicating a high reliability of TMT-based quantitative proteomics results. Areas under the ROC curve (AUC) results confirmed that SAA1 and CD248 combination as early immune diagnosis biomarkers of SLE presented excellent sensitivity and specificity.

Proteomics Insights into the Gene Network of cis9, trans11-Conjugated Linoleic Acid Biosynthesis in Bovine Mammary Gland Epithelial Cells.

Simple SummaryCis9, trans11-conjugated linoleic acid (c9, t11-CLA) is a bioactive compound that is mainly found in ruminant products and has a variety of beneficial biological functions in human health. However, the gene network of c9, t11-CLA biosynthesis in the mammary gland is still not well documented. Therefore, this study aimed to elucidate the stearoyl-coenzyme A desaturase (SCD1)-dependent gene network of c9, t11-CLA biosynthesis in MAC-T cells from the perspective of energy metabolism. The results showed that the deficiency of stearoyl-coenzyme A desaturase (SCD1), led by CAY10566, blocked the biosynthesis of c9, t11-CLA. In total, 60 SCD1-related proteins that were mainly involved in energy metabolism pathways were primary screened by Tandem mass tag-based quantitative proteomics analysis. Moreover, 17 proteins were validated under the parallel reaction monitoring analysis. Then, 11 genes involved in energy metabolism pathways were verified to have negative relationships with SCD1 after small RNA interference analysis. Based on the above results, we concluded that the 11 genes involved in energy metabolism pathways had an impact on the SCD1-dependent molecular mechanism of c9, t11-CLA biosynthesis. This study provided a fresh understanding of the gene network of c9, t11-CLA biosynthesis in the mammary gland from a metabolism perspective.The objective of the study was to elucidate the stearoyl-coenzyme A desaturase (SCD1)-dependent gene network of c9, t11-CLA biosynthesis in MAC-T cells from an energy metabolism perspective. The cells were divided into the CAY group (firstly incubated with CAY10566, a chemical inhibitor of SCD1, then incubated with trans-11-octadecenoic acid, (TVA)), the TVA group (only TVA), and the control group (without CAY, TVA). The c9, t11-CLA, and TVA contents were determined by gas chromatography. The mRNA levels of SCD1 and candidate genes were analyzed via real-time PCR. Tandem mass tag (TMT)-based quantitative proteomics, bioinformatic analysis, parallel reaction monitoring (PRM), and small RNA interference were used to explore genes involved in the SCD1-dependent c9, t11-CLA biosynthesis. The results showed that the SCD1 deficiency led by CAY10566 blocked the biosynthesis of c9, t11-CLA. In total, 60 SCD1-related proteins mainly involved in energy metabolism pathways were primarily screened by TMT-based quantitative proteomics analysis. Moreover, 17 proteins were validated using PRM analysis. Then, 11 genes were verified to have negative relationships with SCD1 after the small RNA interference analysis. Based on the above results, we concluded that genes involved in energy metabolism pathways have an impact on the SCD1-dependent molecular mechanism of c9, t11-CLA biosynthesis.

Quantitative Proteomics Analysis Reveals Proteins Associated with High Melatonin Content in Barley Seeds under NaCl-Induced Salt Stress.

Soil salinization limits hull-less barley cultivation in the Qinghai-Tibet Plateau of China. However, some wild hull-less barley seeds accumulate high melatonin (MEL) during germination with improved salt tolerance; but the mechanism of melatonin-mediated salt tolerance in hull-less barley is not well understood at the protein level. This study investigated proteome changes resulting in high melatonin content in germinating hull-less barley seeds under high saline conditions. The proteome profiles of seed treatment with 240 mM-NaCl (N), water (H), and control (C) taken 7 days after germination were compared using the TMT-based quantitative proteomics. Our results indicate that salt stress-induced global changes in the proteomes of germinating hull-less barley seeds, altering the expression and abundance of proteins related to cell cycle and control, carbohydrate and energy metabolism, and amino acid transport and metabolism including proteins related to melatonin production. Furthermore, proteins associated with cellular redox homeostasis, osmotic stress response, and secondary metabolites derived primarily from amino acid metabolism, purine degradation, and shikimate pathways increased significantly in abundance and may contribute to the high melatonin content in seeds under salt stress. Consequently, triggering the robust response to oxidative stress occasioned by the NaCl-induced salt stress, improved seed germination and strong adaptation to salt stress.

Tandem mass tag-based proteomics analysis reveals the effects of Guri Gumu-13 pill on drug-induced liver injury

The incidence of drug-induced liver injury (DILI) is second only to viral hepatitis and steatohepatitis in China, and DILI has become a serious public health problem that cannot be ignored. Guri Gumu-13 pill (GRGM) is a traditional Chinese medicine (TCM), which has a protective effect on liver diseases. However, the underlying therapeutic mechanisms of GRGM for DILI are still vague. In this study, the protective effect of GRGM on acetaminophen (APAP)-induced DILI was investigated based on the proteomics clues. The effects of GRGM on APAP-induced DILI in rats were studied using tandem mass tag (TMT)-based quantitative proteomics technology. Besides, western blotting was exerted to verify related proteins. Using the TMT-based quantitative proteomics approach, 237 proteins were identified as regulated in APAP-induced DILI and 58 proteins were regulated by GRGM. The 17 overlapping differentially expressed proteins (DEPs) were identified, and 7 proteins were inversely regulated. Enrichment analysis of KEGG indicated that metabolic pathways, linoleic acid metabolism, and retinol metabolism might be affected in DILI. Next, Cyp2c11, Aldh1a1, and Fads2 were verified with molecular biotechnology. GRGM exerts therapeutic effects through multi-pathways regulation in the treatment of DILI. This work may provide proteomics clues for the continuation of research on DILI treatment with GRGM.

TMT-based quantitative proteomics reveals protein biomarkers from cultured Pacific abalone (Haliotis discus hannai) in different regions.

Due to latitude, the growth cycle of abalone in southern China is significantly lower than that in the northern regions. Therefore, it often occurs merchants use southern abalone to disguise as northern abalone. This study aims to explore the differences in the muscle proteome of Pacific abalone (Haliotis discus hannai) in different regions. A total of 1,569 proteins were detected and 729 proteins were identified as differential abundance proteins (DAPs) in Haliotis discus hannai cultured in Northern (Liaoning Province) and Southern (Fujian Province) China. Bioinformatics analysis revealed and Western blot verified that fatty acid synthase, troponin I, calpain small subunit 1, and myosin light chain 6 are candidate biomarkers for abalone cultured in different regions. This study provides a deeper understanding of how to distinguish which region abalone is harvested from to improve abalone quality controls, and prevent food fraud.

Proteomic changes induced by ascorbic acid treatment on porcine immature Sertoli cells

Somatic Sertoli cells constitute the microenvironment and produce essential substances, to support male germ cell development and maturation in testis. We previously found that ascorbic acid treatment of porcine immature Sertoli cells enhances its proliferation and secretion of reproductive hormones and metabolites, and reprograms the global transcriptome. Proteomics is a powerful tool to systematically profile the underlying protein changes. Here, by employing the TMT-based quantitative proteomics method, we identified 96 and 64 significantly up- and down-regulated proteins in porcine immature Sertoli cells treated by ascorbic acid, respectively. Gene enrichment (GO and KEGG) and protein-protein interaction analyses revealed important molecular pathways (dioxygenase activity, sterol biosynthetic process, PI3K-Akt, negative regulation of peptide hormone secretion, extracellular matrix etc.). Further validation of three proteins, HMGCS1 (cholesterol synthesis), P4HA1 (glycolysis) and KDM5A (demethylation of histone 3 at lysine 4), confirmed their significant differential abundance, respectively. Taken together, our findings show that ascorbic acid can alter multiple important protein molecules and related signaling pathways, which could explain partially phenotypic changes (proliferation, apoptosis, nucleic acid methylation, lactate and reproductive hormone secretion) of porcine immature Sertoli cells as induced by ascorbic acid.

Pancreatic INS-1 β-Cell Response to Thapsigargin and Rotenone: A Comparative Proteomics Analysis Uncovers Key Pathways of β-Cell Dysfunction.

Insulin-secreting β-cells in the pancreatic islets are exposed to various endogenous and exogenous stressing conditions, which may lead to β-cell dysfunction or apoptosis and ultimately to diabetes mellitus. However, the detailed molecular mechanisms underlying β-cell's inability to survive under severe stresses remain to be explored. This study used two common chemical stressors, thapsigargin and rotenone, to induce endoplasmic reticulum (ER) and mitochondria stress in a rat insuloma INS-1 832/13 β-cell line, mimicking the conditions experienced by dysfunctional β-cells. Proteomic changes of cells upon treatment with stressors at IC50 were profiled with TMT-based quantitative proteomics and further verified using label-free quantitive proteomics. The differentially expressed proteins under stress conditions were selected for in-depth bioinformatic analysis. Thapsigargin treatment specifically perturbed unfolded protein response (UPR) related pathways; in addition, 58 proteins not previously linked to the UPR related pathways were identified with consistent upregulation under stress induced by thapsigargin. Conversely, rotenone treatment resulted in significant proteome changes in key mitochondria regulatory pathways such as fatty acid β-oxidation, cellular respiration, citric acid cycle, and respiratory electron transport. Our data also demonstrated that both stressors increased reactive oxygen species production and depleted adenosine triphosphate synthesis, resulting in significant dysregulation of oxidative phosphorylation signaling pathways. These novel dysregulated proteins may suggest an alternative mechanism of action in β-cell dysfunction and provide potential targets for probing ER- and mitochondria stress-induced β-cell death.

Asporin Interacts With HER2 to Promote Thyroid Cancer Metastasis via the MAPK/EMT Signaling Pathway.

Approximately 85% of histological subtypes of thyroid cancer are papillary thyroid cancer (PTC), and the morbidity and mortality of PTC patients rapidly increased due to lymph node metastases or distant metastasis. Therefore, it needs to distill an enhanced understanding of the pathogenesis of PTC patients with lymph node metastases or distant metastasis. We employed the TMT-based quantitative proteomics approach to identify and analyze differentially expressed proteins in PTC with different degrees of lymph node metastases. Compared with paired normal tissues, asporin is overexpressed in PTC-N0, PTC-N1a, and PTC-N1b tumorous tissues via proteomics, western blotting, and immunohistochemistry assays. Functionally, asporin is mainly expressed in the extracellular matrix, cell membrane, and cytoplasm of PTC tumorous tissues, and promotes thyroid cancer cell proliferation, migration, and invasion. Mechanistically, asporin, interacting with HER2, co-localizes HER2 on the cell membrane and cytoplasm, and the asporin/HER2/SRC/EGFR axis upregulate the expression of EMT-activating transcription factors through the MAPK signaling pathway. Clinically, asporin can be regarded as a serological biomarker to identify PTC patients with or without lymph node metastasis, and high expression of asporin in PTC tumorous tissues is a risk factor for poor prognosis.

TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J

BackgroundCo-infection with the avian leukosis virus subgroup J (ALV-J) and the reticuloendotheliosis virus (REV) increases mutual viral replication, causing a more serious pathogenic effect by accelerating the progression of neoplasia and extending the tumor spectrum. However, the molecular mechanism underlying the synergistic replication of ALV-J and REV remains unclear.ResultsHere, we performed this study to compare the differentially expressed proteins among CEF cells infected with ALV-J, REV or both at the optimal synergistic infection time using TMT-based quantitative proteomics. We identified a total of 719 (292 upregulated and 427 downregulated) and 64 (35 upregulated and 29 downregulated) proteins by comparing co-infecting both viruses with monoinfecting ALV-J and REV, respectively. GO annotation and KEGG pathway analysis showed the differentially expressed proteins participated in virus-vector interaction, biological adhesion and immune response pathways in the synergistic actions of ALV-J and REV at the protein levels. Among the differentially expressed proteins, a large number of integrins were inhibited or increased in the co-infection group. Further, eight integrins, including ITGα1, ITGα3, ITGα5, ITGα6, ITGα8, ITGα9, ITGα11 and ITGβ3, were validated in CEF cells by qRT-PCR or western blot.ConclusionsThese findings proved that integrins may be key regulators in the mechanism of synergistic infection of REV and ALV-J, which will provide more insight into the pathogenesis of synergism of REV and ALV-J at protein level.

Integration Analysis of Transcriptome and Proteome Reveal the Mechanisms of Goat Wool Bending.

Zhongwei goat is a unique Chinese native goat breed for excellent lamb fur. The pattern of flower spikes of the lamb fur was significantly reduced due to the reduction of the bending of the hair strands with growth. In order to explore the molecular mechanism underlying hair bending with growth, we performed the comprehensive analysis of transcriptome and proteome of skins from 45-days, 108-days and 365-days goat based on TMT-based quantitative proteomics and RNA-seq methods. In the three comparison groups, 356, 592 and 282 differentially expressed proteins (DEPs) were screened, respectively. KEGG pathway analysis indicated that DEPs were significantly enriched in a set of signaling pathways related to wool growth and bending, such as ECM-receptor interaction, PI3K-Akt signaling pathway, PPAR signaling pathway, protein digestion and absorption, and metabolic pathways. In addition, 20 DEPs abundance of goat skin at three development stages were examined by PRM method, which validated the reliability of proteomic data. Among them, KRT and collagen alpha family may play an important role in the development of goat hair follicle and wool bending. COL6A1, COL6A2, CRNN, TNC and LOC102178129 were identified as candidate genes based on combined analysis of transcriptome and proteome data and PRM quantification. Our results identify the differential expressed proteins as well as pathways related to the wool bending of Zhongwei goats and provide a theoretical basis for further revealing the molecular mechanism underlying wool bending of goats.

Revealing therapeutic targets and mechanism of baicalin for anti-chronic gastritis using proteomic analysis of the gastric tissue

BackgroundBaicalin (BCL) is a natural compound associated with antioxidant, anti-inflammatory and immunomodulatory activities, among many others. To investigate the therapeutic effect of BCL treatment in ethanol-induced chronic gastritis, we investigated proteomic changes in the gastric tissue to elucidate the therapeutic targets of BCL in chronic gastritis using tandem mass tag (TMT)-based quantitative proteomics. MethodsSprague–Dawley (SD) rats received 8.7 ml/kg body weight of 56% ethanol intragastrically, which induced chronic gastritis model. Then, BCL (50 mg/kg) or omeprazole (20 mg/kg) was orally administered for 7 days to treat the induced chronic gastritis. After sacrifice, the total protein of the gastric antrum was determined. In addition, a tandem tag labelling for relative and absolute quantification (TMT)-based liquid chromatography with tandem mass spectrometry analysis was performed on the sample to identify differentially expressed proteins (DEPs) between therapy and model groups. Furthermore, the potential protein targets, signalling pathways and protein–protein interaction (PPI) network were analysed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, some potential targets were validated using Western blotting. ResultsA total of 4,452 proteins were identified and quantified in the gastric antrum tissue of SD rats using TMT-based quantitative proteomics. Of these, 107 DEPs, including 44 upregulated and 63 downregulated proteins, were discovered in the BCL-treated group compared with the untreated group with ethanol-induced gastritis, of these were 33 callback proteins. Biological information analysis demonstrated that the selected differential proteins were involved in the enriched pathways, including MAPK, PI3K-Akt and NF-κB. Furthermore, the expression of TPM2, GIMAP4, ICAM-1 and Mpc1 was validated using Western blotting, which was consistent with the proteomics results. The study results confirmed the reliability of the proteomic analysis. Additionally, BCL could decrease the production of interleukin (IL)-2, IL-8 and tumour necrosis factor-α while increasing the expression of epidermal growth factor and B-cell lymphoma-2. Notably, PPI network analysis revealed widespread interactions mediated by BCL. ConclusionsWe investigated the effects and potential mechanism of BCL in chronic gastritis. Proteomic technology was used to explore BCL-affected proteins and some signalling pathways. The results may provide important insights into discovering potential target proteins for treating chronic gastritis.

TMT-Based Quantitative Proteomics Analysis Reveals the Panoramic Pharmacological Molecular Mechanism of β-Elemonic Acid Inhibition of Colorectal Cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide but has limited available therapeutic methods; therefore, there is a need to develop highly efficient prevention and treatment strategies. Here, we investigated the anti-cancer activity of β-elemonic acid (EA) in CRC in vitro and in vivo. Our results showed that EA inhibited cell proliferation and migration in the CRC cell lines SW480 and HCT116. Moreover, EA significantly suppressed the growth of transplanted colorectal tumors in nude mice. Interestingly, high-throughput tandem mass tag (TMT)-based quantitative proteomics indicated that EA mainly targets tumor mitochondria and attenuates the translation of 54 mitochondrial ribosome proteins, many of which are discovered significantly upregulated in clinical CRC patients. More interestingly, EA at a low concentration (lower than 15 μg/ml) repressed the cell cycle by downregulating CDK1, CDK6, and CDC20, whereas at a high concentration (higher than 15 μg/ml), caused a non-apoptotic cell death—ferroptosis via downregulating ferritin (FTL) and upregulating transferrin (TF), ferroxidase (CP), and acyl-CoA synthetase long-chain family member 4 (ACSL4). This is the first report on the panoramic molecular mechanism of EA against CRC, which would make great contributions to developing a novel drug for colorectal cancer therapy.