TMT-based proteomics analysis reveals the efficacy of jiangzhuo formula in improving the lipid profiles of dyslipidemia rats

Integrative analysis of network pharmacology and proteomics reveal the protective effect of Xiaoqinglong Decotion on neutrophilic asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Xiaoqinglong Decotion (XQLD) is a commonly used Chinese herbal formula in clinical practice, especially for allergic diseases such as asthma. However, its intrinsic mechanism for the treatment of neutrophilic asthma (NA) remains unclear.

AIM OF THE STUDY

The aim of this study was to evaluate the efficacy and potential mechanisms of XQLD on NA using network pharmacology and in vivo experiments.

MATERIALS AND METHODS

First, the active compounds, potential targets and mechanisms of XQLD against NA were initially elucidated by network pharmacology. Then, OVA/CFA-induced NA mice were treated with XQLD to assess its efficacy. Proteins were then analyzed and quantified using a Tandem Mass Tags approach for differentially expressed proteins (DEPs) to further reveal the mechanisms of NA treatment by XQLD. Finally, the hub genes, critical DEPs and potential pathways were validated.

RESULTS

176 active compounds and 180 targets against NA were identified in XQLD. Protein-protein interaction (PPI) network revealed CXCL10, CX3CR1, TLR7, NCF1 and FABP4 as hub genes. In vivo experiments showed that XQLD attenuated inflammatory infiltrates, airway mucus secretion and remodeling in the lungs of NA mice. Moreover, XQLD significantly alleviated airway neutrophil inflammation in NA mice by decreasing the expression of IL-8, MPO and NE. XQLD also reduced the levels of CXCL10, CX3CR1, TLR7, NCF1 and FABP4, which are closely associated with neutrophil inflammation. Proteomics analysis identified 28 overlapping DEPs in the control, NA and XQLD groups, and we found that XQLD inhibited ferroptosis signal pathway (elevated GPX4 and decreased ASCL3) as well as the expression of ARG1, MMP12 and SPP1, while activating the Rap1 signaling pathway.

CONCLUSION

This study revealed that inhibition of ARG1, MMP12 and SPP1 expression as well as ferroptosis pathways, and activation of the Rap1 signaling pathway contribute to the therapeutic effect of XQLD on NA.

Sanghuangporus vaninii extract ameliorates hyperlipidemia in rats by mechanisms identified with transcriptome analysis

The increasing incidence of hyperlipidemia is a serious threat to public health. The development of effective and safe lipid-lowering drugs with few side effects is necessary. The purpose of this study was to assess the lipid-lowering activity of Sanghuangporus vaninii extract (SVE) in rat experiments and reveal the molecular mechanism by transcriptome analysis. Hyperlipidemia was induced in the animals using a high-fat diet for 4 weeks. At the end of the 4th week, hyperlipidemic rats were assigned into two control groups (model and positive simvastatin control) and three treatment groups that received SVE at 200, 400, or 800 mg kg-1 day-1 for another 4 weeks. A last control group comprised normal chow-fed rats. At the end of the 8th week, rats were sacrificed and lipid serum levels, histopathology, and liver transcriptome profiles were determined. SVE was demonstrated to relieve the lipid disorder and improve histopathological liver changes in a dose-dependent manner. The transcriptomic analysis identified changes in hepatocyte gene activity for major pathways including steroid biosynthesis, bile secretion, cholesterol metabolism, AMPK signaling, thyroid hormone signaling, and glucagon signaling. The changed expression of crucial genes in the different groups was confirmed by qPCR. Collectively, this study revealed that SVE could relieve hyperlipidemia in rats, the molecular mechanism might be to promote the metabolism of lipids and the excretion of cholesterol, inhibit the biosynthesis of cholesterol by activating the AMPK signaling pathway, the thyroid hormone signaling pathway, and the glucagon signaling pathway.

Label-free quantitative proteomics reveals the potential mechanisms of insoluble dietary fiber from okara in improving hepatic lipid metabolism of high-fat diet-induced mice

The high purity insoluble dietary fiber (IDF) from okara is a natural component with a potentially positive effect on a high-fat diet (HFD)-induced hepatic metabolic disorders, although its regulatory mechanism remains unclear. This study aims to elucidate the potential pathways and key proteins of IDF for the amelioration of hepatic lipid metabolism in mice fed with HFD. Here, we used label-free quantitative proteomics technology to quantity and identify differentially expressed proteins in the liver that are associated with IDF treatment. The differentially expressed proteins were assessed by GO annotation and KEGG pathways. Western blot and qRT-PCR analyses were conducted to validate the potential targets regulated by IDF. In total, 73 differentially expressed proteins were identified, of which 27 were up-regulated (FC > 1.5) and 46 were down-regulated (FC < 0.667). GO analysis suggested that differentially expressed proteins were mainly located in the cell and organelles, regulated biological processes, and were associated with enzyme activity and molecular binding. The KEGG pathway enrichment analysis further demonstrated glycolysis/gluconeogenesis, pyruvate metabolism, TCA cycle, arginine biosynthesis, alanine, aspartate and glutamate metabolism, and retinol metabolism were affected. The combination of proteomics, Western blot, and qRT-PCR suggested that ACS, ACLY, GOT1, GLS2, NAGS, CYP4A10, CYP3A25, and CYP2A5 in these pathways might be key proteins for IDF intervention. Taken together, our findings elucidate new mechanisms involved in how IDF affects hepatic metabolism, provide important information for the functional food industries, and improve the added value of okara. SIGNIFICANCE: Okara is evidenced as a high-quality by-product with several nutritional components, especially dietary fiber (50-60%) labeled as "The Seventh Nutrient". Previous studies have shown that IDF has a positive potential effect on a high-fat diet (HFD)-induced hepatic metabolic disorders, but its molecular mechanism remains unclear. To elucidate the therapeutic mechanism of IDF at the protein level, a label-free quantitative proteomic analysis was used to identify the dynamic changes of the liver proteome between HIDF and HFD groups in this study. These results provide a new perspective for exploring the therapeutic mechanism of IDF at the protein level and enlightenment for promoting the comprehensive utilization of okara.

Polystyrene microplastics aggravate acute pancreatitis in mice

Microplastics (MPs) with a diameter of < 5mm are emerging as a new type of environmental pollutants. With the discovery of MPs in human tissues, the health risks of MPs have attracted considerable attention in recent years. In this study, we aimed to investigate the impact of MPs on acute pancreatitis (AP). We exposed male mice to 100 and 1000μg/L polystyrene MPs for 28 days, then intraperitoneally injected mice with cerulein to develop acute pancreatitis (AP). The results demonstrated that MPs dose-dependently exacerbated pancreatic injuries and inflammation in AP. High-dose MPs significantly increased intestinal barrier disruption in AP mice, which may be partly responsible for the aggravation of AP. Moreover, through tandem mass tag (TMT)- based proteomics of pancreatic tissues, we screened 101 differentially expressed proteins (DEPs) between AP mice and high-dose MPs-treated AP mice. Gene Ontology and KEGG Pathway analysis revealed that the DEPs were mainly implicated in the molecular events including cytoskeleton organization, acute inflammatory response, arginine metabolism, etc. These mechanisms may also contribute to the aggravating AP effects of MPs. Collectively, our data provide new evidence for the harmful potential of MPs.

Anti-melanoma effect and action mechanism of a novel chitosan-based composite hydrogel containing hydroxyapatite nanoparticles

Hydroxyapatite nanoparticles (HANPs) have been increasingly regarded and reported due to their potential anti-tumor ability. Previously, we found that the rod-like HANPs had good application potential for cutaneous melanoma (CMM). To satisfy the actual requirements in repairing post-operative skin defects and inhibiting CMM recurrence after tumorectomy, we constructed a novel chitosan/alginate (CS/Alg) hydrogel containing the aforementioned HANPs. The in vitro cell experiments confirmed that activated mitochondrial-dependent apoptosis was tightly related to the anti-tumor ability of HANPs. Specifically, we further discovered several target proteins might be involved in abnormal activating Wnt, proteoglycans in cancer, oxidative phosphorylation and p53 signaling pathways. The in vivo animal experiments demonstrated that the HANPs-loaded CS/Alg hydrogel (CS/Alg/HANPs) had a similar effect on inhibiting tumor growth as HANPs, and CS/Alg hydrogel as well as phosphate buffered saline (PBS) group (control) not showed any effect, proving the key role of HANPs. The immunohistochemical staining demonstrated a tumor inhibition via the mitochondria-mediated apoptosis pathway, consistent with the in vitro evaluation. Moreover, CS/Alg/HANPs exhibited no additional biosafety risk to the functions of major organs. Overall, this CS/Alg/HANPs hydrogel has substantial application potential for treating CMM.

Tandem mass tag-based proteomic profiling revealed potential therapeutic targets and mechanisms of liraglutide for the treatment of impaired glucose tolerance

OBJECTIVE

Based on the tandem mass tag (TMT) technique, our study investigated the potential therapeutic targets of Liraglutide (LIRA) on streptozotocin (STZ) induced impaired glucose tolerance (IGT) in rats and discuss the biological mechanism of the drug against IGT.

METHODS

10 rats were randomly selected from 31 male wistar rats of specific pathogen free (SPF) grade as control group and fed with conventional chow, offered the remaining rats a high fat and high sugar (HFSD) diet combined with an intraperitoneal injection of STZ to establish the IGT model, and excluded 2 non-model rats. Specifically, the model rats were randomly divided into Model group (n=10) and LIRA group (n=9). In addition, the LIRA group was subcutaneously injected with 0.06 mg/kg LIRA, during which the metabolic parameters including body weight and fasting blood glucose were recorded. After 8 weeks, samples were taken under anesthesia. Then, the cell morphology was observed using HE staining, and immunofluorescence was performed on the pancreatic tissues of the three groups of rats. Besides, the expression of differential proteins in pancreatic tissues of the three groups of rats was determined by the TMT proteomic labeling. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological function analysis were performed on the intersection of Model and LIRA differential proteins.

RESULTS

LIRA could not only significantly reduce blood glucose levels but also improve islet cell morphology and function in IGT rats. Among the differential proteins between the model group and the blank group, 44 were reversed after LIRA treatment, of which 14 were up-regulated, while 30 were down-regulated, including PPIF, MPRIP, CYP51, TXNL1, BCL-2, etc. (FC>1.1 or<0.909, P<0.05). According to the GO and KEGG analysis results, it was related to biological processes such as fatty acid metabolism and adipocyte generation, which involved multiple signaling pathways regulating the function of islet cells, such as MAPK, PI, Ras, FcγR, and unsaturated fatty acids, and pyruvate metabolism.

CONCLUSION

To sum up, LIRA participated in anti-IGT therapy through regulation of multiple target proteins and biological functions. This study is of great reference for further exploring the mechanism of action of LIRA at the protein level of IGT.

A global and physical mechanism of gastric cancer formation and progression

Gastric cancer is regarded as a major health issue for human being nowadays. The Helicobacter pylori (H. pylori) infection has been found to accelerate the development of gastritis and gastric cancer. Significant efforts have been made towards the understanding of the biology of gastric cancer on both genetic and epigenetic levels. However the physical mechanism behind the gastric cancer formation is still elusive. In this study, we constructed a model for investigating gastric cancer formation by explored the gastric cancer landscape and the flow flux. We uncovered three stable state attractors on the landscape: normal, gastritis and gastric cancer. The definition of each attractor is based on the biological function and gene expression levels. The global stabilities and the switching processes were quantified through the barrier heights and dominant kinetic paths. To investigate the underlying mechanism of the process from normal through the gastritis to the gastric cancer caused by genetic or epigenetic factors, we simulate the oncogenesis of gastric cancer through changes of several gene regulation strengths and H. pylori infection. The simulated results can illustrate the developmental and metastasis process of gastric cancer. Different H. pylori infection degrees accelerating the process from gastritis to gastric cancer can be quantified. Then we applied global sensitivity analysis, one key gene and four key regulations were found. These results are consist with the experimental results and can be used to design the polygenic anti-cancer agents through multiple key genes or regulations. The landscape approach provides a physical and simple strategy for analyzing gastric cancer in a systematic and quantitative way. It also offers new insight into treatment strategy for gastric cancer by adjusting relevant polygenic genes and regulations.