Identification of neoantigens and immunological subtypes in clear cell renal cell carcinoma for mRNA vaccine development and patient selection.

Clear cell renal cell carcinoma (ccRCC) is a common urological malignancy with diverse histological types. This study aimed to detect neoantigens in ccRCC to develop mRNA vaccines and distinguish between ccRCC immunological subtypes for construction of an immune landscape to select patients suitable for vaccination. Using The Cancer Genome Atlas SpliceSeq database, The Cancer Genome Atlas, and the International Cancer Genome Consortium cohorts, we comprehensively analysed potential tumour antigens of ccRCC associated with aberrant alternative splicing, somatic mutation, nonsense-mediated mRNA decay factors, antigen-presenting cells, and overall survival. Immune subtypes (C1/C2) and nine immune gene modules of ccRCC were identified by consistency clustering and weighted correlation network analysis. The immune landscape as well as molecular and cellular characteristics of immunotypes were assessed. Rho-guanine nucleotide exchange factor 3 (ARHGEF3) was identified as a new ccRCC antigen for development of an mRNA vaccine. A higher tumour mutation burden, differential expression of immune checkpoints, and immunogenic cell death were observed in cases with the C2 immunotype. Cellular characteristics increased the complexity of the immune environment, and worse outcomes were observed in ccRCC cases with the C2 immunotype. We constructed the immune landscape for selecting patients with the C2 immunotype suitable for vaccination.

Combinational study with network pharmacology, molecular docking and preliminary experiments on exploring common mechanisms underlying the effects of weijing decoction on various pulmonary diseases.

Objective: 'Homotherapy for heteropathy' is a theory by which different diseases with similar pathogenesis can be treated with one Chinese formula. We aimed to explore the key components and core targets of Weijing decoction (WJD) in treating various lung diseases, namely, pneumonia, chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), pulmonary fibrosis, pulmonary tuberculosis and non-small cell lung cancer (NSCLC), via network pharmacology, molecular docking and some experiments. Significance: This is the first study on the mechanism of WJD in treating various lung diseases by 'homotherapy for heteropathy'. This study is helpful for the transformation of TCM formula and development of new drugs. Methods: Active components and therapeutic targets of WJD were obtained via TCMSP and UniProt databases. Targets of the six pulmonary diseases were harvested from the GeneCards TTD, DisGeNet, UniProt and OMIM databases. Drug-disease intersection targets, corresponding Venn diagrams, herb-component-target networks and protein-protein interaction networks were established. Furthermore, GO biological function and KEGG enrichment analysis were completed. Moreover, the binding activity between main compounds and core targets was measured through molecular docking. Finally, the xenograft NSCLC mouse model was established. Immune responses were evaluated by flow cytometry and mRNA expression levels of critical targets were measured by real-time PCR. Results: JUN, CASP3 and PTGS2 were the most critical targets in six pulmonary diseases. The active compounds beta-sitosterol, tricin and stigmasterol stably bound to many active sites on target proteins. WJD had extensive pharmacological regulation, involving pathways related to cancer, inflammation, infection, hypoxia, immunity and so on. Conclusions: Effects of WJD against various lung diseases involve lots of compounds, targets and pathways. These findings will facilitate further research as well as clinical application of WJD.

Akkermansia muciniphila ameliorates chronic kidney disease interstitial fibrosis via the gut-renal axis.

CONTEXT: Chronic kidney disease (CKD) affects approximately 10% of the global population. The abundance of Akkermansia muciniphila (AKK) is significantly reduced in CKD patients. OBJECTIVE: This study investigated the effects of AKK bacteria on kidney damage and the renal interstitium in rats with CKD. MATERIALS AND METHODS: CKD model 5/6 nephrectomy rats were used. CKD rats were supplemented with AKK (2 × 108 cfu/0.2 mL) for 8 weeks. RESULTS: AKK administration significantly suppressed epithelial-mesenchymal transition (EMT), and high-throughput 16S rRNA pyrosequencing showed that AKK supplementation restored the disordered intestinal microecology in CKD rats. AKK also enhanced the intestinal mucosal barrier function. AKK may regulate the intestinal microecology and reduce renal interstitial fibrosis by enhancing the abundance of probiotics and reducing damage to the intestinal mucosal barrier. CONCLUSION: The results suggest that AKK administration could be a novel therapeutic strategy for treating renal fibrosis and CKD.

Network Pharmacology-Based Exploration on the Intervention of Qinghao Biejia Decoction on the Inflammation-Carcinoma Transformation Process of Chronic Liver Disease via MAPK and PI3k/AKT Pathway.

Chronic liver disease(CLD) is a slow-developing and long-term disease that can cause serious damage to the liver. Thus far, it has been associated with viral hepatitis, non-alcoholic fatty liver disease(NAFLD), alcoholic liver disease(ALD), hepatic fibrosis(HF), liver cirrhosis (LC), and liver cancer. Qinghao Biejia Decoction (QBD) is a classic ancient Chinese herbal prescription with strong immune-enhancing, anti-inflammatory, and anti-tumor effects. In this study, we used a network pharmacology approach to investigate the molecular mechanisms of QBD in the inflammation-carcinoma transformation process of chronic liver disease. Two key drug targets, MAPK1 and PIK3CA, were screened using network pharmacology and molecular docking techniques, revealing dihydroartemisinin, artesunate, 12-O-Nicotinoylisolineolone, caffeic acid, and diincarvilone A as active ingredients involved in QBD mechanisms. The main signaling pathways involved were the PI3K-AKT signaling pathway and MAPK signaling pathway. In summary, our results indicated that QBD affects the inflammatory transformation of chronic liver disease through MAPK1 and PIK3CA and signaling pathways MAPK and PI3K/AKT. These data provide research direction for investigating the mechanisms underlying the inflammation-carcinoma transformation process in QBD for chronic liver disease.

Chemical profiling of Houttuynia cordata Thunb. by UPLC-Q-TOF-MS and analysis of its antioxidant activity in C2C12 cells.

Houttuynia cordata Thunb. ("Yu-Xing-Cao"), a traditional Chinese medicinal herb, has long been used to treat various diseases. However, detailed information regarding the chemical constituents of H. cordata aqueous extract is lacking, and the molecular basis of its beneficial effects on muscle is unknown. To investigate these points, in this study, we used ultra-performance liquid chromatography coupled with quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) in positive and negative ion modes to profile and identify the major constituents of H. cordata water extract. A total of 63 peaks were identified based on mass and fragmentation characteristics, including 29 organic acids and their glycosides, 17 flavonoids, 7 volatiles, 4 pyrimidine and purine derivatives, 2 alkaloids, 2 amino acids, 1 isovanillin, and 1 coumarin. The total flavonoid and polyphenol contents of the extract were 4.77 and 139.15 mg/mL, respectively, by ultraviolet spectrophotometry. The cytoprotective activity of H. cordata aqueous extract was evaluated using C2C12 cells treated with tumor necrosis factor (TNF)-α to induce oxidative challenge. The TNF-α induced decrease in cell viability was reversed by treatment for 48 h with the extract; moreover, superoxide dismutase activity was increased while reactive oxygen species level was decreased. These results provide molecular-level evidence for the antioxidant effect of H. cordata extract and highlight its therapeutic potential for the treatment of muscle injury or diseases caused by oxidative stress.

Camptothecin-based nanodrug delivery systems.

The drug camptothecin has a wide range of antitumor effects in cancers including gastric cancer, rectal and colon cancer, liver cancer, and lung cancer. Camptothecin-based drugs inhibit topoisomerase 1 (Topo 1), leading to destruction of DNA, and are currently being used as important chemotherapeutic agents in clinical antitumor treatment. However, the main obstacle associated with cancer therapy is represented by systemic toxicity of conventional anticancer drugs and their low accumulation at the tumor site. In addition, low bioavailability, poor water solubility, and other shortcomings hinder their anticancer activity. Different from traditional pharmaceutical preparations, nanotechnology-dependent nanopharmaceutical preparations have become one of the main strategies for different countries worldwide to overcome drug development problems. In this review, we summarized the current hotspots and discussed a variety of camptothecin-based nanodrugs for cancer therapy. We hope that through this review, more efficient drug delivery systems could be designed with potential applications in clinical cancer therapy.