Potential application of Nardostachyos Radix et Rhizoma-Rhubarb for the treatment of diabetic kidney disease based on network pharmacology and cell culture experimental verification.

BACKGROUND: Diabetic kidney disease (DKD) is one of the serious complications of diabetes mellitus, and the existing treatments cannot meet the needs of today's patients. Traditional Chinese medicine has been validated for its efficacy in DKD after many years of clinical application. However, the specific mechanism by which it works is still unclear. Elucidating the molecular mechanism of the Nardostachyos Radix et Rhizoma-rhubarb drug pair (NRDP) for the treatment of DKD will provide a new way of thinking for the research and development of new drugs. AIM: To investigate the mechanism of the NRDP in DKD by network pharmacology combined with molecular docking, and then verify the initial findings by in vitro experiments. METHODS: The Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to screen active ingredient targets of NRDP. Targets for DKD were obtained based on the Genecards, OMIM, and TTD databases. The VENNY 2.1 database was used to obtain DKD and NRDP intersection targets and their Venn diagram, and Cytoscape 3.9.0 was used to build a "drug-component-target-disease" network. The String database was used to construct protein interaction networks. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology analysis were performed based on the DAVID database. After selecting the targets and the active ingredients, Autodock software was used to perform molecular docking. In experimental validation using renal tubular epithelial cells (TCMK-1), we used the Cell Counting Kit-8 assay to detect the effect of NRDP on cell viability, with glucose solution used to mimic a hyperglycemic environment. Flow cytometry was used to detect the cell cycle progression and apoptosis. Western blot was used to detect the protein expression of STAT3, p-STAT3, BAX, BCL-2, Caspase9, and Caspase3. RESULTS: A total of 10 active ingredients and 85 targets with 111 disease-related signaling pathways were obtained for NRDP. Enrichment analysis of KEGG pathways was performed to determine advanced glycation end products (AGEs)-receptor for AGEs (RAGE) signaling as the core pathway. Molecular docking showed good binding between each active ingredient and its core targets. In vitro experiments showed that NRDP inhibited the viability of TCMK-1 cells, blocked cell cycle progression in the G0/G1 phase, and reduced apoptosis in a concentration-dependent manner. Based on the results of Western blot analysis, NRDP differentially downregulated p-STAT3, BAX, Caspase3, and Caspase9 protein levels (P < 0.01 or P < 0.05). In addition, BAX/BCL-2 and p-STAT3/STAT3 ratios were reduced, while BCL-2 and STAT3 protein expression was upregulated (P < 0.01). CONCLUSION: NRDP may upregulate BCL-2 and STAT3 protein expression, and downregulate BAX, Caspase3, and Caspase9 protein expression, thus activating the AGE-RAGE signaling pathway, inhibiting the vitality of TCMK-1 cells, reducing their apoptosis. and arresting them in the G0/G1 phase to protect them from damage by high glucose.

HDAC11 deficiency resists obesity by converting adipose-derived stem cells into brown adipocyte-like cells.

Obesity, with complications such as type 2 diabetes, dyslipidemia, and even cancer, is rampant worldwide. Histone deacetylases (HDACs) have been extensively studied as key players in the epigenetic regulation of cellular metabolism. However, the function of HDAC11 has long been focused on the immune and nervous systems and cancer development, and its potential role in obesity has been poorly studied. We found that the expression of HDAC11 was highly upregulated in the white adipose tissue (WAT) of obese mice and was closely related to the progression of obesity. Knockdown of HDAC11 by lentiviral injection in high-fat diet-fed mice attenuated the development of obesity. Furthermore, knockdown of HDAC11 ameliorated WAT hypertrophy and induced WAT browning. At the cellular level, silencing of HDAC11 promoted the differentiation of adipose-derived stem cells (ADSCs) into brown adipocyte-like cells and inhibited the proliferation of ADSCs. More interestingly, HDAC11 expression was elevated in ADSCs isolated from obese mice, and silencing of HDAC11 facilitated the spontaneous differentiation of ADSCs into mesoderm, which is the source of adipocytes. This also superficially and effectively demonstrates the exciting prospect of HDAC11 silencing in obesity research and treatment, as a valve for "energy saving and flow reduction".

Exploring the targets and molecular mechanism of glycyrrhetinic acid against diabetic nephropathy based on network pharmacology and molecular docking.

BACKGROUND: Diabetic nephropathy (DN) stands as the most prevalent chronic microvascular complication of diabetes mellitus. Approximately 50% of DN patients progress to end-stage renal disease, posing a substantial health burden. AIM: To employ network pharmacology and molecular docking methods to predict the mechanism by which glycyrrhetinic acid (GA) treats DN, subsequently validating these predictions through experimental means. METHODS: The study initially identified GA targets using Pharm Mapper and the TCMSP database. Targets relevant to DN were obtained from the Genecards, OMIM, and TTD databases. The Venny database facilitated the acquisition of intersecting targets between GA and DN. The String database was used to construct a protein interaction network, while DAVID database was used to conducted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis. Molecular docking experiments were performed using Autodock software with selected proteins. Experimental validation was conducted using renal proximal tubular cells (HK-2) as the study subjects. A hyperglycemic environment was simulated using glucose solution, and the effect of GA on cell viability was assessed through the cell counting kit-8 method. Flow cytometry was employed to detect cell cycle and apoptosis, and protein immunoblot (western blot) was used to measure the expression of proteins of the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway and insulin resistance pathway, including insulin receptor (INSR), PI3K, p-PI3K, AKT, p-AKT, and glycogen synthase kinase-3 (GSK3). RESULTS: A total of 186 intersecting targets between GA and DN were identified, which were associated with 144 KEGG-related enrichment pathways, 375 GO biological process entries, 45 GO cellular component entries, and 112 GO cellular function entries. Molecular docking demonstrated strong binding of GA to mitogen-activated protein kinase (MAPK)-1, SRC, PIK3R1, HSP90AA1, CASPASE9, HARS, KRAS, and MAPK14. In vitro experiments revealed that GA inhibited HK-2 cell viability, induced cell cycle arrest at the G2/M phase, and reduced apoptosis with increasing drug concentration. Western blot analysis showed that GA differentially up-regulated GSK3 protein expression, up-regulated AKT/p-AKT expression, down-regulated INSR, AKT, p-AKT, PI3K, and p-PI3K protein expression, and reduced p-PI3K/PI3K levels under high glucose conditions. CONCLUSION: GA may protect renal intrinsic cells by modulating the PI3K/AKT signaling pathway, thereby inhibiting HK-2 cell viability, reducing HK-2 cell apoptosis, and inducing cell cycle arrest at the G0/G1 phase.

Gut microbiota mediates the anti-obesity effect of intermittent fasting by inhibiting intestinal lipid absorption.

The prevention and treatment of obesity have been one of the most difficult problems in the world. Intermittent fasting (IF) has received wide attention as an effective diet strategy. Existing studies have shown that IF could improve obesity and diabetes-related metabolic disorders. Here, we show that IF can change the composition and metabolic function of intestinal microbes, and reduce lipid absorption by inhibiting PI3K/AKT signaling pathway, with the participation of arginine. Arginine concentration in feces of fasted mice is inversely correlated with Akkermansia muciniphila abundance. Antibiotic-induced clearance of intestinal microbiota greatly inhibits the effect of IF. Furthermore, the colonization test of Akkermansia muciniphila again activates the browning of white adipose tissue and restores the improvement of metabolism to alleviate obesity. These phenomena indicate that every-other-day fasting regimen inhibits intestinal lipid absorption and promotes the browning of white adipose tissue in mice to ameliorate the risk of obesity and metabolic disorders through the microbial flora-metabolite-fat signaling axis. And the above results demonstrate new directions for the treatment of obesity and other metabolic disorders.

Anti-tumor effect of coix seed based on the theory of medicinal and food homology.

Coix seed is a dry and mature seed of Coix lacryma-jobi L.var.ma-yuen (Roman.) Stapf in the Gramineae family. Coix seed has a sweet, light taste, and a cool nature. Coix seed enters the spleen, stomach, and lung meridians. It has the effects of promoting diuresis and dampness, strengthening the spleen to prevent diarrhea, removing arthralgia, expelling pus, and detoxifying and dispersing nodules. It is used for the treatment of edema, athlete's foot, poor urination, spleen deficiency and diarrhea, dampness and obstruction, lung carbuncle, intestinal carbuncle, verruca, and cancer. The medicinal and health value is high, and it has been included in the list of medicinal and food sources in China, which has a large development and application space. This article reviews the current research achievements in the processing methods and anti-tumor activities of Coix seed and provides examples of its clinical application in ancient and modern times, aiming to provide reference for further research on Coix seed and contribute to its clinical application and development. Through the analysis of the traditional Chinese patent medicines, and simple preparations and related health food of Coix seed queried by Yaozhi.com, the source, function, and dosage form of Coix seed were comprehensively analyzed, with a view of providing a reference for the development of Coix seed medicine and food.

Serum flavin mononucleotide but not riboflavin is inversely associated with the risk of colorectal cancer.

Vitamin B2 is essential for DNA methylation, stability and repair, which may influence the development and pathogenesis of several cancers. However, data regarding the associations of circulating vitamin B2 with colorectal cancer risk are limited. The purpose of this study was to investigate the associations between serum vitamin B2 and colorectal cancer risk, particularly among participants with different serum levels of vitamin B6 or folate. A hospital-based case-control study, including 1009 colorectal cancer cases and 1182 controls matched by age and sex, was conducted in Guangdong Province, China. Vitamin B2 including riboflavin and flavin mononucleotide (FMN), the vitamin B6 indicator pyridoxal-5'-phosphate (PLP) and folate in serum samples were measured by ultra-high-performance liquid chromatography-tandem mass spectrometry. Vitamin B2 sum was calculated as the sum of riboflavin plus FMN. A significant inverse association was observed between serum FMN, but not serum riboflavin or vitamin B2 sum, and colorectal cancer risk. The adjusted odds ratio (OR) and 95% confidence interval (95% CI) of serum FMN, by comparing the highest with the lowest quartile, was 0.63 (0.46-0.85, Ptrend = 0.001). Stratified analysis by serum PLP and folate levels indicated that serum FMN was inversely associated with colorectal cancer risk among participants with lower serum PLP or higher folate levels. This study added supporting data to the limited evidence that vitamin B2 could play a preventive role in colorectal carcinogenesis among the Chinese population, primarily by FMN. Individuals with a lower PLP level or an adequate folate level could be more sensitive to the protective role of vitamin B2.

Melatonin relieves hepatic lipid dysmetabolism caused by aging via modifying the secondary bile acid pattern of gut microbes.

It has been reported that aging-generated gut microecosystem may promote host hepatic lipid dysmetabolism through shaping the pattern of secondary bile acids (BAs). Then as an oral drug, melatonin (Mel)-mediated beneficial efforts on the communication between gut microbiota and aging host are still not clearly. Here, we show that aging significantly shapes the pattern of gut microbiota and BAs, whereas Mel treatment reverses these phenotypes (P < 0.05), which is identified to depend on the existence of gut microbiota. Mechanistically, aging-triggered high-level expression of ileac farnesoid X receptor (FXR) is significantly decreased through Mel-mediated inhibition on Campylobacter jejuni (C. jejuni)-induced deconjugation of tauroursodeoxycholic acid (TUDCA) and glycoursodeoxycholic acid (GUDCA) (P < 0.05). The aging-induced high-level of serum taurine chenodeoxycholic acid (TCDCA) activate trimethylamine-N-oxide (TMAO)-triggered activating transcriptional factor 4 (ATF4) signaling via hepatic FXR, which further regulates hepatic BAs metabolism, whereas TUDCA inhibits aging-triggered high-level of hepatic ATF4. Overall, Mel reduces C. jejuni-mediated deconjugation of TUDCA to inhibit aging-triggered high-level expression of hepatic FXR, which further decreases hepatic TMAO production, to relieve hepatic lipid dysmetabolism.

Association of Serum Pyridoxal-5'-Phosphate, Pyridoxal, and PAr with Colorectal Cancer Risk: A Large-Scale Case-Control Study.

Previous epidemiological studies have focused on the association of dietary vitamin B6 or circulating pyridoxal-5'-phosphate (PLP) with colorectal cancer risk. This study aimed to investigate the vitamin B6 in relation to colorectal cancer risk combining the biomarkers of PLP, pyridoxal (PL) plus PLP, and PAr (the ratio of 4-pyridoxic acid over the sum of PLP and PL). A large-scale hospital-based case-control study was conducted in Guangdong Province, China, which included 1233 colorectal cancer cases and 1245 sex and age frequency-matched controls. Serum PLP, PL, and 4-pyridoxic acid (PA) were detected with ultra-high-performance liquid chromatography−tandem mass spectrometry. Unconditional logistic regression models were used to assess the odds ratios (ORs) and 95% confidence intervals (95% CIs). Serum PLP and the sum of PLP and PL were inversely associated with colorectal cancer risk, while PAr was positively associated with colorectal cancer risk. Comparing the highest with the lowest quartile, the adjusted OR (95% CI) was 0.26 (0.20−0.33, Ptrend < 0.001) for serum PLP, 0.51 (0.40−0.66, Ptrend < 0.001) for serum PLP plus PL, and 2.90 (2.25−3.75, Ptrend < 0.001) for PAr. Serum PLP and PAr had significantly stronger associations with colorectal cancer risk in the male group and smoking group. Our results supported the protective role of vitamin B6 in colorectal cancer risk among Chinese people. The positive association of PAr with colorectal cancer risk suggested the potential role of inflammation and oxidative stress in colorectal carcinogenesis.

Transcriptome analysis reveals the effects of strigolactone on shoot regeneration of apple.

KEY MESSAGE: We have demonstrated that strigolactone inhibitor, Tis108, could be used to improve shoot regeneration of apple, and provided insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Lack of an efficient transformation system largely stagnated the application of transgenic and CRISPR technology in apple rootstock. High shoot regeneration ability is an important basis for establishing an effective transformation system. In this study, we first demonstrated the inhibitory effects of strigolactones on the adventitious shoot formation of apple rootstock M26. Next, we successfully verified that strigolactone-biosynthesis inhibitor, Tis108, could be used to improve the shoot regeneration of woody plants. Our results also suggest strigolactone-biosynthesis gene, MdCCD7, can be a target gene for biotechnological improvements of shoot regeneration capacity. Furthermore, we have employed transcriptome analysis to reveal the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Differentially expressed genes associated with photosynthesis, secondary growth, and organ development were identified. WGCNA suggests SLs might affect shoot regeneration through interaction with other hormones, especially, auxin, cytokinin, and ethylene. We were able to identify important candidate genes mediating the cross-talk between strigolactone and other hormones during the process of adventitious shoot formation. Overall, our findings not only propose a useful chemical for improving shoot regeneration in practice but also provide insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation.

PP1A prevents ROS-induced pyroptosis by inhibiting MAPK/caspase-3 in mouse adipose tissue.

Pyroptosis is a type of programmed cell death triggered by a variety of exogenous stimuli, playing important roles in the development of cells. Recent studies have shown that pyroptosis also occurs in human and mouse adipocytes. The serine/threonine protein phosphatase 1 catalytic subunit α (PP1A) is located in the nucleus and functions in the regulation of cell development, glucose metabolism and protein synthesis. PP1A can also target important proteins in the process of apoptosis. However, it is still unclear whether PP1A participates in the regulation of pyroptosis in mouse adipocytes. In the present study, we investigated the function of PP1A in reactive oxygen species-induced pyroptosis and the related mechanism in mouse adipose tissue. Our results demonstrated that PP1A suppressed pyroptosis in adipocytes by inhibiting the reactive oxygen species/mitogen-activated protein kinase/caspase-3 signaling pathway and promoting M2 macrophage polarization. This experiment provides a theoretical basis for understanding the regulatory function and mechanism of PP1A in pyroptosis caused by oxidative stress in adipocytes.

Identification of Immune-Related Genes Associated With Bladder Cancer Based on Immunological Characteristics and Their Correlation With the Prognosis.

BACKGROUND: To identify the immune-related genes of bladder cancer (BLCA) based on immunological characteristics and explore their correlation with the prognosis. METHODS: We downloaded the gene and clinical data of BLCA from the Cancer Genome Atlas (TCGA) as the training group, and obtained immune-related genes from the Immport database. We downloaded GSE31684 and GSE39281 from the Gene Expression Omnibus (GEO) as the external validation group. R (version 4.0.5) and Perl were used to analyze all data. RESULT: Univariate Cox regression analysis and Lasso regression analysis revealed that 9 prognosis-related immunity genes (PIMGs) of differentially expressed immune genes (DEIGs) were significantly associated with the survival of BLCA patients (p < 0.01), of which 5 genes, including NPR2, PDGFRA, VIM, RBP1, RBP1 and TNC, increased the risk of the prognosis, while the rest, including CD3D, GNLY, LCK, and ZAP70, decreased the risk of the prognosis. Then, we used these genes to establish a prognostic model. We drew receiver operator characteristic (ROC) curves in the training group, and estimated the area under the curve (AUC) of 1-, 3- and 5-year survival for this model, which were 0.688, 0.719, and 0.706, respectively. The accuracy of the prognostic model was verified by the calibration chart. Combining clinical factors, we established a nomogram. The ROC curve in the external validation group showed that the nomogram had a good predictive ability for the survival rate, with a high accuracy, and the AUC values of 1-, 3-, and 5-year survival were 0.744, 0.770, and 0.782, respectively. The calibration chart indicated that the nomogram performed similarly with the ideal model. CONCLUSION: We had identified nine genes, including PDGFRA, VIM, RBP1, RBP1, TNC, CD3D, GNLY, LCK, and ZAP70, which played important roles in the occurrence and development of BLCA. The prognostic model based on these genes had good accuracy in predicting the OS of patients and might be promising candidates of therapeutic targets. This study may provide a new insight for the diagnosis, treatment and prognosis of BLCA from the perspective of immunology. However, further experimental studies are necessary to reveal the underlying mechanisms by which these genes mediate the progression of BLCA.

Photochemical mechanism of 1,5-benzodiazepin-2-one: electronic structure calculations and nonadiabatic surface-hopping dynamics simulations.

Due to the significant applications in bioimaging, sensing, optoelectronics etc., photoluminescent materials have attracted more and more attention in recent years. 1,5-Benzodiazepin-2-one and its derivatives have been used as fluorogenic probes for the detection of biothiols. However, their photochemical and photophysical properties have remained ambiguous until now. In this work, we have adopted combined static electronic structure calculations and nonadiabatic surface-hopping dynamics simulations to study the photochemical mechanism of 1,5-benzodiazepin-2-one. Firstly, we optimized minima and conical intersections in S0 and S1 states; then, we proposed three nonadiabatic decay pathways that efficiently populate the ground state from the Franck-Condon region based on computed electronic structure information and dynamics simulations. In the first pathway, upon photoexcitation to the S1 state, the system proceeds with an ultrafast excited-state intramolecular proton transfer (ESIPT) process. Then, the molecule tends to rotate around the C-C bond until it encounters keto conical intersections, from which the system can easily decay to the ground state. The other two pathways involve the enol channels in which the S1 system hops to the ground state via two enol S1/S0 conical intersections, respectively. These three energetically allowed S1 excited-state deactivation pathways are responsible for the decrease of fluorescence quantum yield. The present work will provide detailed mechanistic information of similar systems.

Electronic structure calculations and nonadiabatic dynamics simulations of excited-state relaxation of Pigment Yellow 101.

Pigment Yellow 101 (PY101) is widely used as a typical pigment due to its excellent excited-state properties. However, the origin of its photostability is still elusive. In this work, we have systematically investigated the photodynamics of PY101 by performing combined electronic structure calculations and trajectory-based nonadiabatic dynamics simulations. On the basis of the results, we have found that upon photoexcitation to the S1 state, PY101 undergoes an essentially barrierless excited-state intramolecular single proton transfer generating an S1 keto species. In the keto region, there is an energetically accessible S1/S0 conical intersection that funnels the system to the S0 state quickly. In the S0 state, the keto species either goes back to its trans-enol species through a ground-state reverse hydrogen transfer or arrives at the cis-keto region. In addition, we have found an additional excited-state decay channel for the S1 enol species, which is directly linked to an S1/S0 conical intersection located in the enol region. This mechanism has also been confirmed by our dynamics simulations, in which about 54% of the trajectories decay to the S0 state via the enol S1/S0 conical intersection; while the remaining ones employ the keto S1/S0 conical intersection. The gained mechanistic information helps us understand the photostability of the PY101 chromophore and its variants with the same molecular scaffold.

Aberrations in circulating inflammatory cytokine levels in patients with Down syndrome: a meta-analysis.

Evidence suggests that immune system alterations in Down syndrome (DS) may be early events that drive neuropathological and cognitive changes of Alzheimer's disease. The primary objective of this meta-analysis was to investigate whether there is an abnormal cytokine profile in DS patients when compared with healthy control (HC) subjects. A systematic search of Pubmed and Web of Science identified 19 studies with 957 DS patients and 541 HC subjects for this meta-analysis. Random effects meta-analysis demonstrated that patients with DS had significantly increased circulating tumor necrosis factor-α (Hedges' g = 1.045, 95% confidence interval (CI) = 0.192 to 1.898, p = 0.016), interleukin (IL)-1ß (Hedges' g = 0.696, 95% confidence CI = 0.149 to 1.242, p = 0.013), interferon-γ (Hedges' g = 0.978, 95% CI = 0.417 to 1.539, p = 0.001) and neopterin (Hedges' g = 0.815, 95% CI = 0.423 to 1.207, p < 0.001) levels compared to HC subjects. No significant differences were found between patients with DS and controls for concentrations of IL-4, IL-6, IL8 and IL-10. In addition, most of the cytokine data in this meta-analysis were from children with DS and HC, and subgroup analysis showed that children with DS had elevated tumor necrosis factor-α, IL-1ß and interferon-γ levels when compared with controls. Taken together, these results demonstrated that patients (children) with DS are accompanied by increased circulating cytokine tumor necrosis factor-α, IL-1ß and interferon-γ levels, strengthening the clinical evidence that patients (children) with DS are accompanied by an abnormal inflammatory response.