Primary Bile Acid Biosynthesis Research Articles

Based on Serum Pharmacochemistry and Metabolomics Studied the Pharmacodynamic Material Basis and Mechanism of Rubi Fructus (Fupenzi) in Improving the Symptom of Kidney-Yang Deficiency.

Rubi fructus (Fupenzi) is the immature fruit of East China Rubi fructus, which is widely used in medicine, food, health food and other fields. Since ancient times, Fupenzi has been considered to be an important medicine for tonifying the kidney in terms of nourishing the liver and kidney, fixing essence and reducing urine, but its effective components and mechanism are not clear. In this paper, the effective components of Rubi fructus were analyzed by detecting the components of Fupenzi in vivo and in vitro. Adenine was used to replicate the model of kidney yang deficiency, and organ index, biochemical index and histopathology were used to evaluate the effect of different doses of Fupenzi on tonifying kidney yang. Metabonomics technique was used to analyze the metabolic regulation mechanism of Fupenzi in improving kidney yang deficiency syndrome. The results showed that 61 chemical constituents of Fupenzi were identified in vitro, including 18 flavonoids, 19 organic acids, 5 coumarins, 8 terpenoids, 7 amino acids and 4 other components. A total of 51 chemical components were identified, including 30 prototype components and 21 metabolic components, which may be the effective components of Fupenzi. The results of pharmacodynamics showed that compared with the model group, the renal index, testicular index and epididymal index of rats in each Fupenzi group were significantly improved (p<0.01), cAMP significantly increased (p<0.05), cGMP decreased (p<0.05) and cAMP/cGMP ratio increased significantly (p<0.05). The content of ACTH in low dose group increased significantly (p<0.05), while the content of ACTH in middle and high dose groups increased, but there was no significant difference. The results of HE staining showed that compared with the model group, the kidney, testis and epididymis of rats in each treatment group were significantly improved. In general, these changes may be mainly through primary bile acid biosynthesis, linoleic acid metabolism, steroid hormone biosynthesis, β-alanine metabolism, glutathione metabolism, porphyrin and chlorophyll metabolism, unsaturated fatty acid biosynthesis, arachidonic acid metabolism, arginine and proline metabolism and other metabolic pathways to improve adenine-induced metabolic disorders in rats with kidney-yang deficiency syndrome.

Antioxidative and Cytoprotective Effects of Rosa Roxburghii and Metabolite Changes in Oxidative Stress-Induced HepG2 Cells Following Rosa Roxburghii Intervention.

Rosa Roxburghii (RR), a traditional Chinese medicinal fruit, is rich in bioactive substances that make it a potential natural antioxidant resource. This research aimed to study the antioxidant properties of RR by in vitro experiments and through intracellular assessment in H2O2-induced HepG2 cells. A non-targeted metabolic analysis was conducted to indicate changes in intracellular and extracellular metabolites. Differential metabolites and metabolic pathways were explored using PCA, PLS-DA, and KEGG pathway analysis. The results showed that RR rich in bioactive substances exhibited a significant antioxidative property in vitro and intracellularly. This property may be achieved by scavenging free radicals, increasing the activity of catalase (CAT), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and the levels of bicinchoninic acid (BCA) while reducing the reactive oxygen species (ROS) generation. This study identified 13 differential metabolites intracellularly and 7 extracellularly, among which the key differential metabolites included D-glucopyranose, D-mannose, fructose, citric acid, malic acid, cholesterol, and cholestenone. These key metabolites primarily regulated glucose-related metabolism, the citrate cycle, and the primary bile acid biosynthesis pathway in H2O2-induced HepG2 cells. These findings provide potential application evidence of RR in the development of natural resources for functional foods.

Macrophage MST4 exacerbates cardiac microvascular ischaemia/reperfusion injury by phosphorylating ACLY

Abstract Background Cardiac microvascular dysfunction is a contributing factor in the development of cardiac ischaemia/reperfusion (I/R) injury. The STE20-type kinases play important role in cardiovascular diseases. However, the impact of mammalian Ste20-like kinase 4 (MST4) on cardiac microvascular I/R injury remains unknown. Purpose To decipher the role of MST4 in cardiac microvascular I/R injury and the underlying mechanisms. Methods Single-cell RNA sequencing of I/R mouse heart was performed to explore the expression changes of MST4 in different cell types. MST4 flox (MST4 f/Y) mice was crossed with myeloid-specific LysM-Cre mice to generate myeloid-specific MST4 knockout mice (MST4 CKO). Bone marrow transplantation was used to testify the role of myeloid-derived MST4 in cardiac microvascular I/R injury. Bone-marrow-derived macrophage (BMDM) and cardiac microvascular endothelial cell (CMEC) were used to dissect molecular mechanisms. Adeno-associated virus and adenovirus were constructed to overexpress ATP Citrate Lyase (ACLY) with mutation of serine 455 (S455A) in vivo and in vitro, respectively. Phosphoproteomics, coimmunoprecipitation coupled with liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis and metabolomics were performed to decipher the downstream of MST4. Results MST4 is dominantly upregulated in CCR2+ monocyte-derived macrophages. Myeloid-specific deficiency of MST4 improves cardiac performance in I/R mouse model. Wild type (WT) mice transplanted with BMDM from MST4 CKO mice also exhibited improved cardiac function after I/R, however, MST4 CKO mice transplanted with BMDM from WT mice showed deteriorated cardiac performance. Metabolomics showed that primary bile acid biosynthesis pathway was upregulated in BMDM overexpressing MST4. The level of 7α-hydroxyl3-oxo-4-cholestenoic acid (7-HOCA), an intermediate of bile acid, was dramatically increased in I/R mice or BMDM overexpressing MST4, which can be reversed by knocking down MST4. Phosphoproteomics and LC-MS/MS analysis discovered that ACLY was one of the most important substrates of MST4 in the process of I/R injury. ACLY was directly phosphorylated by MST4 at serine 455, which increased ACLY enzyme activity. Mechanistically, ACLY promoted cholesterol catabolism through the bile acid synthesis pathway, leading to the accumulation of 7-HOCA in the macrophage-endothelial cell microenvironment. High level of 7-HOCA was able to promote endothelial cell mtDNA release, leading to endothelial cell pyroptosis through inflammasome pathway. However, mutation of serine 455 of ACLY blocked the role of MST4. Conclusions Our data defined a previously unrecognized role of MST4/ACLY pathway in cardiac microvascular I/R injury. MST4 led to the accumulation of 7-HOCA by phosphorylating ACLY, furthermore, 7-HOCA promoted endothelial cell injury. Targeting MST4/ACLY pathway ameliorated microvascular I/R injury, which may provide a novel therapeutic strategy for I/R injury.

High-concentrate diet decreases lamb fatty acid contents by regulating bile acid composition

Feeding sheep with high-concentrate diet (HCD) to shorten production cycle is a well-developed feeding strategy to increase lamb production. Here, metabolomics were performed to explore the mechanism that HCD changes lamb nutrition composition. Differential metabolites were enriched in primary bile acid biosynthesis. Significantly higher content of bile acids including taurodeoxycholic acid sodium salt (TDCA), taurochenodeoxycholic acid sodium salt (TCDCA) and taurocholic acid (TCA) was observed in lamb of HCD, while the content of lithocholic acid (LCA), cholic acid (CA), chenodeoxycholic acid (CDCA) and Chenodeoxycholic acid-3-beta-D-glucuronide (CDCA-3Gln) were higher in the controls. Furthermore, a significantly decreased content of fatty acids was observed in lamb of HCD group. Finally, primary skeletal cells treated with CA or TCA showed a significant decrease in contents of fatty acids, while TCA showed a stronger effect in decreasing fatty acid contents. Collectively, we suggest that HCD decreases lamb fatty acid contents by regulating bile acid composition.

Effects of complex probiotics on intestinal function and its regulatory mechanism in patients with constipation.

Chronic constipation is a multi-symptomatic, multifactorial, and heterogeneous gastrointestinal disorder. Current pharmacological treatments for chronic constipation are limited and might negatively impact the patients' quality of life. Although probiotics have been shown to improve constipation symptoms, their specific regulatory mechanisms remain unclear. This study sought to explore how probiotic complexes may affect chronic constipation by improving patients' defecation habits. Furthermore, microbial profiles and non-targeted metabolites were assessed to explore the metabolic pathways involved in the improvement of constipation by probiotics. Patients with chronic constipation were treated using a single-blind, randomised, placebo-controlled trial design. The experimental group was administered Lactobacillus powder prepared from 15 probiotic products, and maltodextrin was used as a placebo. Samples were collected twice daily for 4 weeks, and faecal samples were analysed using 16S rRNA sequencing and untargeted metabolic histology. Probiotic treatment changed the makeup of the gut microbiota, enhanced the quantity of Bifidobacterium and Lactobacillus, and markedly reduced clinical symptoms. The 16S rRNA analysis revealed that the abundance of Bifidobacterium and Prevotella increased while that of Thickettsia declined. Moreover, there was a decrease in the abundance of Faecalibacterium and Roseburia. Non-targeted metabolomics analysis identified several differential metabolites, including succinic acid, fumaric acid, cholesterol, xanthurenic acid, 3-alpha,7-alpha-trihydroxy-5beta-cholestan-26-oic, and N-methyltryptamine. KEGG analysis showed that these metabolites were mainly associated with metabolic pathways such as primary bile acid biosynthesis, tryptophan metabolism, alanine, aspartate and glutamate metabolism, phenylalanine metabolism, cholesterol metabolism, and propanoate metabolism. In this study, gut microbiome and non-targeted metabolome analyses were performed on collected faecal samples to compare characteristic microorganisms and differential metabolites to provide new insights and references for probiotic intervention in constipation. Trial registered at chictr.org.cn under number: ChiCTR2200056274.

Explore the mechanism of yishenjiangya formula in the treatment of senile hypertension based on multi-omics technology

Ethnopharmacological relevanceThe Yishenjiangya formula (YSJ) is a traditional Chinese medicine (TCM) primarily composed of qi-tonifying components. This classic formula is commonly utilized to treat kidney qi deficiency in elderly patients with hypertension. According to TCM, maintaining a balance between qi and blood is crucial for stable blood pressure. Kidney qi deficiency can disrupt this balance, altering fluid shear force and, ultimately, leading to hypertension, particularly in elderly populations. Despite YSJ's efficacy in treating hypertension, its specific anti-hypertensive mechanisms remain unclear. Aim of the studyYSJ is commonly prescribed for elderly patients with hypertension. Earlier metabolomics studies demonstrated that YSJ exerts antihypertensive effects by influencing four key pathways: linoleic acid metabolism, glycerol phospholipid metabolism, arginine and proline metabolism, and steroid hormone biosynthesis. This study aims to combine metabolomic and proteomic analyses to thoroughly understand the molecular biological mechanisms responsible for YSJ's anti-hypertensive properties. MethodsUltra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) metabolomics, combined with Label-Free Quantitation (LFQ) proteomics, was employed to analyze serum samples from elderly individuals with and without hypertension pre- and post-YSJ intervention. Serum levels of candidate proteins were assessed using enzyme-linked immunosorbent assay, and receiver operating characteristic curves were used to evaluate the diagnostic performance of the target proteins. ResultsEight differentially expressed metabolites and three differentially expressed proteins were identified as potential therapeutic targets of YSJ. These substances are primarily involved in unsaturated fatty acid metabolism, fluid shear stress and atherosclerosis pathway, primary bile acid biosynthesis, proline metabolism, apoptosis, and endoplasmic reticulum stress. YSJ exerts its therapeutic effects on hypertension in the elderly by modulating these pathways. ConclusionsYSJ effectively treats senile hypertension. By analyzing the correlation between therapeutic targets and pathways, YSJ's anti-hypertensive effect was achieved by inhibiting lipid peroxidation and matrix degeneration. Combining metabolomics and proteomics provides an effective method for uncovering YSJ's anti-hypertensive mechanisms.

Safflower dietary fiber alleviates functional constipation in rats via regulating gut microbiota and metabolism

A functional constipation rat model was established by loperamide hydrochloride (LOP), and then safflower dietary fiber (SDF) was supplemented to constipated rats. The results revealed that SDF increased the serum levels of excitatory gastrointestinal active peptides such as motilin (MTL), gastrin (GAS), and substance P (SP), while concurrently decreasing the levels of inhibitory peptides like somatostatin (SS) and vasoactive intestinal peptide (VIP). SDF restored the ratio of Firmicutes/Bacteriodetes (F/B), upregulated the relative abundance of Lactobacillus and Clostridium, and downregulated the relative abundance of Oscillopira, Ruminococcus, Coprococcus, and Akkermansia; analysis of metabolites revealed that the levels of bile acid, deoxycholic acid, chenodeoxycholic acid, and taurocholic acid were notably elevated after SDF treatment, while the levels of indole-3-lactic acid, putrescine, and L-arginine were significantly decreased. Pathway enrichment analysis found that SDF regulates Taurine and hypotaurine metabolism, Primary bile acid biosynthesis, and Bile secretion. Correlation analysis between gut microbiota and metabolites revealed that Fusibacter and Actinomyces may contribute to alleviating constipation by regulating the level of bile acid in the intestine. SDF intervention increased the mRNA expressions of FABP1 and SLC1A5 in constipated rats. Furthermore, SDF exhibited notable abilities in retaining water and undergoing swelling. The above results showed that SDF helped the intestine lock water and promoted intestinal peristalsis by increasing friction. On the other hand, SDF supplementation increased the relative abundance of Lactobacillus and Clostridium, decreased the relative abundance of Oscillopira, increased the levels of various bile acids such as deoxycholic acid and chenodeoxycholic acid, further regulated intestinal lipid metabolism, up-regulated FABP1 mRNA expression, promoted intestinal cell proliferation, restored intestinal homeostasis, and thus alleviated constipation.

Integrating metabolomics with network pharmacology to reveal the mechanism of Poria cocos in hyperuricemia treatment

Ethnopharmacological relevanceHyperuricemia is a chronic condition characterized by persistently elevated uric acid levels, often leading to gouty arthritis and renal insufficiency. Poria cocos F.A.Wolf, a traditional Chinese medicinal herb, possesses notable diuretic and anti-inflammatory properties and is widely used to treat edema, inflammation, viral infections, and tumors. Recent studies suggest that Poria cocos has the potential to lower uric acid levels and mitigate kidney damage, making it a promising candidate for hyperuricemia treatment. However, its pharmacological mechanisms require further exploration. Aim of the studyThis study aims to elucidate the mechanisms by which Poria cocos alleviates hyperuricemia, using metabolomics and network pharmacology approaches. Materials and methodsHyperuricemia was induced in rats via a high-yeast diet combined with potassium oxonate. The effects of Poria cocos were assessed by measuring serum uric acid, creatinine, urea nitrogen levels, hepatic xanthine oxidase activity, and renal tissue morphology. Non-targeted metabolomics was employed to identify differential metabolites and explore the metabolic pathways involved in its therapeutic effects. Network pharmacology was utilized to analyze potential targets and signaling pathways, which were validated through molecular docking and ELISA analysis. ResultsPoria cocos extract significantly reduced serum uric acid, creatinine, and urea nitrogen levels, inhibited xanthine oxidase activity, and attenuated kidney damage. Metabolomics combined with network pharmacology identified xanthine dehydrogenase and fatty acid synthase as key targets, while purine metabolism, fatty acid biosynthesis, and primary bile acid biosynthesis were identified as critical pathways. ELISA confirmed that Poria cocos suppressed xanthine dehydrogenase and fatty acid synthase expression in hyperuricemic rats. Molecular docking further verified strong binding interactions between core compounds and key targets. ConclusionsPoria cocos alleviates hyperuricemia by modulating multiple compounds, targets, and pathways. Through network pharmacology and metabolomics, it reveals that Poria cocos selectively regulates xanthine dehydrogenase and fatty acid synthase, influencing purine metabolism, fatty acid biosynthesis, and primary bile acid biosynthesis pathways. These findings provide insights into its therapeutic mechanisms, supporting the clinical application of Poria cocos in treating metabolic disorders and kidney damage associated with hyperuricemia.

PSV-2 Rumen fluid metabolomics of dairy cows fed combinations of essential oil blend, onion peel extract and prebiotics using the RUSITEC system

Abstract Dairy products have a crucial role in the diets of over 6 billion people worldwide, providing essential nutrients such as energy, high-quality protein, and micronutrients. With dairy cows accounting for nearly 81% of global milk production, strategies to increase milk production sustainably are vital, especially with the U.S. being the second-largest producer. Essential oil blends (EOB), onion peel extract (OPE), and prebiotics such as mannan oligosaccharides (MOS) and galacto-oligosaccharides (GOS) offer promising avenues to enhance bovine milk production. These additives have the potential to modify rumen ecology and fermentation activity, while also mitigating greenhouse gas emissions in dairy cows. Therefore, this study investigated the effects of combining EOB, OPE, GOS, and/or MOS on specific rumen metabolites and metabolic pathways using the rumen simulation technique (RUSITEC) system. Rumen-cannulated non-lactating Holstein Friesian cows (n = 3) were used as rumen fluid donors. Total mixed ration (TMR) consisted of corn silage (60%), alfalfa hay (20%), and concentrate (20%). Using a completely randomized design, 16 fermentation vessels were divided into 4 groups with 4 replicates each over a 9-d period. The treatments included a control group (CON; TMR only), GEO (TMR+GOS+EOB+OPE), MEO (TMR+MOS+EOB+OPE), and OLEO (TMR+OLG+EOB+OPE). The EOB comprised of garlic, lemongrass, cumin, lavender, and nutmeg (4:2:2:1:1), while OLG contained GOS and MOS in equal proportions. EOB was added at 10 µL/g, and OPE, GOS, MOS, and OLG were included at 30 mg/g TMR. Rumen effluents were collected over 5 d for quantitative untargeted metabolome analysis. Analysis of rumen effluents using liquid chromatography-mass spectrometry and MetaboAnalyst 5.0 revealed 495 detected and identified metabolites. Volcano plot analysis showed no significant differences (P ≥ 0.05) in metabolite abundance between the CON and MEO, GEO, or OLEO treatments. Partial least squares-discriminant analysis (PLS-DA) also indicated no clear separation between the CON and treatment groups, suggesting no significant alteration in the metabolome. Compared with CON, the relative concentrations of dopamine 4-O-glucuronide, proline, and histamine were less while pyrocatechol was greater in MEO group. Isomer 1 of 2-hydroxyhepta-2,4-dienedioic acid, histamine, and dopamine 4-O-glucuronide were less while 2-aminomuconic acid and isomer 1 of hulupinic acid were greater in the GEO group. Histamine was less and hydroxypyridine was greater in the OLEO group. Phosphonate and phosphinate metabolism tended to be upregulated in OLEO. Meanwhile, metabolic pathways related to amino acids, vitamins, nitrogen metabolism, and primary bile acid biosynthesis remained unaltered by MEO, GEO and OLEO treatments. In summary, the study demonstrated that the inclusion of MEO, GEO, and OLEO had no adverse effects on rumen metabolites. Future research should focus on combinations of nutraceuticals that could positively impact nutrient metabolism and production performance of dairy cows.

40 The gut microbiota modifies host-parasite interactions

Abstract It is well documented that parasitic infections induce a profound change in the structure and function of host gut microbiota, likely due to infection-associated perturbations in the gut microenvironment. However, the mechanisms remain largely unknown. Here we aim to understand how the gut microbiota is modified by host-parasite relationships or vice versa using an integrated multi-omics analysis in a swine-Ascaris infection model. Female pigs (n = 30; 6 to 8 mo of age) were randomly divided into three groups (n = 10 per group). One group served as normal uninfected controls (NU); the remaining 20 pigs were inoculated per os with ~10,000 infective A. suum eggs; and the infection was allowed to progress for 35 d post-inoculation (dpi). At 21 dpi, one of the infected groups (IP) was treated with a single daily dose of an anthelmintic drug, Panacur, for three consecutive days while the other infected pigs remained untreated (IU). At necropsy, intestine tissue, serum and fecal samples were collected for untargeted metabolome analysis using UPLC-MS/MS and the fecal microbiota was characterized using full-length 16S rRNA gene-based sequencing with DADA2. Fecal and serum metabolites were categorized for their origin using MetOrigin. An integrated multi-omics analysis was performed using DIABLO algorithms and NetCoMi networking tools. Our results showed that A. suum worms were well developed in pigs from the IU group, which harbored a significantly reduced microbiota alpha diversity (Simpson, P &amp;lt; 0.005) compared with NU. The infection altered the abundance of at least 17 bacterial species/strains, including multiple butyrate-producing Clostridium spp., such as C. butyricum. The infection also dysregulated 51 fecal metabolites, including microbiota-derived metabolites such as glutaric acid and p-Cresol sulfate, and succinate of mixed origin. Moreover, the anthelmintic treatment was efficacious and eliminated all worms from the gut. Nevertheless, 11 pathways of both host and microbiota origin were significantly enriched in the gut of pigs from the IP group, including peptidoglycan biosynthesis, histidine metabolism (in both feces and serum), and primary bile acid biosynthesis, suggesting the infection-induced alterations may not be transient. In conclusion, the host microbiota modified swine-Ascaris interactions via three different mechanisms. First, microbiota-derived metabolites directly regulate host gene expression, which in turn affects host physiology and immune responses. Second, plasticity of the gut microbiota allows the exploitation of the niche differentiated upon infection, resulting in blossom of certain strains in the gut of post-treated animals. Lastly, the host microbiota is likely one of the key determinants of parasite gut microbiota, indirectly exerting its effect on parasite physiology and nutrition. Further studies aiming to understand reciprocal yet complex relations between the gut microbiota, the host, and parasites (including parasite gut microbiota) will be conducive to the design of next-generation functional anthelmintics.

Polysaccharides from Lanzhou Lily Attenuate Nonalcoholic Fatty Liver Disease Modifying the Gut Microbiota and Metabolite Profile.

Nonalcoholic fatty liver disease (NAFLD) is closely related to gut microbiota due to the hepatic portal system, and utilizing natural polysaccharides as prebiotics has become a prospective strategy for treating NAFLD. However, the therapeutic effects and potential molecular mechanisms of Lanzhou Lily polysaccharides (LLP) on NAFLD remains unclear. Therefore, the alleviating effects of LLP on NAFLD induced by high-fat diet (HFD) were investigated. LLP treatment greatly ameliorated NAFLD by significantly reducing lipid accumulation and the levels of liver function markers in HFD-induced NAFLD mice, as evidenced by decreased serum levels of TG, TC, HDL-C and LDL-C. Furthermore, LLP administration reduced hepatic steatosis, as shown by H&E and Oil red O staining. LLP also inhibited the TNF-α and IL-1β expression, thereby reducing levels of hepatic proinflammatory cytokines. Furthermore, LLP restored gut microbiota dysbiosis (up-regulated Bacteroidota, Proteobacteria, Alistipes and Lachnospiraceae abundances, down-regulated Firmicutes, Verrucomicrobiota, Desulfobacterota and Turicibacter abundances), and regulated microbial metabolic pathways such as primary bile acid biosynthesis and amino acid metabolism. In addition, the resultes of Spearman's correlation analysis found that some key metabolites in these metabolic pathways were associated with intestinal microorganisms such as Desulfobacterota, Prevotellaceae-UCG-001, Colidextribacter and Alistipes. Therefore, our study suggests that LLP may has potential applications in the treatment of NAFLD by regulating gut microbiota and its metabolite profile.

Metabolomics Unveils Disrupted Pathways in Parkinson's Disease: Toward Biomarker-Based Diagnosis.

Parkinson's disease (PD) is a neurodegenerative disorder characterized by diverse symptoms, where accurate diagnosis remains challenging. Traditional clinical observation methods often result in misdiagnosis, highlighting the need for biomarker-based diagnostic approaches. This study utilizes ultraperformance liquid chromatography coupled to an electrospray ionization source and quadrupole time-of-flight untargeted metabolomics combined with biochemometrics to identify novel serum biomarkers for PD. Analyzing a Brazilian cohort of serum samples from 39 PD patients and 15 healthy controls, we identified 15 metabolites significantly associated with PD, with 11 reported as potential biomarkers for the first time. Key disrupted metabolic pathways include caffeine metabolism, arachidonic acid metabolism, and primary bile acid biosynthesis. Our machine learning model demonstrated high accuracy, with the Rotation Forest boosting model achieving 94.1% accuracy in distinguishing PD patients from controls. It is based on three new PD biomarkers (downregulated: 1-lyso-2-arachidonoyl-phosphatidate and hypoxanthine and upregulated: ferulic acid) and surpasses the general 80% diagnostic accuracy obtained from initial clinical evaluations conducted by specialists. Besides, this machine learning model based on a decision tree allowed for visual and easy interpretability of affected metabolites in PD patients. These findings could improve the detection and monitoring of PD, paving the way for more precise diagnostics and therapeutic interventions. Our research emphasizes the critical role of metabolomics and machine learning in advancing our understanding of the chemical profile of neurodegenerative diseases.

Multi-omics reveal toxicity mechanisms underpinning nanoplastic in redclaw crayfish (Cherax quadricarinatus)

We investigated the effects of different nanoplastic (NP, size = 100 nm) concentrations on red crayfish (Cherax quadricarinatus) and examined toxicity mechanisms. We established four concentration groups (control (CK): 0 μg/L; Low: 100 μg/L; Medium: 500 μg/L; and High: 1000 μg/L) and analyzed toxicity effects in C. quadricarinatus hepatopancreas using histopathological, transcriptomic, metabolomic, and fluorescence methods. NP exposure caused histological lesions and oxidative stress in hepatopancreas, and also significantly decreased glutathione (GSH) (P < 0.05) but significantly increased malondialdehyde content (MDA) (P < 0.05) in NP-treated groups. By analyzing different metabolic indicators, total cholesterol (T-CHO) content significantly increased (P < 0.05) and triglyceride (TG) content significantly decreased in Medium and High (P < 0.05). Transcriptomic analyses revealed that NPs influenced apoptosis, drug metabolism-cytochrome P450, and P53 signaling pathways. Metabolomic analyses indicated some metabolic processes were affected by NPs, including bile secretion, primary bile acid biosynthesis, and cholesterol metabolism. Caspase 3, 8, and 9 distribution levels in hepatopancreatic tissues were also determined by immunofluorescence; positive caspase staining increased with increased NP concentrations. Additionally, by examining relative Bcl-2, Bax, Apaf-1, and p53 mRNA expression levels, Bcl-2 expression was significantly decreased with increasing NP concentrations; and the expression of Bcl-2 was increasing significantly with the NPs concentration increasing. Bax expression in Low, Medium, and High groups was also significantly higher when compared with the CK group (P < 0.05); with High group levels significantly higher than in Low and Medium groups (P < 0.05). P53 expression was significantly increased in Low, Medium, and High groups (P < 0.05). Thus, NPs induced apoptosis in C. quadricarinatus hepatopancreatic cells, concomitant with increasing NP concentrations. Therefore, we identified mechanisms underpinning NP toxicity in C. quadricarinatus and provide a theoretical basis for exploring NP toxicity in aquatic organisms.

Cross-Omics Analyses Reveal the Effects of Ambient PM2.5 Exposure on Hepatic Metabolism in Female Mice.

Ambient particulate matter (PM2.5) is a potential risk factor for metabolic damage to the liver. Epidemiological studies suggest that elevated PM2.5 concentrations cause changes in hepatic metabolism, but there is a lack of laboratory evidence. Here, we aimed to evaluate the effects of PM2.5 exposure on liver metabolism in C57BL/6j female mice (10 months old) and to explore the mechanisms underlying metabolic alterations and differential gene expressions by combining metabolomics and transcriptomics analyses. The metabolomics results showed that PM2.5 exposure notably affected the metabolism of amino acids and organic acids and caused hepatic lipid and bile acid accumulation. The transcriptomic analyses revealed that PM2.5 exposure led to a series of metabolic pathway abnormalities, including steroid biosynthesis, steroid hormone biosynthesis, primary bile acid biosynthesis, etc. Among them, the changes in the bile acid pathway might be one of the causes of liver damage in mice. In conclusion, this study clarified the changes in liver metabolism in mice caused by PM2.5 exposure through combined transcriptomic and metabolomic analyses, revealed that abnormal bile acid metabolism is the key regulatory mechanism leading to metabolic-associated fatty liver disease (MAFLD) in mice, and provided laboratory evidence for further clarifying the effects of PM2.5 on body metabolism.

Metabolomics Profiling of Serum and Urine from Chuanzang Black Pigs with Different Residual Feed Intake.

This study was conducted to evaluate associations of blood variables and urine variables with different residual feed intakes (RFIs) in growing Chuanzang black (CB) pigs. A total of 228 growing CB boars from 99 days were used. The same basal diet was offered ad libitum and individual feed intake and body weight were measured over a period of 181 d. The CB pigs were categorized based on their residual feed intake values, with six individuals each from the high and low ends selected and divided into two groups: the low residual feed intake group (LS) and the high residual feed intake group (HS). Serum and urine samples were collected at the end of the experiment for determination of metabolomics profiling. Results showed that there were significantly different metabolites in serum and urine of different RFI groups (fold-change, FC > 2.0 or FC < 0.5, and p < 0.05), and 21 metabolites were identified in serum and 61 in urine. Cluster analysis showed that 20 metabolites were up-regulated and one metabolite was down-regulated in serum; 44 metabolites were up-regulated and 17 metabolites were down-regulated in urine. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differential metabolites of serum were enriched in linoleic acid metabolism, and the differential metabolites of urine were enriched in steroid hormone biosynthesis, taurine and hypotaurine metabolism, and primary bile acid biosynthesis. The correlations between serum metabolites and urine metabolites indicated a significant positive correlation between all fatty acyls in serum metabolites and L-glutamate in urine. However, no compelling genetic or blood biomarkers have been found to explain the differences in RFI, suggesting multiple approaches to effective feed use in pigs. This study provides new insights into the subsequent assessment of RFI by metabolomics profiling, as well as the development of novel feed additives for the factors that will facilitate future research directions in CB pigs.

Fufang Muji Granules Ameliorate Liver Fibrosis by Reducing Oxidative Stress and Inflammation, Inhibiting Apoptosis, and Modulating Overall Metabolism.

Fufang Muji granules (FMGs) are a prominent modern prescription Chinese patent formulation derived from the Muji decoction. Utilized in clinical practice for nearly four decades, FMGs have demonstrated efficacy in treating liver diseases. However, the precise mechanism of action remains unclear. This study investigates the hepatoprotective effects of FMGs against liver fibrosis in rats based on untargeted metabolomics and elucidates their underlying mechanisms. A comprehensive model of liver fibrosis was established with 30% CCl4 (2 mL/kg) injected intraperitoneally, and a fat and sugar diet combined with high temperatures and humidity. Rats were orally administered FMGs (3.12 g/kg/d) once daily for six weeks. FMG administration resulted in improved liver fibrosis and attenuated hepatic oxidative stress and apoptosis. Furthermore, FMGs inhibited hepatic stellate cell activation and modulated transforming growth factor β1/Smad signaling. Additionally, FMG treatment influenced the expression levels of interleukin-6, interleukin-1β, and tumour necrosis factor alpha in the injured liver. Metabolic pathways involving taurine and hypotaurine metabolism, as well as primary bile acid biosynthesis, were identified as mechanisms of action for FMGs. Immunohistochemistry, quantitative reverse transcription polymerase chain reaction (RT-qPCR), and quantitative analysis also revealed that FMGs regulated taurine and hypotaurine metabolism and bile acid metabolism. These findings provide a valuable understanding of the role of FMGs in liver fibrosis management.

Core biomarkers analysis benefit for diagnosis on human intrahepatic cholestasis of pregnancy

BackgroundThe pregnant women with intrahepatic cholestasis were at high risk of fetal distress, preterm birth and unexpected stillbirth. Intrahepatic cholestasis of pregnancy (ICP) was mainly caused by disorder of bile acid metabolism, whereas the specific mechanism was obscure.MethodsWe performed proteomics analysis of 10 ICP specimens and 10 placenta specimens from patients without ICP through data-independent acquisition (DIA) technique to disclose differentially expressed proteins. We executed metabolomic analysis of 30 ICP specimens and 30 placenta specimens from patients without ICP through UPLC-MS/MS to identify differentially expressed metabolites. Enrichment and correlation analysis was used to obtain the direct molecular insights of ICP development. The ICP rat models were constructed to validate pathological features.ResultsThe heatmap of proteomics analysis showed the top 30 up-regulated and 30 down-regulated proteins. The metabolomic analysis revealed 20 richer and 4 less abundant metabolites in ICP samples compared with placenta specimens from patients without ICP, and enrichment pathways by these metabolites included primary bile acid biosynthesis, cholesterol metabolism, bile secretion, nicotinate and nicotinamide metabolism, purine metabolism and metabolic pathways. Combined analysis of multiple omics results demonstrated that bile acids such as Glycohyocholic acid, Glycine deoxycholic acid, beta-Muricholic acid, Noncholic acid, cholic acid, Gamma-Mercholic Acid, alpha-Muricholic acid and Glycochenodeoxycholic Aicd were significantly associated with the expression of GLRX3, MYL1, MYH7, PGGT1B, ACTG1, SP3, LACTB2, C2CD5, APBB2, IPO9, MYH2, PPP3CC, PIN1, BLOC1S1, DNAJC7, RASAL2 and ATCN3 etc. The core protein ACAT2 was involved in lipid metabolic process and animal model showed that ACAT2 was up-regulated in placenta and liver of pregnant rats and fetal rats. The neonates had low birth weight and Safranin O-Fast green FCF staining of animal models showed that poor osteogenic and chondrogenic differentiation of fetal rats.ConclusionMultiple metabolites-alpha-Muricholic acid, beta-Muricholic acid, Glycine deoxycholic acid and Glycochenodeoxycholic Acid etc. were perfect biomarkers to predict occurrence of ICP. Bile acids were significantly associated with varieties of protein expression and these proteins were differentially expressed in ICP samples. Our study provided several biomarkers for ICP detection and potential therapeutic targets for ICP development.

Metabolomic profiling analysis reveals the benefits of ginseng berry intake on mitochondrial function and glucose metabolism in the liver of obese mice.

Ginseng berry (GB) has previously been demonstrated to improve systemic insulin resistance and regulate hepatic glucose metabolism and steatosis in mice with diet-induced obesity (DIO). In this study, the role of GB in metabolism was assessed using metabolomics analysis on the total liver metabolites of DIO mice. Metabolomic profiling was performed using capillary electrophoresis time-of-flight mass spectrometry (CE-TOF/MS) of liver tissue from mice on a 12-wk normal chow diet (NC), high-fat diet (HFD), and HFD supplemented with 0.1% GB (HFD + GB). The detected metabolites, its pathways, and functions were analyzed through partial least square discriminant analysis (PLS-DA), the small molecular pathway database (SMPDB), and MetaboAnalyst 5.0. The liver metabolite profiles of NC, HFD, and GB-fed mice (HFD + GB) were highly compartmentalized. Metabolites involved in major liver functions, such as mitochondrial function, gluconeogenesis/glycolysis, fatty acid metabolism, and primary bile acid biosynthesis, showed differences after GB intake. The metabolites that showed significant correlations with fasting blood glucose (FBG), insulin, and homeostatic model assessment for insulin resistance (HOMA-IR) were highly associated with mitochondrial membrane function, energy homeostasis, and glucose metabolism. Ginseng berry intake increased the levels of metabolites involved in mitochondrial membrane function, decreased the levels of metabolites related to glucose metabolism, and was highly correlated with metabolic phenotypes. This study demonstrated that long-term intake of GB changed the metabolite of hepatosteatotic livers in DIO mice, normalizing global liver metabolites involved in mitochondrial function and glucose metabolism and indicating the potential mechanism of GB in ameliorating hyperglycemia in DIO mice.

Naringenin Against Cadmium Toxicity in Fibroblast Cells: An Integrated Network Pharmacology and In Vitro Metabolomics Approach.

Cadmium, a heavy metal, disrupts cellular homeostasis and is highly toxic, with no effective treatments currently available against its toxicity. According to studies, phytochemicals provide a promising strategy for mitigating cadmium toxicity. Naringenin (NG), a potent antioxidant found primarily in citrus fruits, showed protective properties against cadmium toxicity in rats. Nonetheless, the precise mechanism of cadmium cytotoxicity in fibroblasts remains unknown. This study evaluated NG against cadmium (CdCl2) toxicity utilizing network pharmacology and in silico molecular docking, and was further validated experimentally in rat fibroblast F111 cells. Using network pharmacology, 25 possible targets, including the top 10 targets of NG against cadmium, were identified. Molecular docking of interleukin 6 (IL6), the top potential target with NG, showed robust binding with an inhibition constant (Ki) of 58.76 μM, supporting its potential therapeutic potential. Pathway enrichment analysis suggested that "response to reactive oxygen species" and "negative regulation of small molecules metabolic process" were the topmost pathways targeted by NG against cadmium. In vitro analysis showed that NG (10 μM) attenuated CdCl2-induced oxidative stress by reducing altered intracellular ROS, mitochondrial mass, and membrane potential. Also, NG reversed CdCl2-mediated nuclear damage, G2/M phase arrest, and apoptosis. GC/MS-based metabolomics of F111 cells revealed CdCl2 reduced cholesterol levels, which led to alterations in primary bile acid, steroid and steroid hormone biosynthesis pathways, whereas, NG restored these alterations. In summary, combined in silico and in vitro analysis suggested that NG protected cells from CdCl2 toxicity by mitigating oxidative stress and metabolic pathway alterations, providing a comprehensive understanding of its protective mechanisms against cadmium-induced toxicity.

The mechanism of bile acid metabolism regulating lipid metabolism and inflammatory response in T2DM through the gut-liver axis

AimsThe main objective of this study was to analyze the changes of intestinal microflora and how bile acid metabolic pathways affect lipid metabolism in T2DM through the gut-liver axis. MethodsFirstly, 16S rRNA sequencing, metabolomics and transcriptomic sequencing were performed on plasma and feces of clinical subjects to determine the changes of intestinal flora and its metabolites. Finally, T2DM mice model was verified in vivo. ResultsT2DM patients have significant intestinal flora metabolism disorders. The differential fecal metabolites were mainly enriched in primary bile acid biosynthesis and cholesterol metabolism pathways in T2DM patients. After verification, the changes in gut microbiota and metabolites in T2DM patients (including up-regulated bacteria associated with BA metabolism, such as lactobacillus and bifidobacterial, and down-regulated bacteria capable of producing SCFAs such as Faecalibacterium, Bacteroides, Romboutsia and Roseburia); and the changes in the flora and metabolites that result in impairment of intestinal barrier function and changes of protein expression in the blood, intestine and liver of T2DM patients (including FGFR4↑, TRPM5↑ and CYP27A1↓, which are related to BA and lipid metabolism homeostasis, and TLR6↑, MYD88↑ and NF-κB↑, which are related to inflammatory response). These aspects together contribute to the development of further disorders of glucolipid metabolism and systemic inflammation in T2DM patients. ConclusionsChanges in intestinal flora and its metabolites may affect lipid metabolism and systemic inflammatory response in T2DM patients through the gut-liver axis mediated by bile acids.