Metabolomic-proteomic combination analysis reveals the targets and molecular pathways associated with hydrogen sulfide alleviating NAFLD

Integrative analysis of metabolomics and proteomics reveals mechanism of berberrubine-induced nephrotoxicity

Berberrubine (BRB), a main metabolite of berberine, has stronger hypoglycemic and lipid-lowering activity than its parent form. We previously found that BRB could cause obvious nephrotoxicity, but the molecular mechanism involved remains unknown. In this study, we systematically integrated metabolomics and quantitative proteomics to reveal the potential mechanism of nephrotoxicity caused by BRB. Metabolomic analysis revealed that 103 significant- differentially metabolites were changed. Among the mentioned compounds, significantly upregulated metabolites were observed for phosphorylcholine, sn-glycerol-3-phosphoethanolamine, and phosphatidylcholine. The top three enriched KEGG pathways were the mTOR signaling pathway, central carbon metabolism in cancer, and choline metabolism in cancer. ERK1/2 plays key roles in all three metabolic pathways. To further confirm the main signaling pathways involved, a proteomic analysis was conducted to screen for key proteins (such as Mapk1, Mapk14, and Caspase), indicating the potential involvement of cellular growth and apoptosis. Moreover, combined metabolomics and proteomics analyses revealed the participation of ERK1/2 in multiple metabolic pathways. These findings indicated that ERK1/2 regulated the significant- differentially abundant metabolites determined via metabolomics analysis. Notably, through a cellular thermal shift assay (CETSA) and molecular docking, ERK1/2 were revealed to be the direct binding target involved in BRB-induced nephrotoxicity. To summarize, this study sheds light on the understanding of severe nephrotoxicity caused by BRB and provides scientific basis for its safe use and rational development.

Hydrogen Sulfide and Liver Health: Insights into Liver Diseases

Significance: Hydrogen sulfide (H2S) is a recently recognized gasotransmitter involved in physiological and pathological conditions in mammals. It protects organs from oxidative stress, inflammation, hypertension, and cell death. With abundant expression of H2S-production enzymes, the liver is closely linked to H2S signaling. Recent Advances: Hepatic H2S comes from various sources, including gut microbiota, exogenous sulfur salts, and endogenous production. Recent studies highlight the importance of hepatic H2S in liver diseases such as nonalcoholic fatty liver disease (NAFLD), liver injury, and cancer, particularly at advanced stages. Endogenous H2S production deficiency is associated with severe liver disease, while exogenous H2S donors protect against liver dysfunction. Critical Issues: However, the roles of H2S in NAFLD, liver injury, and liver cancer are still debated, and its effects depend on donor type, dosage, treatment duration, and cell type, suggesting a multifaceted role. This review aimed to critically evaluate H2S production, metabolism, mode of action, and roles in liver function and disease. Future Direction: Understanding H2S's precise roles and mechanisms in liver health will advance potential therapeutic applications in preclinical and clinical research. Targeting H2S-producing enzymes and exogenous H2S sources, alone or in combination with other drugs, could be explored. Quantifying endogenous H2S levels may aid in diagnosing and managing liver diseases. Antioxid. Redox Signal. 40, 122-144.

The Mechanism Underlying the Hypoglycemic Effect of Epimedin C on Mice with Type 2 Diabetes Mellitus Based on Proteomic Analysis

Type 2 diabetes mellitus (T2DM) has become a worldwide public health problem. Epimedin C is considered one of the most important flavonoids in Epimedium, a famous edible herb in China and Southeast Asia that is traditionally used in herbal medicine to treat diabetes. In the present study, the therapeutic potential of epimedin C against T2DM was ascertained using a mouse model, and the mechanism underlying the hypoglycemic activity of epimedin C was explored using a label-free proteomic technique for the first time. Levels of fasting blood glucose (FBG), homeostasis model assessment of insulin resistance (HOMA-IR), and oral glucose tolerance, as well as contents of malondialdehyde (MDA) and low-density lipoprotein cholesterol (LDL-C) in the 30 mg·kg-1 epimedin C group (EC30 group), were significantly lower than those in the model control group (MC group) (p < 0.05), while the contents of hepatic glycogen, insulin, and high-density lipoprotein cholesterol (HDL-C), as well as activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in the EC30 group were notably higher than those in the MC group (p < 0.05). The structures of liver cells and tissues were greatly destroyed in the MC group, whereas the structures of cells and tissues were basically complete in the EC30 group, which were similar to those in the normal control group (NC group). A total of 92 differentially expressed proteins (DEPs) were enriched in the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In the EC30 vs. MC groups, the expression level of cytosolic phosphoenolpyruvate carboxykinase (Pck1) was down-regulated, while the expression levels of group XIIB secretory phospholipase A2-like protein (Pla2g12b), apolipoprotein B-100 (Apob), and cytochrome P450 4A14 (Cyp4a14) were up-regulated. According to the KEGG pathway assay, Pck1 participated in the gluconeogenesis and insulin signaling pathways, and Pla2g12b, Apob, and Cyp4a14 were the key proteins in the fat digestion and fatty acid degradation pathways. Pck1, Pla2g12b, Apob, and Cyp4a14 seemed to play important roles in the prevention and treatment of T2DM. In summary, epimedin C inhibited Pck1 expression to maintain FBG at a relatively stable level, promoted Pla2g12b, Apob, and Cyp4a14 expressions to alleviate liver lipotoxicity, and protected liver tissues and cells from oxidant stress possibly by its phenolic hydroxyl groups.

Recent Insights into the Biomarkers, Molecular Targets and Mechanisms of Non-Alcoholic Steatohepatitis-Driven Hepatocarcinogenesis

Non-alcoholic fatty liver disease (NAFLD) or metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatitis (NASH) are chronic hepatic conditions leading to hepatocellular carcinoma (HCC) development. According to the recent "multiple-parallel-hits hypothesis", NASH could be caused by abnormal metabolism, accumulation of lipids, mitochondrial dysfunction, and oxidative and endoplasmic reticulum stresses and is found in obese and non-obese patients. Recent translational research studies have discovered new proteins and signaling pathways that are involved not only in the development of NAFLD but also in its progression to NASH, cirrhosis, and HCC. Nevertheless, the mechanisms of HCC developing from precancerous lesions have not yet been fully elucidated. Now, it is of particular importance to start research focusing on the discovery of novel molecular pathways that mediate alterations in glucose and lipid metabolism, which leads to the development of liver steatosis. The role of mTOR signaling in NASH progression to HCC has recently attracted attention. The goals of this review are (1) to highlight recent research on novel genetic and protein contributions to NAFLD/NASH; (2) to investigate how recent scientific findings might outline the process that causes NASH-associated HCC; and (3) to explore the reliable biomarkers/targets of NAFLD/NASH-associated hepatocarcinogenesis.

Gasotransmitters in non-alcoholic fatty liver disease: just the tip of the iceberg

Non-alcoholic fatty liver disease (NAFLD) is a clinicopathological syndrome characterized by fatty lesions and fat accumulation in hepatic parenchymal cells, which is in the absence of excessive alcohol consumption or definite liver damage factors. The exact pathogenesis of NAFLD is not fully understood, but it is now recognized that oxidative stress, insulin resistance, and inflammation are essential mechanisms involved in the development and treatment of NAFLD. NAFLD therapy aims to stop, delay or reverse disease progressions, as well as improve the quality of life and clinical outcomes of patients with NAFLD. Gasotransmitters are produced by enzymatic reactions, regulated through metabolic pathways in vivo, which can freely penetrate cell membranes with specific physiological functions and targets. Three gasotransmitters, nitric oxide, carbon monoxide, and hydrogen sulfide have been discovered. Gasotransmitters exhibit the effects of anti-inflammatory, anti-oxidant, vasodilatory, and cardioprotective agents. Gasotransmitters and their donors can be used as new gas-derived drugs and provide new approaches to the clinical treatment of NAFLD. Gasotransmitters can modulate inflammation, oxidative stress, and numerous signaling pathways to protect against NAFLD. In this paper, we mainly review the status of gasotransmitters research on NAFLD. It provides clinical applications for the future use of exogenous and endogenous gasotransmitters for the treatment of NAFLD.

Regulation mechanism of lipids for extracellular yellow pigments production by Monascus purpureus BWY-5

The biosynthesis and secretion of Monascus pigments are closely related to the integrity of the cell membrane, which determines the composition of lipids and its content in cell membrane. The present study aimed to thoroughly describe the changes of lipid profiling in Monascus purpureus BWY-5, which was screened by carbon ion beam irradiation (¹²C⁶⁺) to almost single yield extracellular Monascus yellow pigments (extra-MYPs), by absolute quantitative lipidomics and tandem mass tags (TMT) based quantitative proteomic. ¹²C⁶⁺ irradiation caused non-lipid oxidation damage to Monascus cell membrane, leading to an imbalance in cell membrane lipid homeostasis. This imbalance was attributed to significant changes not only in the composition but also in the content of lipids in Monascus, especially the inhibition of glycerophospholipid biosynthesis. Integrity of plasma membrane was maintained by the increased production of ergosterol, monogalactosylmonoacylglycerol (MGMG) and sulfoquinovosylmonoacylglycerol (SQMG), while mitochondrial membrane homeostasis was maintained by the increase of cardiolipin production. The growth and extra-MYPs production of Monascus BWY-5 have been regulated by the promotion of sphingolipids (ceramide and sulfatide) biosynthesis. Simultaneous, energy homeostasis may be achieved by increase of TG synthesis and Ca²⁺/Mg²⁺-ATPase activity. These finding suggest ergosterol, cardiolipin, sphingolipids, MGMG and SQMG play a key facilitating role in cytomembrane lipid homeostasis maintaining for Monascus purpureus BWY-5, and then it is closely related to cell growth and extra-MYPs production. KEY POINTS: 1. Energy homeostasis in Monascus purpureus BWY-5 was achieved by increase of TG synthesis and Ca²⁺/Mg²⁺-ATPase activity. 2. Integrity of plasma membrane in Monascus purpureus BWY-5 was maintained by the increased production of ergosterol. 3. Mitochondrial membrane homeostasis in Monascus purpureus BWY-5 was maintaed by the increase of cardiolipin synthesis.

Study on the mechanism of Shuganzhi Tablet against nonalcoholic fatty liver disease and lipid regulation effects of its main substances in vitro

ETHNOPHARMACOLOGICAL RELEVANCE

Shuganzhi Tablet (SGZT) originates from a famous traditional Chinese herbal formula Chaihu Decoction which can be applied to treat liver diseases, however, the pharmacodynamic mechanism of SGZT needs to be evaluated.

AIM OF THIS STUDY

To study the mechanism of SGZT in the treatment of non-alcoholic fatty liver disease (NAFLD), and screen out its effective ingredients.

MATERIALS AND METHODS

In this study, firstly, the main components of SGZT were analyzed qualitatively. And a rat model of NAFLD was established by feeding high-fat diet. Serum biochemical indexes and liver pathological analysis were used to evaluate the pharmacodynamic effect of SGZT in the treatment of NAFLD. In order to explore the pharmacodynamic mechanism, proteomics and metabolomics analysis were used. Western blotting was used to verify the expression of important differential proteins. And L02 cells were treated with free fatty acids (FFA) and the main substances of SGZT to establish the cell model of NAFLD in vitro and to reveal the pharmacodynamic substance of SGZT.

RESULTS

Twelve components were detected in SGZT, and according to the results of serum biochemical indexes and liver pathological analysis, SGZT could effectively treat NAFLD. Combined with the results of bioinformatics analysis, we found that 133 differentially expressed proteins were reversed in liver samples of rats treated with SGZT. The important proteins in PPAR signaling pathway, steroid biosynthesis, cholesterol metabolism and fatty acid metabolism were mainly regulated to maintain cholesterol homeostasis and improve lipid metabolism. SGZT also affected various metabolites in rat liver, including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and taurine. In addition, the main components contained in SGZT (hesperidin, polydatin, naringin, emodin, specnuezhenide, saikosaponin A) and a metabolite (resveratrol) could significantly reduce FFA-induced intracellular lipid accumulation.

CONCLUSION

SGZT effectively treated NAFLD, and PPAR-γ, Acsl4, Plin2 and Fads1 may be the main targets of SGZT. And Fads1-EPA/DHA-PPAR-γ may be the potential pharmacodynamic pathway. Cell experiments in vitro revealed that the main components of SGZT and their metabolites, such as hesperidin, polydatin, naringin, emodin, specnuezhenide, saikosaponin A and resveratrol may be the main components of its efficacy. Further research is needed to reveal and validate the pharmacodynamic mechanism.

Serine hydroxymethyltransferase 2 knockdown induces apoptosis in ccRCC by causing lysosomal membrane permeabilization via metabolic reprogramming

Serine hydroxymethyltransferase 2 (SHMT2) plays an important role in converting serine to glycine and supplying carbon to one-carbon metabolism to sustain cancer cell proliferation. However, the expression, function, and underlying mechanisms of SHMT2 in clear cell renal cell carcinoma (ccRCC) remain largely unknown. In this study, we demonstrated that SHMT2 was upregulated in ccRCC tissues compared with controls and associated with patient survival. SHMT2 knockdown inhibited proliferation, migration, and invasion in ccRCC cells. Overexpression of SHMT2 promoted tumor progression. Mechanistically, SHMT2 depletion disrupted one-carbon metabolism, increased reactive oxygen species (ROS) levels, and decreased ATP levels via metabolic reprogramming, which destroyed cell homeostasis. The SHMT2 knockdown-induced stress activated autophagy. A mass of autophagosomes fused with lysosomes, resulting in lysosomal membrane permeabilization (LMP) and leakage of lysosomal contents into the cytoplasm, which eventually led to apoptosis. Our work reveals that SHMT2 functions as an oncogenic gene to promote ccRCC progression. SHMT2 depletion induces apoptosis by causing LMP through excessive activation of the autophagy-lysosome pathway via metabolic reprogramming.

Protective Effects of Clinacanthus nutans (Burm.f.) Lindau Aqueous Extract on HBV Mouse Model by Modulating Gut Microbiota and Liver Metabolomics

Background

Clinacanthus nutans (Burm.f.) Lindau (C. nutans) has been used in the therapy of hepatitis B (HB) and is effective; however, the mechanism of action has not been elucidated.

Objective

To investigate the protective effects of C. nutans aqueous extract on the hepatitis B virus (HBV) mouse model based on correlation analysis between gut microbiota and liver metabolomics.

Materials and Methods

We firstly constructed the animal model by high-pressure injection of pcDNA3.1(+)/HBV plasmid into the tail vein and treated it with C. nutans. The biomarkers and inflammatory cytokines of HB were detected by enzyme-linked immunosorbent assay and quantitative PCR; the Illumina-MiSeq platform was used for investigating gut microbiota; the LC-MS/MS method was utilized on screening liver tissue metabolites; multiomics joint analysis was performed using the R program.

Results

Compared with the modeling group, C. nutans significantly decreased the expression levels of HBsAg, IL-1β, TNF-α(P < 0.05) in the serum, and cccDNA (P < 0.05) in the liver tissues of mice. C. nutans dramatically reduced the ratio of Firmicutes and Bacteroidetes (P < 0.05) and significantly declined the proportion of Lactobacillaceae and Lactobacillus(P < 0.05), dramatically increasing the relative abundance of Bacteroidales_S24-7_group, Rikenellaceae, and Alistipes(P < 0.05); LC-MS/MS analysis results showed that C. nutans dramatically upregulate hippuric acid, L-histidine, trehalose, D-threitol, and stachyose and downregulate uridine 5'-diphosphate, cholic acid, trimethylamine N-oxide, CDP-ethanolamine, and phosphorylcholine (P < 0.05). The correlation analysis revealed that C. nutans affects the related metabolite levels of hippuric acid and cholic acid through the modulation of crucial bacteria (Alistipes) (P < 0.01), exerting specific anti-inflammatory effects.

Conclusion

These results suggest that C. nutans exerts protective effects in HBV model mice, showing the therapeutic potential for anti-HBV infection.

Hydrogen Sulfide and Its Donors: Keys to Unlock the Chains of Nonalcoholic Fatty Liver Disease

Hydrogen sulfide (H2S) has emerged as the third “gasotransmitters” and has a crucial function in the diversity of physiological functions in mammals. In particular, H2S is considered indispensable in preventing the development of liver inflammation in the case of excessive caloric ingestion. Note that the concentration of endogenous H2S was usually low, making it difficult to discern the precise biological functions. Therefore, exogenous delivery of H2S is conducive to probe the physiological and pathological roles of this gas in cellular and animal studies. In this review, the production and metabolic pathways of H2S in vivo, the types of donors currently used for H2S release, and study evidence of H2S improvement effects on nonalcoholic fatty liver disease are systematically introduced.

Hydrogen Sulfide Plays an Important Role by Regulating Endoplasmic Reticulum Stress in Diabetes-Related Diseases

Endoplasmic reticulum (ER) plays important roles in protein synthesis, protein folding and modification, lipid biosynthesis, calcium storage, and detoxification. ER homeostasis is destroyed by physiological and pharmacological stressors, resulting in the accumulation of misfolded proteins, which causes ER stress. More and more studies have shown that ER stress contributes to the pathogenesis of many diseases, such as diabetes, inflammation, neurodegenerative diseases, cancer, and autoimmune diseases. As a toxic gas, H₂S has, in recent years, been considered the third most important gas signal molecule after NO and CO. H₂S has been found to have many important physiological functions and to play an important role in many pathological and physiological processes. Recent evidence shows that H₂S improves the body’s defenses to many diseases, including diabetes, by regulating ER stress, but its mechanism has not yet been fully understood. We therefore reviewed recent studies of the role of H₂S in improving diabetes-related diseases by regulating ER stress and carefully analyzed its mechanism in order to provide a theoretical reference for future research.

Protective Effects of Abrus cantoniensis Hance on the Fatty Liver Hemorrhagic Syndrome in Laying Hens Based on Liver Metabolomics and Gut Microbiota

As a metabolic disease, fatty liver hemorrhagic syndrome (FLHS) has become a serious concern in laying hens worldwide. Abrus cantoniensis Hance (AC) is a commonly used plant in traditional medicine for liver disease treatment. Nevertheless, the effect and mechanism of the decoction of AC (ACD) on FLHS remain unclear. In this study, ultra-high performance liquid chromatography analysis was used to identify the main phytochemicals in ACD. FLHS model of laying hens was induced by a high-energy low-protein (HELP) diet, and ACD (0.5, 1, 2 g ACD/hen per day) was given to the hens in drinking water at the same time for 48 days. Biochemical blood indicators and histopathological analysis of the liver were detected and observed to evaluate the therapeutic effect of ACD. Moreover, the effects of ACD on liver metabolomics and gut microbiota in laying hens with FLHS were investigated. The results showed that four phytochemicals, including abrine, hypaphorine, vicenin-2, and schaftoside, were identified in ACD. ACD treatment ameliorated biochemical blood indicators in laying hens with FLHS by decreasing aspartate aminotransferase, alanine aminotransferase, triglycerides, low-density lipoprotein cholesterol, and total cholesterol, and increasing high-density lipoprotein cholesterol. In addition, lipid accumulation in the liver and pathological damages were relieved in ACD treatment groups. Moreover, distinct changes in liver metabolic profile after ACD treatment were observed, 17 endogenous liver metabolites mainly associated with the metabolism of arachidonic acid, histidine, tyrosine, and tryptophan were reversed by ACD. Gut microbiota analysis revealed that ACD treatment significantly increased bacterial richness (Chao 1, P < 0.05; Ace, P < 0.01), and upregulated the relative abundance of Bacteroidetes and downregulated Proteobacteria, improving the negative effects caused by HELP diet in laying hens. Taken together, ACD had a protective effect on FLHS by regulating blood lipids, reducing liver lipid accumulation, and improving the dysbiosis of liver metabolomics and gut microbiota.

Hydrogen sulphide in liver glucose/lipid metabolism and non-alcoholic fatty liver disease

BACKGROUND

For a long time, hydrogen sulphide (H₂ S) was considered only as a toxic gas, inhibiting mitochondrial respiration at the level of cytochrome c oxidase, and an environmental pollutant. Nowadays, H₂ S is recognized as the third mammalian gasotransmitter, playing an important role in inflammation, septic shock, ischaemia reperfusion events, cardiovascular disease and more recently in liver physiology and chronic liver diseases such as non-alcoholic fatty liver disease (NAFLD).

METHODS

This narrative review is based on literature search using PubMed.

RESULTS

From a bioenergetic perspective, H₂ S is a very unique molecule, serving as a mitochondrial poison at high concentrations or as an inorganic mitochondrial substrate at low concentrations. By using transgenic animal models to specifically modulate liver H₂ S biosynthesis or exogenous compounds that release H₂ S, several studies demonstrated that H₂ S is a key player in liver glucose and lipid metabolism. Liver H₂ S content and biosynthesis were also altered in NAFLD animal models with the in vivo administration of H₂ S-releasing molecules preventing the further escalation into non-alcoholic-steatohepatitis. Liver steady-state levels of H₂ S, and hence its cell signalling properties, are controlled by a tight balance between its biosynthesis, mainly through the transsulphuration pathway, and its mitochondrial oxidation via the sulphide oxidizing unit. However, studies investigating mitochondrial H₂ S oxidation in liver dysfunction still remain scarce.

CONCLUSIONS

Since H₂ S emerges as a key regulator of liver metabolism and metabolic flexibility, further understanding the physiological relevance of mitochondrial H₂ S oxidation in liver energy homeostasis and its potential implication in chronic liver diseases are of great interest.

Untargeted and targeted metabolomics profiling reveals the underlying pathogenesis and abnormal arachidonic acid metabolism in laying hens with fatty liver hemorrhagic syndrome

As a metabolic disease, fatty liver hemorrhagic syndrome (FLHS) has become the major factor responsible for the noninfectious cause of mortality in laying hens, which lead to huge economic losses to poultry industry. However, the pathogenesis of FLHS remains unclear. The aim of present study was to identify novel liver metabolites associated with FLHS. Twenty healthy Chinese commercial Jing Fen laying hens aged 90 d were used in present study. After acclimatization for 2 wk, the hens were divided into 2 treatments (n = 10): control group (normal diet) and FLHS group (high-energy low-protein diet). The experiment lasted for 48 d, and the laying hens were killed for blood and liver sampling at the end of the experiment. Blood biochemical indicators and liver pathological changes were examined. Meanwhile, the changes in liver metabolic profile were investigated with the application of metabolomics approach. Significant increased levels of alanine aminotransferase, aspartate aminotransferase, low density lipoprotein, total cholesterol and triglycerides, decreased high density lipoprotein (P < 0.01), and hepatic steatosis were observed in hens of FLHS group, which suggested FLHS was successfully established in this study. Distinct changes in metabolite patterns in liver between control and FLHS group were observed by partial least-squares discriminant analysis. In total, 42 liver metabolites including tyrosine, glutathione, carnitine, linoleic acid, uric acid, arachidonic acid (ARA), lactate and lysophosphatidylcholine (14: 0) were identified and considered to be related with pathogenesis of FLHS. Pathway analysis revealed that these metabolites were mainly involved in amino acid metabolism, fatty acid metabolism, ARA metabolism, glucose metabolism and glycerophospholipid metabolism. Furthermore, targeted metabolomics found that ARA metabolites such as prostaglandins and hydroxyeicosatetraenoic acids were significantly increased in FLHS group (P < 0.05). In conclusion, our data showed that liver metabolites and ARA metabolism were linked to the pathophysiology of FLHS, which provided a basis for understanding the pathogenesis of FLHS in laying hens.