Metabolomic Profiling of Autoimmune Hepatitis: The Diagnostic Utility of Nuclear Magnetic Resonance Spectroscopy

Navigating liver health with metabolomics: A comprehensive review

Non-alcoholic fatty liver disease (NAFLD) is the main cause of chronic liver disease worldwide, affecting one-fourth of the world's population. With more than half of the world's population, the Asia-Pacific region contributed 62.6 % of liver-related fatal incidents in 2015. Currently, liver imaging techniques such as computed tomography (CT), nuclear magnetic resonance (NMR) spectroscopy, and ultrasound are non-invasive imaging methods to diagnose the disease. A liver biopsy is the gold standard test for establishing the definite diagnosis of non-alcoholic steatohepatitis (NASH). However, there are still significant problems with sample variability and the procedure's invasiveness. Numerous studies have indicated various non-invasive biomarkers for both fibrosis and steatosis to counter the invasiveness of diagnostic procedures. Metabolomics could be a promising method for detecting early liver diseases, investigating pathophysiology, and developing drugs. Metabolomics, when utilized with other omics technologies, can result in a deeper understanding of biological systems. Metabolomics has emerged as a prominent research topic, offering extensive opportunities to investigate biomarkers for liver diseases that are both sensitive and specific. In this review, we have described the recent studies involving the use of a metabolomics approach in the diagnosis of liver diseases, which would be beneficial for the early detection and treatment of liver diseases.

Metabolome and Transcriptome Profiling Reveals Age-Associated Variations in Meat Quality and Molecular Mechanisms of Taihe Black-Bone Silky Fowls

To explore the changes in meat quality and molecular mechanisms during the growth and development of Taihe black-bone silky fowl, this study employed liquid chromatography-mass spectrometry (LC-MS/MS) metabolomics to elucidate the dynamic changes of key differential metabolites (DMs) affecting meat quality, indicating that chicken at D120 had higher levels of ω-3 polyunsaturated fatty acids (PUFAs), creatine, anserine, and homocarnosine, while D150 had the most stachydrine and D210 had the most acylcarnitines. Additionally, D120 and D180 had more umami and sweet compounds. Furthermore, key metabolic pathways influenced by age included purine metabolism, the pentose phosphate pathway, nicotinate and nicotinamide metabolism, and taurine and hypotaurine metabolism. Transcriptomic identified differential expression genes (DEGs) are predominantly enriched in focal adhesion, the TGF-β signaling pathway, and the MAPK signaling pathway. Integrated metabolomics and transcriptomics revealed complex regulatory networks of DEGs and DMs in key metabolic pathways. This research enhanced our understanding of the biology of Taihe black-bone silky fowl meat quality, revealing possible biomarkers.

Transcriptome-metabolome reveals the molecular changes in meat production and quality in the hybrid populations of Sichuan white goose

Hybrid breeding has proven to enhance meat quality and is extensively utilized in goose breeding. Nevertheless, there is a paucity of research investigating the molecular mechanisms that underlie the meat quality of hybrid geese. In this study, we employed the Sichuan White Goose as the maternal line for hybridization with the Zhedong White Goose and Tianfu Meat Goose P3 line. We assessed the growth and slaughter meat quality performance of 10-wk-old hybrid offspring in comparison to Sichuan white goose purebred offspring. The results indicate that hybrid geese have significantly improved performance in growth and slaughter meat quality. Furthermore, we conducted a comprehensive analysis of the chest muscles of hybrid offspring through transcriptomics and metabolomics to unravel the effects of hybrid breeding on growth and meat quality. A total of 673 differentially expressed genes (DEGs), and 93 differentially expressed metabolites were identified. The joint analysis highlighted the significant enrichment of DEGs AMPD1, AMPD3, RRM2, ENTPD3, and the metabolite UMP in the nucleotide metabolism pathway. These findings underscore the crucial role of these genetic and metabolic factors in regulating muscle growth and meat quality in hybrid populations.

Exploration of Synergistic Regulation Mechanisms of Cerebral Ganglion and Muscle in Eriocheir sinensis Activated in Response to Alkalinity Stress

The cerebral ganglion and muscle are important regulatory tissues in Eriocheir sinensis. Therefore, it is of great significance to explore their synergistic roles in this organism's anti-stress response. In this study, proteomics, metabolomics, and combination analyses of the cerebral ganglion and muscle of E. sinensis under alkalinity stress were performed. The cerebral ganglion and muscle played a significant synergistic regulatory role in alkalinity adaptation. The key regulatory pathways involved were amino acid metabolism, energy metabolism, signal transduction, and the organismal system. They also played a modulatory role in the TCA cycle, nerve signal transduction, immune response, homeostasis maintenance, and ion channel function. In conclusion, the present study provides a theoretical reference for further research on the mechanisms regulating the growth and development of E. sinensis in saline-alkaline environments. In addition, it provides theoretical guidelines for promoting the vigorous development of the E. sinensis breeding industry in saline-alkaline environments in the future.

Exploration of the Synergistic Regulation Mechanism in Cerebral Ganglion and Heart of Eriocheir sinensis on Energy Metabolism and Antioxidant Homeostasis Maintenance under Alkalinity Stress

(1) The development and utilization of the vast saline-alkali land worldwide is an important way to solve the worsening food crisis. Eriocheir sinensis, due to its strong osmotic regulation capability and its characteristics of being suitable for culturing in alkaline water, has become a potential aquaculture species in saline-alkali water. The brain and heart are the key tissues for signal transduction and energy supply under environmental stress. (2) This study is the first to explore the synergistic regulatory molecular mechanism by integrated analysis on cerebral ganglion proteomics and heart metabolomics of Eriocheir sinensis under alkalinity stress. (3) The results indicate that the cerebral ganglion and heart of E. sinensis were closely related in response to acute alkalinity stress. The differential regulatory pathways mainly involved regulation of energy metabolism, amino acid metabolism, and homeostasis maintenance. Importantly, alkalinity stress induced the regulation of antioxidants and further adjusted longevity and rhythm in the cerebral ganglion and heart, reflecting that the cerebral ganglion and heart may be the key tissues for the survival of Eriocheir sinensis under an alkalinity environment. (4) This study provides a theoretical reference for research on the regulation mechanism of E. sinensis under alkalinity condition and contributes to the development of aquaculture in saline-alkali water.

NMR-based metabolomic signature: An important tool for the diagnosis and study of pathogenesis of autoimmune hepatitis

BACKGROUND AND AIMS

Metabolomics is used to predict, diagnose, and monitor metabolic disorders but altered metabolomic signatures have also been reported in diverse diseases, including autoimmune disorders. However, the metabolomic profile in autoimmune hepatitis (AIH) has not been investigated in depth. Therefore, we investigated the metabolomic signature of AIH and its significance as a diagnostic and pathogenetic tool.

APPROACH AND RESULTS

Metabolites in plasma samples from 50 patients with AIH at diagnosis, 43 healthy controls, 72 patients with primary biliary cholangitis (PBC), 26 patients with metabolic dysfunction-associated liver disease, and 101 patients with chronic viral hepatitis were determined by 1 H NMR (nuclear magnetic resonance) spectroscopy. Fifty-two metabolites were quantified, and metabolic pathway analysis was performed. Multivariate analysis revealed that AIH could be differentiated from healthy controls and each of the disease controls ( p <0.001). Fifteen metabolites differentiated AIH from disease controls (PBC+chronic viral hepatitis+metabolic dysfunction-associated liver disease) (95% sensitivity and 92% specificity). Ten distinct metabolic pathways were altered in AIH compared to disease controls. The metabolic pathway of branched-chain amino acids (lower valine, leucine, and isoleucine levels and their catabolic intermediates in PBC), methionine (lower methionine, 2-aminobutyrate, and 2-hydroxybutyrate levels in PBC), alanine-aspartate-glutamate (lower metabolites in PBC), and that of metabolites associated with gut microbiota (lower choline, betaine, and dimethylamine levels in PBC) were significantly different between AIH and PBC ( p <0.01).

CONCLUSIONS

1 H NMR spectroscopy could be a promising novel tool to diagnose and study AIH pathogenesis as there is no need for much sample handling, is highly reproducible with high sensitivity and specificity, and low cost.

Drying enhances the antioxidant activity of Allium mongolicum Regel through the phenylpropane and AA-MA pathway as shown by metabolomics

Fresh Allium mongolicum Regel (FA) and dried A. mongolicum Regel (DA) are significantly different in antioxidant activity. However, the relevant mechanisms have not yet been explored. We evaluated the antioxidant activities of two varieties of FA and DA and characterized their metabolites using targeted metabolomics. The effect of different metabolites on the antioxidant activity of A. mongolicum Regel was investigated by multivariate analysis. A total of 713 metabolites were detected in all samples. Pearson correlation analysis demonstrated that the key primary metabolites were directly and significantly correlated with the total phenolic content (TPC) and total flavonoid content (TFC), while the secondary metabolites were directly correlated with antioxidant activity. The higher antioxidant activity of DA may be mainly attributed to the higher TPC and TFC. This study revealed the potential mechanism by which drying enhances the antioxidant activity of A. mongolicum Regel.

Effects of Low-Salinity Stress on Histology and Metabolomics in the Intestine of Fenneropenaeus chinensis

Metabolomics has been used extensively to identify crucial molecules and biochemical effects induced by environmental factors. To understand the effects of acute low-salinity stress on Fenneropenaeus chinensis, intestinal histological examination and untargeted metabonomic analysis of F. chinensis were performed after exposure to a salinity of 15 ppt for 3, 7, and 14 d. The histological examination revealed that acute stress resulted in most epithelial cells rupturing, leading to the dispersion of nuclei in the intestinal lumen after 14 days. Metabolomics analysis identified numerous differentially expressed metabolites (DEMs) at different time points after exposure to low-salinity stress, in which some DEMs were steadily downregulated at the early stage of stress and then gradually upregulated. We further screened 14 overlapping DEMs, in which other DEMs decreased significantly during low-salinity stress, apart from L-palmitoylcarnitine and vitamin A, with enrichments in phenylalanine, tyrosine and tryptophan biosynthesis, fatty acid and retinol metabolism, and ABC transporters. ABC transporters exhibit significant abnormalities and play a vital role in low-salinity stress. This study provides valuable insights into the molecular mechanisms underlying the responses of F. chinensis to acute salinity stress.

Genome-wide profiling of WRKY genes involved in flavonoid biosynthesis in Erigeron breviscapus

The transcription factors of WRKY genes play essential roles in plant growth, stress responses, and metabolite biosynthesis. Erigeron breviscapus, a traditional Chinese herb, is abundant in flavonoids and has been used for centuries to treat cardiovascular and cerebrovascular diseases. However, the WRKY transcription factors that regulate flavonoid biosynthesis in E. breviscapus remain unknown. In this study, a total of 75 EbWRKY transcription factors were predicted through comprehensive genome-wide characterization of E. breviscapus and the chromosomal localization of each EbWRKY gene was investigated. RNA sequencing revealed transient responses of 74 predicted EbWRKY genes to exogenous abscisic acid (ABA), salicylic acid (SA), and gibberellin 3 (GA3) after 4 h of treatment. In contrast, the expression of key structural genes involved in flavonoid biosynthesis increased after 4 h in GA3 treatment. However, the content of flavonoid metabolites in leaves significantly increased at 12 h. The qRT-PCR results showed that the expression patterns of EbWRKY11, EbWRKY30, EbWRKY31, EbWRKY36, and EbWRKY44 transcription factors exhibited a high degree of similarity to the 11 structural genes involved in flavonoid biosynthesis. Protein-DNA interactions were performed between the key genes involved in scutellarin biosynthesis and candidate WRKYs. The result showed that F7GAT interacts with EbWRKY11, EbWRKY36, and EbWRKY44, while EbF6H has a self-activation function. This study provides comprehensive information on the regulatory control network of flavonoid accumulation mechanisms, offering valuable insights for breeding E. breviscapus varieties with enhanced scutellarin content.

Physiological, Biochemical, and Molecular Analyses Reveal Dark Heartwood Formation Mechanism in Acacia melanoxylon

Acacia melanoxylon is highly valued for its commercial applications, with the heartwood exhibiting a range of colors from dark to light among its various clones. The underlying mechanisms contributing to this color variation, however, have not been fully elucidated. In an effort to understand the factors that influence the development of dark heartwood, a comparative analysis was conducted on the microstructure, substance composition, differential gene expression, and metabolite profiles in the sapwood (SW), transition zone (TZ), and heartwood (HW) of two distinct clones, SR14 and SR25. A microscopic examination revealed that heartwood color variations are associated with an increased substance content within the ray parenchyma cells. A substance analysis indicated that the levels of starches, sugars, and lignin were more abundant in SP compared to HW, while the concentrations of phenols, flavonoids, and terpenoids were found to be higher in HW than in SP. Notably, the dark heartwood of the SR25 clone exhibited greater quantities of phenols and flavonoids compared to the SR14 clone, suggesting that these compounds are pivotal to the color distinction of the heartwood. An integrated analysis of transcriptome and metabolomics data uncovered a significant accumulation of sinapyl alcohol, sinapoyl aldehyde, hesperetin, 2', 3, 4, 4', 6'-peptahydroxychalcone 4'-O-glucoside, homoeriodictyol, and (2S)-liquiritigenin in the heartwood of SR25, which correlates with the up-regulated expression of CCRs (evm.TU.Chr3.1751, evm.TU.Chr4.654_667, evm.TU.Chr4.675, evm.TU.Chr4.699, and evm.TU.Chr4.704), COMTs (evm.TU.Chr13.3082, evm.TU.Chr13.3086, and evm.TU.Chr7.1411), CADs (evm.TU.Chr10.2175, evm.TU.Chr1.3453, and evm.TU.Chr8.1600), and HCTs (evm.TU.Chr4.1122, evm.TU.Chr4.1123, evm.TU.Chr8.1758, and evm.TU.Chr9.2960) in the TZ of A. melanoxylon. Furthermore, a marked differential expression of transcription factors (TFs), including MYBs, AP2/ERFs, bHLHs, bZIPs, C2H2s, and WRKYs, were observed to be closely linked to the phenols and flavonoids metabolites, highlighting the potential role of multiple TFs in regulating the biosynthesis of these metabolites and, consequently, influencing the color variation in the heartwood. This study facilitates molecular breeding for the accumulation of metabolites influencing the heartwood color in A. melanoxylon, and offers new insights into the molecular mechanisms underlying heartwood formation in woody plants.

Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems

Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.

The role of amino acid metabolism in autoimmune hepatitis

Autoimmune hepatitis (AIH) is an inflammatory chronic liver disease with persistent and recurrent immune-mediated liver injury. The exact cause of AIH is still not fully understood, but it is believed to be primarily due to an abnormal activation of the immune system, leading to autoimmune injury caused by the breakdown of autoimmune tolerance. Although the pathogenesis of AIH remains unclear, recent studies have shown that abnormalities in amino acid metabolism play significant roles in its development. These abnormalities in amino acid metabolism can lead to remodeling of metabolic processes, activation of signaling pathways, and immune responses, which may present new opportunities for clinical intervention in AIH. In this paper, we first briefly outline the recent progress of clinically relevant research on AIH, focusing on the role of specific amino acid metabolism (including glutamine, cysteine, tryptophan, branched-chain amino acids, etc.) and their associated metabolites, as well as related pathways, in the development of AIH. Furthermore, we discuss the scientific issues that remain to be resolved regarding amino acid metabolism, AIH development and related clinical interventions, with the aim of contributing to the future development of amino acid metabolism-based as a new target for the clinical diagnosis and treatment of AIH.

Multi-omics approaches for drug-response characterization in primary biliary cholangitis and autoimmune hepatitis variant syndrome

BACKGROUND

Primary biliary cholangitis (PBC) and autoimmune hepatitis (AIH) variant syndrome (VS) exhibit a complex overlap of AIH features with PBC, leading to poorer prognoses than those with PBC or AIH alone. The biomarkers associated with drug response and potential molecular mechanisms in this syndrome have not been fully elucidated.

METHODS

Whole-transcriptome sequencing was employed to discern differentially expressed (DE) RNAs within good responders (GR) and poor responders (PR) among patients with PBC/AIH VS. Subsequent gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for the identified DE RNAs. Plasma metabolomics was employed to delineate the metabolic profiles distinguishing PR and GR groups. The quantification of immune cell profiles and associated cytokines was achieved through flow cytometry and immunoassay technology. Uni- and multivariable logistic regression analyses were conducted to construct a predictive model for insufficient biochemical response. The performance of the model was assessed by computing the area under the receiver operating characteristic (AUC) curve, sensitivity, and specificity.

FINDINGS

The analysis identified 224 differentially expressed (DE) mRNAs, 189 DE long non-coding RNAs, 39 DE circular RNAs, and 63 DE microRNAs. Functional pathway analysis revealed enrichment in lipid metabolic pathways and immune response. Metabolomics disclosed dysregulated lipid metabolism and identified PC (18:2/18:2) and PC (16:0/20:3) as predictors. CD4+ T helper (Th) cells, including Th2 cells and regulatory T cells (Tregs), were upregulated in the GR group. Pro-inflammatory cytokines (IFN-γ, TNF-α, IL-9, and IL-17) were downregulated in the GR group, while anti-inflammatory cytokines (IL-10, IL-4, IL-5, and IL-22) were elevated. Regulatory networks were constructed, identifying CACNA1H and ACAA1 as target genes. A predictive model based on these indicators demonstrated an AUC of 0.986 in the primary cohort and an AUC of 0.940 in the validation cohort for predicting complete biochemical response.

CONCLUSION

A combined model integrating genomic, metabolic, and cytokinomic features demonstrated high accuracy in predicting insufficient biochemical response in patients with PBC/AIH VS. Early recognition of individuals at elevated risk for insufficient response allows for the prompt initiation of additional treatments.

Antibiotic intervention exacerbated oxidative stress and inflammatory responses in SD rats under hypobaric hypoxia exposure

The gut microbiota plays a crucial role in maintaining host nutrition, metabolism, and immune homeostasis, particularly in extreme environmental conditions. However, the regulatory mechanisms of the gut microbiota in animal organisms hypobaric hypoxia exposure require further study. We conducted a research by comparing SD rats treated with an antibiotic (ABX) cocktail and untreated SD rats that were housed in a low-pressure oxygen chamber (simulating low pressure and hypoxic environment at 6000 m altitude) for 30 days. After the experiment, blood, feces, and lung tissues from SD rats were collected for analysis of blood, 16S rRNA amplicon sequencing, and non-targeted metabolomics. The results demonstrated that the antibiotic cocktail-treated SD rats exhibited elevated counts of neutrophil (Neu) and monocyte (Mon) cells, an enrichment of sulfate-reducing bacteria (SBC), reduced levels of glutathione, and accumulated phospholipid compounds. Notably, the accumulation of phospholipid compounds, particularly lysophosphatidic acid (LPA), lipopolysaccharide (LPS), and lysophosphatidylcholine (LPC), along with the aforementioned changes, contributed to heightened oxidative stress and inflammation in the organism. In addition, we explored the resistance mechanisms of SD rats in low-oxygen and low-pressure environments and found that increasing the quantity of the Prevotellaceae and related beneficial bacteria (especially Lactobacillus) could reduce oxidative stress and inflammation. These findings offer valuable insights into enhancing the adaptability of low-altitude animals under hypobaric hypoxia exposure.

Hepatotoxicity effects of Ageratina adenophora, as indicated by network toxicology combined with metabolomics and transcriptomics

Ageratina adenophora (A. adenophora), one of the prominent invasive plants in the Asian continent has shown toxicity in animals. However, studies examining the gene expression and metabolic profiles of animals that ingest A. adenophora have not yet been reported in the literature. Therefore, considering the wide distribution of A. adenophora, it is necessary to elucidate the toxic mechanisms of A. adenophora via multiomics approach. In this study, we identified and evaluated the toxic mechanisms of action associated with bioactive compounds in A. adenophora by using network toxicology studies combined with metabolomics and transcriptomics and found that 2-deoxo-2-(acetyloxy)- 9-oxoageraphorone, 10Hβ-9-oxo-agerophorone, 10Hα-9-oxo-agerophorone, nerolidol, 9-oxo-10,11-dehydro-agerophorone were the main active toxic compounds in A. adenophora. In addition, using metabolomics approach we identified differential metabolites such as L-pyroglutamic acid, 1-methylhistidine, prostaglandin F2alpha and hydrocortisone from A. adenophora and these metabolites were involved in amino acid metabolism, lipid metabolism and signal conducting media regulation. Based on network toxicological analysis, we observed that, A. adenophora can affect the Ras signaling, Phospholipase D signaling and MAPK signaling pathways by regulating EGFR, PDGFRB, KIT and other targets. From the results of this study we concluded that A. adenophora induces liver inflammatory damage by activating the EGFR expression and Ras/Raf/MEK/ERK signaling pathways as well as affect nutrients metabolism and neuron conduction.

Plasma metabolomic profiling of patients with transient ischemic attack reveals positive role of neutrophils in ischemic tolerance

BACKGROUND

Transient ischemic attack (TIA) induces ischemic tolerance that can reduce the subsequent ischemic damage and improve prognosis of patients with stroke. However, the underlying mechanisms remain elusive. Recent advances in plasma metabolomics analysis have made it a powerful tool to investigate human pathophysiological phenotypes and mechanisms of diseases. In this study, we aimed to identify the bioactive metabolites from the plasma of patients with TIA for determination of their prophylactic and therapeutic effects on protection against cerebral ischemic stroke, and the mechanism of TIA-induced ischemic tolerance against subsequent stroke.

METHODS

Metabolomic profiling using liquid chromatography-mass spectrometry was performed to identify the TIA-induced differential bioactive metabolites in the plasma samples of 20 patients at day 1 (time for basal metabolites) and day 7 (time for established chronic ischemic tolerance-associated metabolites) after onset of TIA. Mouse middle cerebral artery occlusion (MCAO)-induced stroke model was used to verify their prophylactic and therapeutic potentials. Transcriptomics changes in circulating neutrophils of patients with TIA were determined by RNA-sequencing. Multivariate statistics and integrative analysis of metabolomics and transcriptomics were performed to elucidate the potential mechanism of TIA-induced ischemic tolerance.

FINDINGS

Plasma metabolomics analysis identified five differentially upregulated metabolites associated with potentially TIA-induced ischemic tolerance, namely all-trans 13,14 dihydroretinol (atDR), 20-carboxyleukotriene B4, prostaglandin B2, cortisol and 9-KODE. They were associated with the metabolic pathways of retinol, arachidonic acid, and neuroactive ligand-receptor interaction. Prophylactic treatment of MCAO mice with these five metabolites significantly improved neurological functions. Additionally, post-stroke treatment with atDR or 9-KODE significantly reduced the cerebral infarct size and enhanced sensorimotor functions, demonstrating the therapeutic potential of these bioactive metabolites. Mechanistically, we found in patients with TIA that these metabolites were positively correlated with circulating neutrophil counts. Integrative analysis of plasma metabolomics and neutrophil transcriptomics further revealed that TIA-induced metabolites are significantly correlated with specific gene expression in circulating neutrophils which showed prominent enrichment in FoxO signaling pathway and upregulation of the anti-inflammatory cytokine IL-10. Finally, we demonstrated that the protective effect of atDR-pretreatment on MCAO mice was abolished when circulating neutrophils were depleted.

INTERPRETATION

TIA-induced potential ischemic tolerance is associated with upregulation of plasma bioactive metabolites which can protect against cerebral ischemic damage and improve neurological functions through a positive role of circulating neutrophils.

FUNDING

National Natural Science Foundation of China (81974210), Science and Technology Planning Project of Guangdong Province, China (2020A0505100045), Natural Science Foundation of Guangdong Province (2019A1515010671), Science and Technology Program of Guangzhou, China (2023A03J0577), and Natural Science Foundation of Jiangxi, China（20224BAB216043).

Alteration of Gut Microbiota in Individuals at High-Risk for Rheumatoid Arthritis Associated With Disturbed Metabolome and the Initiation of Arthritis Through the Triggering of Mucosal Immunity Imbalance

OBJECTIVE

In this study, we aimed to decipher the gut microbiome (GM) and serum metabolic characteristic of individuals at high risk for rheumatoid arthritis (RA) and to investigate the causative effect of GM on the mucosal immune system and its involvement in the pathogenesis of arthritis.

METHODS

Fecal samples were collected from 38 healthy individuals and 53 high-risk RA individuals with anti-citrullinated protein antibody (ACPA) positivity (Pre-RA), 12 of 53 Pre-RA individuals developed RA within 5 years of follow-up. The differences in intestinal microbial composition between the healthy controls and Pre-RA individuals or among Pre-RA subgroups were identified by 16S ribosomal RNA sequencing. The serum metabolite profile and its correlation with GM were also explored. Moreover, antibiotic-pretreated mice that received GM from the healthy control or Pre-RA groups were then evaluated for intestinal permeability, inflammatory cytokines, and immune cell populations. Collagen-induced arthritis (CIA) was also applied to test the effect of fecal microbiota transplantation (FMT) from Pre-RA individuals on arthritis severity in mice.

RESULTS

Stool microbial diversity was lower in Pre-RA individuals than in healthy controls. The bacterial community structure and function significantly differed between healthy controls and Pre-RA individuals. Although there were differences to some extent in the bacterial abundance among the Pre-RA subgroups, no robust functional differences were observed. The metabolites in the serum of the Pre-RA group were dramatically different from those in the healthy controls group, with KEGG pathway enrichment of amino acid and lipid metabolism. Moreover, intestinal bacteria from the Pre-RA group increased intestinal permeability in FMT mice and zonula occludens-1 expression in the small intestine and Caco-2 cells. Moreover, Th17 cells in the mesenteric lymph nodes and Peyer's patches were also increased in mice receiving Pre-RA feces compared to healthy controls. The changes in intestinal permeability and Th17-cell activation prior to arthritis induction enhanced CIA severity in PreRA-FMT mice compared with HC-FMT mice.

CONCLUSION

Gut microbial dysbiosis and metabolome alterations already occur in individuals at high risk for RA. FMT from preclinical individuals triggers intestinal barrier dysfunction and changes mucosal immunity, further contributing to the development of arthritis.

Alteration of Meibum Lipidomics Profiling in Patients With Chronic Ocular Graft-Versus-Host Disease

Purpose

To investigate the characteristics of the lipid profiling in meibum of patients with chronic ocular graft-versus-host disease (coGVHD) and to detect the potential influence of anti-inflammatory therapy on these differential lipids.

Methods

This cross-sectional study included 25 coGVHD patients and 13 non-coGVHD after allogeneic hematopoietic stem cell transplantation. Among those with coGVHD, 14 had prior topical treatment (coGVHD(T)), and 11 did not (coGVHD(WT)). All participants completed ocular surface disease index questionnaire and received slit lamp examination, Schirmer's test without anesthesia, ocular surface interferometer, and meibography. Binocular meibum was collected and pooled for lipidomic analysis by liquid chromatography-mass spectrometry.

Results

One hundred and twenty differential lipid species were found among the three groups (96 of coGVHD(WT) vs. non-coGVHD, 78 of coGVHD(WT) vs. coGVHD(T), and three of non-coGVHD vs. coGVHD(T)). Compared with non-coGVHD group, coGVHD(WT) group had a significant abnormality of meibum composition, showing a significant decrease in glycerolipids, and an increase in glycerophospholipids and sphingolipids. Similar changes were also observed when coGVHD(WT) versus coGVHD(T). CoGVHD severity was negatively associated with mono-unsaturated triglycerides (TG), (β = -214.7; 95% CI, -363.9 to -65.5; P = 0.006) and poly-unsaturated TG (β = -4019.9; 95% CI, -7758.1 to -281.6; P = 0.036). Intensity of immunosuppression was negatively associated with mono-unsaturated TG (β = -162.4; 95% CI, -268.6 to -56.2; P = 0.004) and positively associated with phosphatidylcholine (β = 332.0; 95% CI, 19.2-644.8; P = 0.038).

Conclusions

Altered meibum in coGVHD is characterized by a decrease of glycerolipids and an increase of glycerophospholipids and may be significantly reversed by topical anti-inflammatory therapy.

Differences in body wall metabolites of Apostichopus japonicus of different ages in liquid chromatography-tandem mass spectrometry

Apostichopus japonicus is a marine invertebrate with high economic value. Analysis of the effects of age on the structure of this species is important for understanding the status of the population and conservation. In this study, metabolite analysis of the body walls of A. japonicus of three different ages (1, 2, and 3 years) was performed using LC-MS/MS. Metabolite analysis was performed for the KEGG metabolic pathway. The partial least squares-discriminant analysis is clearly distinguished metabolites in the three groups of A. japonicus. A total of 59, 222, and 179 different metabolites were detected in the age 3 vs age 2, age 3 vs age 1, and age 2 vs age 1 controls, respectively (P < 0.05). These metabolic differences involved several metabolic pathways, including phenylalanine metabolism, taurine and hypotaurine metabolism, sulfur metabolism et al. Thiamin, riboflavin, lipoic acid, acetyl l-carnitine levels increase with age, trans-10-heptadecenoic acid, stearic acid, pentadecanoic acid, dibutyl sebacate, and 8,15-diHETE levels decrease with age, which these metabolites can be used as potential markers to determine the age of A. japonicus. Our results provide the foundation for determining the age of A. japonicus and are important for the conservation of germplasm resources of A. japonicus.

Metabolite Alterations in Autoimmune Diseases: A Systematic Review of Metabolomics Studies

Autoimmune diseases, characterized by the immune system's loss of self-tolerance, lack definitive diagnostic tests, necessitating the search for reliable biomarkers. This systematic review aims to identify common metabolite changes across multiple autoimmune diseases. Following PRISMA guidelines, we conducted a systematic literature review by searching MEDLINE, ScienceDirect, Google Scholar, PubMed, and Scopus (Elsevier) using keywords "Metabolomics", "Autoimmune diseases", and "Metabolic changes". Articles published in English up to March 2023 were included without a specific start date filter. Among 257 studies searched, 88 full-text articles met the inclusion criteria. The included articles were categorized based on analyzed biological fluids: 33 on serum, 21 on plasma, 15 on feces, 7 on urine, and 12 on other biological fluids. Each study presented different metabolites with indications of up-regulation or down-regulation when available. The current study's findings suggest that amino acid metabolism may serve as a diagnostic biomarker for autoimmune diseases, particularly in systemic lupus erythematosus (SLE), multiple sclerosis (MS), and Crohn's disease (CD). While other metabolic alterations were reported, it implies that autoimmune disorders trigger multi-metabolite changes rather than singular alterations. These shifts could be consequential outcomes of autoimmune disorders, representing a more complex interplay. Further studies are needed to validate the metabolomics findings associated with autoimmune diseases.

Real-ambient particulate matter exposure-induced FGFR1 methylation contributes to cardiac dysfunction via lipid metabolism disruption

Particulate matter (PM)-induced cardiometabolic disorder contributes to the progression of cardiac diseases, but its epigenetic mechanisms are largely unknown. This study used bioinformatic analysis, in vivo and in vitro multiple models to investigate the role of PM-induced cardiac fibroblast growth factor 1 (FGFR1) methylation and its impact on cardiomyocyte lipid metabolic disruption. Bioinformatic analysis revealed that FGFR1 was associated with cardiac pathologies, mitochondrial function and metabolism, supporting the possibility that FGFR1 may play regulatory roles in PM-induced cardiac functional impairment and lipid metabolism disorders. Individually ventilated cage (IVC)-based real-ambient PM exposure system mouse models were used to expose C57/BL6 mice for six and fifteen weeks. The results showed that PM induced cardiac lipid metabolism disorder, DNA nucleotide methyltransferases (DNMTs) alterations and FGFR1 expression declines in mouse heart. Lipidomics analysis revealed that carnitines, phosphoglycerides and lysophosphoglycerides were most significantly affected by PM exposure. At the cellular level, AC16 cells treated with FGFR1 inhibitor (PD173074) led to impaired mitochondrial and metabolic functions in cardiomyocytes. Inhibition of DNA methylation in cells by 5-AZA partially restored the FGFR1 expression, ameliorated cardiomyocyte injury and mitochondrial functions. These changes involved alterations in AMP-activated protein kinase (AMPK)-peroxisome proliferator activated receptors gamma, coactivator 1 alpha (PGC1α) pathways. Bisulfite sequencing PCR (BSP) and DNA methylation specific PCR (MSP) confirmed that PM exposure induced FGFR1 gene promoter region methylation. These results suggested that, by inducing FGFR1 methylation, PM exposure would affect cardiac injury and deranged lipid metabolism. Overexpression of FGFR1 in mouse heart using adeno-associated virus 9 (AAV9) effectively alleviated PM-induced cardiac impairment and metabolic disorder. Our findings identified that FGFR1 methylation might be one of the potential indicators for PM-induced cardiac mitochondrial and metabolic dysfunction, providing novel insights into underlying PM-related cardiotoxic mechanisms.

Metabolomics and Transcriptomics Reveal the Response Mechanisms of Mikania micrantha to Puccinia spegazzinii Infection

Mikania micrantha is one of the 100 worst invasive species globally and can cause significant negative impacts on agricultural and forestry economics, particularly in Asia and the Pacific region. The rust Puccinia spegazzinii has been used successfully as a biological control agent in several countries to help manage M. micrantha. However, the response mechanisms of M. micrantha to P. spegazzinii infection have never been studied. To investigate the response of M. micrantha to infection by P. spegazzinii, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 74 metabolites, including organic acids, amino acids, and secondary metabolites in M. micrantha infected with P. spegazzinii, were significantly different compared to those in plants that were not infected. After P. spegazzinii infection, the expression of the TCA cycle gene was significantly induced to participate in energy biosynthesis and produce more ATP. The content of most amino acids, such as L-isoleucine, L-tryptophan and L-citrulline, increased. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid, and JA-Ile, accumulated in M. micrantha. A total of 4978 differentially expressed genes were identified in M. micrantha infected by P. spegazzinii. Many key genes of M. micrantha in the PTI (pattern-triggered immunity) and ETI (effector-triggered immunity) pathways showed significantly higher expression under P. spegazzinii infection. Through these reactions, M. micrantha is able to resist the infection of P. spegazzinii and maintain its growth. These results are helpful for us to understand the changes in metabolites and gene expression in M. micrantha after being infected by P. spegazzinii. Our results can provide a theoretical basis for weakening the defense response of M. micrantha to P. spegazzinii, and for P. spegazzinii as a long-term biological control agent of M. micrantha.

Autoimmune serology testing in clinical practice: An updated roadmap for the diagnosis of autoimmune hepatitis

Diagnosis of autoimmune hepatitis (AIH) is in most cases challenging for clinicians as there is not a single specific laboratory or histological marker to diagnose or exclude the presence of the disease. The clinical spectrum of AIH varies from completely asymptomatic to acute-severe or even rarely fulminant hepatic failure, while everybody can be affected irrespective of age, gender, and ethnicity. The old revised and the newer simplified diagnostic scores have been established by the International Autoimmune Hepatitis Group (IAIHG) in 1999 and 2008, respectively, which are based on several clinical, laboratory and histological parameters. Additionally, a thorough differential diagnosis from other diseases mimicking AIH is absolutely indicated. In this context, autoantibodies detection in patients with suspected AIH is mandatory -even though not pathognomonic- not only for AIH diagnosis but furthermore, for AIH classification (AIH-type 1 and AIH-type 2). Although autoimmune serology can be supportive of AIH diagnosis in ≥95% of cases if testing has been performed according to the IAIHG guidelines, this is not the case under real-life circumstances in routine clinical laboratories. Clinicians should be careful both for the importance of the required testing and how to interpret the results and therefore, they should communicate and discuss with the laboratory personnel to achieve the maximum benefit for the patient. Herein, a detailed and updated review of the diagnostic work-up for AIH diagnosis under real-life conditions is given to minimize the underestimation and misdiagnosis of AIH which can result in progression of the disease and unfavourable outcomes.

The DNA adenine methylase of Salmonella Enteritidis promotes their intracellular replication by inhibiting arachidonic acid metabolism pathway in macrophages

Macrophages can participate in immune responses by altering their metabolism, and play important roles in controlling bacterial infections. However, Salmonella Enteritidis can survive and proliferate in macrophages. After the deletion of DNA adenine methylase (Dam), the proliferation of Salmonella Enteritidis in macrophages decreased, the molecular mechanism is still unclear. After infecting macrophages with Salmonella Enteritidis wild type and dam gene deletion strains, intracellular metabolites were extracted and detected by non-targeted metabolomics and fatty acid targeted metabolomics. We found Dam had significant effects on arachidonic acid and related metabolic pathways in macrophages. The dam gene can promote the proliferation of Salmonella Enteritidis in macrophages by inhibiting the metabolic pathway of cytosolic phospholipase A2-mediated arachidonic acid production and conversion to prostaglandin E2 in macrophages, reducing the secretion of the pro-inflammatory factors IL-1β and IL-6. In addition, inhibition of arachidonic acid-related pathways in macrophages by Arachidonyl trifluoromethyl ketone could restore the proliferation of dam gene deletion strains in macrophages. This study explored the role of Dam in the process of Salmonella Enteritidis invading host cells from the perspective of host cell metabolism, and provides new insights into the immune escape mechanism of Salmonella Enteritidis.

Low-dose florfenicol and copper combined exposure during early life induced health risks by affecting gut microbiota and metabolome in SD rats

The potential health risks associated with simultaneous presence of residues of heavy metals and antibiotics in the environment and food have been of wide concern. However, the adverse health effects of combined heavy metal and antibiotic exposure at low doses remain unclear. In this study, the effects of combined exposure to florfenicol and copper at low doses during early life on toxicity, gut microbiota, drug resistance genes, and the fecal metabolome were investigated in Sprague-Dawley (SD) rats. The results showed that combined exposure induced inflammatory responses and visceral injury as well as faster weight gain compared with florfenicol or copper exposure alone. Alpha and beta diversity indices indicated that the composition of the gut microbiota and the abundance of bacteria related to energy intake and disease in the combined exposure group were significantly altered. The increase in resistance genes (floR, fexA) induced by florfenicol exposure was suppressed under combined exposure to florfenicol and copper. The fecal metabolome also demonstrated that metabolic pathways related to energy intake and liver injury were significantly affected in the combined exposure group. In conclusion, this study shows that combined exposure to florfenicol and copper during early life can pose a nonnegligible health risk even if the exposure concentration of florfenicol or copper is below the safe limit.

Colchicine increases intestinal toxic load by disturbing fecal metabolome homeostasis in mice

Colchicine (COL) has been used to treat gout for over a millennium, but its medicinal use has been controversial due to its potent toxicity in the gastrointestinal tract. Nausea, vomiting, and diarrhea are the most prominent external manifestations of COL gastrointestinal toxicity, but the cause of these adverse events remains obscure. In this study, the mice were exposed to COL (2.5 mg/kg b.w./day) for one week to study the mechanism of COL-induced diarrhea from the perspective of intestinal metabolism. The results showed that COL exposure disturbed intestinal metabolic homeostasis, resulting in a significant accumulation of 116 metabolites and, conversely, significant depletion of 64 metabolites, with the number of differential metabolites being one-eighth of the total metabolites (180/1445). Also, it was found that cAMP, Adenosine 5'-monophosphate, GDP, Inositol, and Cortisol are core metabolites that play crucial roles in COL-induced metabolic disorders. These metabolites could be used as biomarkers to differentiate control and COL-treated groups, implying that these metabolites may be closely related to COL-induced diarrhea. Furthermore, changes in the metabolic pathways (Purine metabolism, biosynthesis and metabolism of aromatic amino acids, and Bile secretion) involved in these five core metabolites increased the toxic load in the gut, which was the culprit leading to intestinal metabolic disorders. In addition, the abnormal bile secretion caused by COL exposure may play an important role in COL-induced diarrhea. In conclusion, our study opens new avenues for understanding the mechanisms of COL-induced gastrointestinal adverse reactions and broadens the scientific horizon on the interactions between COL and host metabolism.

Metabolomic Analysis and MRM Verification of Coarse and Fine Skin Tissues of Liaoning Cashmere Goat

One of the critical elements in evaluating the quality of cashmere is its fineness, but we still know little about how it is regulated at the metabolic level. In this paper, we use UHPLC–MS/MS detection and analysis technology to compare the difference in metabolites between coarse cashmere (CT_LCG) and fine cashmere (FT_LCG) skin of Liaoning cashmere goats. According to the data, under positive mode four metabolites were significantly up-regulated and seven were significantly down-regulated. In negative mode, seven metabolites were significantly up-regulated and fourteen metabolites were significantly down-regulated. The two groups’ most significant metabolites, Gly–Phe and taurochenodeoxycholate, may be crucial in controlling cashmere’s growth, development, and fineness. In addition, we enriched six KEGG pathways, of which cholesterol metabolism, primary bile acid biosynthesis, and bile secretion were enriched in positive and negative modes. These findings offer a new research idea for further study into the critical elements influencing cashmere’s fineness.

Chemokines in Primary Liver Cancer

The liver is responsible for extremely important functions in the human body. In the liver’s structure, we distinguish between connective tissue (stroma) and parenchyma, the latter of which is formed from the basic structural and functional units of the liver—hepatocytes. There are many factors, that negatively affect the liver cells, contributing to their damage. This may lead to fibrosis, liver failure and, in consequence, primary liver cancer, which is the sixth most commonly diagnosed malignancy and the fourth leading cause of cancer death worldwide. Chemokines are a large family of secreted proteins. Their main role is to direct the recruitment and migration of cells to sites of inflammation or injury. Some authors suggest that these proteins might play a potential role in the development of many malignancies, including primary liver cancer. The aim of this study was to evaluate and summarize the knowledge regarding liver diseases, especially primary liver cancer (HCC) and the participation of chemokines in the development of this malignancy. Chemokines involved in the initiation of this type of tumor belong mainly to the CC and CXC chemokines. Their significant role in the course of hepatocellular carcinoma proves their usefulness in detecting and monitoring the course and treatment in patients with this disease.

Hypertension of liver-yang hyperactivity syndrome induced by a high salt diet by altering components of the gut microbiota associated with the glutamate/GABA-glutamine cycle

The gut microbiota and metabolites are closely related to hypertension; however, the changes in the composition of the gut microbiome and metabolites linking a high salt diet to elevated blood pressure are not established. In this study, traditional Chinese medicine (TCM) syndrome of hypertension caused by high salt had been diagnosed and the pathogenesis of hypertension was explored from the perspective of intestinal microecology. Rats in a high salt diet-induced hypertension group (CG) and normal group (CZ) were compared by 16S rRNA gene full-length sequencing and liquid chromatography and mass spectrometry to identify differences in the bacterial community structure, metabolites, and metabolic pathways. Hypertension induced by a high salt diet belongs to liver-Yang hyperactivity syndrome. Alpha and beta diversity as well as the composition of microbiota from the phylum to species levels differed substantially between the CG and CZ groups. In an analysis of differential metabolites in the intestines, a high salt diet mainly affected the metabolism of amino acids and their derivatives; in particular, γ-aminobutyric acid (GABA) was down-regulated and glutamic acid and its derivatives were up-regulated under a high salt diet. Based on a KEGG analysis, high salt intake mainly altered pathways related to GABA and the glutamate/glutamine metabolism, such as the GABAergic synapse pathway and glutamatergic synapse pathway. The correlation analysis of differential gut microbes and differential metabolites suggested that a high salt diet promoted hypertension via the inhibition of Clostridiaceae_1 growth and alterations in the GABA metabolic pathway, leading to increased blood pressure. These findings suggest that a high salt diet induces hypertension of liver-Yang hyperactivity syndrome by mediating the microbiota associated with the glutamate/GABA-glutamine metabolic cycle via the gut-brain axis.

The Effects of NAA on the Tuberous Root Yield and Quality of Rehmannia glutinosa and Its Regulatory Mechanism by Transcriptome and Metabolome Profiling

Naphthylacetic acid (NAA) was used to increase the tuberous root yield of Rehmannia glutinosa, but the differences between its NAA-treated and control tuberous roots (NT and CG) and the regulatory mechanism of NAA effect remain unclear. In order to investigate them, NTs and CGs were used as materials, and both yield-related indices were measured; the metabolomics and transcriptomics were used to capture differentially accumulated metabolites (DAM) and to validate them via mining differentially expressed genes (DEGs), respectively. The effects of NAA treatment: increased NT mass per plant by 21.14%, through increasing the number of roots and increasing the mean root diameter; increased catalpol content by 1.2234% (p < 0.05); up-regulated 11DAMs and 596DEGs; and down-regulated 18 DAMs and 517DEGs. In particular, we discovered that NAA regulated its DAMs and biomass via 10 common metabolic pathways, and that the number of NAA-down-regulated DAMs was more than that of NAA-up-regulated DAMs in its tuberous root. Furthermore, HPLC validated the changes of several DAMs and 15 DEGs (4CL, ARF, CCoAOMT, ARGOS, etc.) associated with the yield increase and DAMs were verified by RT-qPCR. This study provided some valuable resources, such as tuberous root indices, key genes, and DAMs of Rehmannia glutinosa in response to NAA for distinguishing the CGs from NTs, and novel insights into the regulatory mechanism of NAA effects on both at the transcriptomic and metabolomic levels, so it will lay a theoretical foundation for NAA-regulated plant yield and quality, and provide references for prohibiting the uses of NAA as a swelling agent in medicinal tuber plants in China.

Comparative Metabolomics and Proteomics Reveal Vibrio parahaemolyticus Targets Hypoxia-Related Signaling Pathways of Takifugu obscurus

Coronavirus disease 2019 (COVID-19) raises the issue of how hypoxia destroys normal physiological function and host immunity against pathogens. However, there are few or no comprehensive omics studies on this effect. From an evolutionary perspective, animals living in complex and changeable marine environments might develop signaling pathways to address bacterial threats under hypoxia. In this study, the ancient genomic model animal Takifugu obscurus and widespread Vibrio parahaemolyticus were utilized to study the effect. T. obscurus was challenged by V. parahaemolyticus or (and) exposed to hypoxia. The effects of hypoxia and infection were identified, and a theoretical model of the host critical signaling pathway in response to hypoxia and infection was defined by methods of comparative metabolomics and proteomics on the entire liver. The changing trends of some differential metabolites and proteins under hypoxia, infection or double stressors were consistent. The model includes transforming growth factor-β1 (TGF-β1), hypoxia-inducible factor-1α (HIF-1α), and epidermal growth factor (EGF) signaling pathways, and the consistent changing trends indicated that the host liver tended toward cell proliferation. Hypoxia and infection caused tissue damage and fibrosis in the portal area of the liver, which may be related to TGF-β1 signal transduction. We propose that LRG (leucine-rich alpha-2-glycoprotein) is widely involved in the transition of the TGF-β1/Smad signaling pathway in response to hypoxia and pathogenic infection in vertebrates as a conserved molecule.

Artesunate attenuates atherosclerosis by inhibiting macrophage M1-like polarization and improving metabolism

OBJECT

Atherosclerosis (AS) is caused by chronic inflammation. Artesunate (ART), a sesquiterpene lactone endoperoxide isolated from Chinese herbal medicine, displays excellent anti-inflammatory activity. In this study, we investigated the effects of artesunate on atherosclerosis in ApoE knock-out mice, and used untargeted metabolomics to determine metabolite changes in these mice following ART treatment.

METHODS

ApoE knock-out mice were fed a western diet and administered ART for eight weeks. Untargeted metabolomics was used to detect differential metabolites following the administration of ART. Oil Red O was used to assess plaque size, western blot and ELISA were used to detect inflammatory factors, and flow cytometry was used to detect the expression of markers on macrophages.

RESULTS

Results of the in vivo experiment suggested that ART reduced atherosclerotic plaques in murine aortic root. In addition both in vivo and vitro experiments suggested that ART reduced the expression levels of inflammating cytokines, but enhanced those of the anti-inflammatory cytokines in macrophages. Untargeted metabolomic analysis demonstrated that multiple metabolic pathways, which were blocked in AS mice, showed different degrees of improvement following ART treatment. Furthermore, bioinformatic analyses showed that the HIF-1α pathway was altered in the AS mice and the ART treatment mice. In vitro experiments confirmed that LPS-induced upregulation of HIF-1α expression and activation of the NF-κB signaling pathways was significantly inhibited by ART treatment.

CONCLUSION

These results suggest that ART exerts anti-atherosclerosis effects by inhibiting M1 macrophage polarization. One of the molecular mechanisms is that ART inhibits M1-like macrophage polarization via regulating HIF-1α and NF-κB signaling pathways.

Metabolomics of Spleen-Yang deficiency syndrome and the therapeutic effect of Fuzi Lizhong pill on regulating endogenous metabolism

ETHNOPHARMACOLOGICAL RELEVANCE

Spleen-Yang deficiency (SYD) is one of the primary causes of many digestive diseases, such as ulcerative colitis (UC), and irritable bowel syndrome (IBS), but its endogenous metabolic characteristics are still unclear. Fuzi Lizhong pill (FLZP) is well-known for its powerful capacity for treating SYD; however, its mechanisms require further study.

AIM OF THE STUDY

Herein, our present study aimed to investigate the essence of SYD from the perspective of metabolomics, and tried to reveal the anti-SYD action mechanisms of FLZP.

MATERIALS AND METHODS

Firstly, the compound factor modeling method with the principle of "indiscipline in diet + excessive fatigue + intragastric administration of Senna water extracts" was used to establish Sprague Dawley (SD) rats as SYD model. Then, the visceral index, motilin (MTL), malonaldehyde (MDA), Interleukin 1 alpha (IL-1α), and Interleukin 6 (IL-6) levels were used to verify the anti-SYD effect of FLZP. In addition, serum samples were analyzed by UPLC-QE/MS metabolomics technique. Finally, the metabolic pathways associated with specific biomarkers were analyzed to research the possible mechanism underlying the action of FLZP.

RESULTS

The expression of MTL, MDA, IL-1α, and IL-6 were regulated by FLZP, which suggested that it has relieved diarrhea and gastrointestinal motility disorder caused by SYD and had an anti-peroxidation, anti-inflammatory, and immune regulation effect. A total of 75 metabolites were found to be the potential biomarkers of SYD. Moreover, FLZP regulates 21 metabolites and 10 vital pathways including the tricarboxylic acid (TCA) cycle, sphingolipid metabolism, and histidine metabolism.

CONCLUSION

SYD primarily causes disorders of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, nucleotide metabolism, and translation. In addition, FLZP regulated carbohydrate, lipid, and amino acid metabolisms, gastrointestinal motility, digestive juice secretion, immune regulation, as well as antioxidant effects. Hence, FLZP had a good therapeutic effect on treatment of SYD. It might be a promising therapeutic agent for the treatment of SYD-related diseases.

Identification of Key Volatiles Differentiating Aromatic Rice Cultivars Using an Untargeted Metabolomics Approach

Non-aromatic rice is often sold at the price of aromatic rice to increase profits, seriously impairing consumer experience and brand credibility. The assessment of rice varieties origins in terms of their aroma traits is of great interest to protect consumers from fraud. To address this issue, the study identified differentially abundant metabolites between non-aromatic rice varieties and each of the three most popular aromatic rice varieties in the market using an untargeted metabolomics approach. The 656 metabolites of five rice grain varieties were determined by headspace solid-phase extraction gas chromatography-mass spectrometry, and the multivariate analyses were used to identify differences in metabolites among rice varieties. The metabolites most differentially abundant between Daohuaxiang 2 and non-aromatic rice included 2-acetyl-1-pyrroline and acetoin; the metabolites most differentially abundant between Meixiangzhan 2 and non-aromatic rice included acetoin and 2-methyloctylbenzene,; and the metabolites most differentially abundant between Yexiangyoulisi and non-aromatic rice included bicyclo[4.4.0]dec,1-ene-2-isopropyl-5-methyl-9-methylene and 2-methylfuran. Overall, acetoin was the metabolite that was most differentially abundant between the aromatic and non-aromatic rice. This study provides direct evidence of the outstanding advantages of aromatic rice and acts a reference for future rice authentication processes in the marketplace.

Serum Metabolomic Analysis of Chronic Drug-Induced Liver Injury With or Without Cirrhosis

Background: Chronic drug-induced liver injury (DILI) occurs in up to 20% of all DILI patients. It presents a chronic pattern with persistent or relapsed episodes and may even progress to cirrhosis. However, its underlying development mechanism is poorly understood. Aims: To find serum metabolite signatures of chronic DILI with or without cirrhosis, and to elucidate the underlying mechanism. Methods: Untargeted metabolomics coupled with pattern recognition approaches were used to profile and extract metabolite signatures from 83 chronic DILI patients, including 58 non-cirrhosis (NC) cases, 14 compensated cirrhosis (CC) cases, and 11 decompensated cirrhosis (DC) cases. Results: Of the 269 annotated metabolites associated with chronic DILI, metabolic fingerprints associated with cirrhosis (including 30 metabolites) and decompensation (including 25 metabolites), were identified. There was a significantly positive correlation between cirrhosis-associated fingerprint (eigenmetabolite) and the aspartate aminotransferase-to-platelet ratio index (APRI) (r = 0.315, P = 0.003). The efficacy of cirrhosis-associated eigenmetabolite coupled with APRI to identify cirrhosis from non-cirrhosis patients was significantly better than APRI alone [area under the curve (AUC) value 0.914 vs. 0.573]. The decompensation-associated fingerprint (eigenmetabolite) can effectively identify the compensation and decompensation periods (AUC value 0.954). The results of the metabolic fingerprint pathway analysis suggest that the blocked tricarboxylic acid cycle (TCA cycle) and intermediary metabolism, excessive accumulation of bile acids, and perturbed amino acid metabolism are potential mechanisms in the occurrence and development of chronic DILI-associated cirrhosis. Conclusions: The metabolomic fingerprints characterize different stages of chronic DILI progression and deepen the understanding of the metabolic reprogramming mechanism of chronic DILI progression to cirrhosis.

Metabolomic Signatures of Autoimmune Hepatitis in the Development of Cirrhosis

Objectives: Autoimmune hepatitis (AIH) can progress into severe outcomes, i.e., decompensated cirrhosis, from remarkable and persistent inflammation in the liver. Considering the energy-expending nature of inflammation, we tried to define the metabolomics signatures of AIH to uncover the underlying mechanisms of cirrhosis development and its metabolic biomarkers. Methods: Untargeted metabolomics analysis was performed on sera samples from 79 AIH patients at the stages (phenotypes) of non-cirrhosis (n = 27), compensated cirrhosis (n = 22), and decompensated cirrhosis (n = 30). Pattern recognition was used to find unique metabolite fingerprints of cirrhosis with or without decompensation. Results: Out of the 294 annotated metabolites identified, 2 metabolic fingerprints were found associated with the development of cirrhosis (independent of the decompensated state, 42 metabolites) and the evolution of decompensated cirrhosis (out of 47 metabolites), respectively. The cirrhosis-associated fingerprints (eigenmetabolite) showed better capability to differentiate cirrhosis from non-cirrhosis patients than the aminotransferase-to-platelet ratio index. From the metabolic fingerprints, we found two pairs of metabolites (Mesobilirubinogen/6-Hydroxynicotinic acid and LysoPA(8:0/0:0)/7alpha-Hydroxycholesterol) calculated as ratio of intensities, which revealed robust abilities to identify cirrhosis or predict decompensated patients, respectively. These phenotype-related fingerprint metabolites featured fundamental energy supply disturbance along with the development of AIH cirrhosis and progression to decompensation, which was characterized as increased lipolysis, enhanced proteolysis, and increased glycolysis. Conclusions: Remodeling of metabolism to meet the liver inflammation-related energy supply is one of the key signatures of AIH in the development of cirrhosis and decompensation. Therefore, drug regulation metabolism has great potential in the treatment of AIH.

Novel approaches to liver disease diagnosis and modeling

Lack of a prompt and accurate diagnosis remains on top of the list of challenges faced by patients with rare liver diseases. Although rare liver diseases affect a significant percentage of the population as a group, when taken singularly they represent unique diseases and the approaches used for diagnosis of common liver diseases are insufficient. However, the development of new methods for the acquisition of molecular and clinical data (i.e., genomic, proteomics, metabolomics) and computational tools for their analysis and integration, together with advances in modeling diseases using stem cell-based technology [i.e., induced pluripotent stem cells (iPSCs) and tissue organoids] represent a promising and powerful tool to improve the clinical management of these patients. This is the goal of precision medicine, a novel approach of modern medicine that aims at delivering a specific treatment based on disease-specific biological insights and individual profile. This review will discuss the application and advances of these technologies and how they represent a new opportunity in hepatology.

Metabolomics Profiling and Diagnosis Biomarkers Searching for Drug-Induced Liver Injury Implicated to Polygonum multiflorum: A Cross-Sectional Cohort Study

Aim: The diagnosis of drug-induced liver injury (DILI) remains a challenge and the cases of Polygonum multiflorum Thunb. (PM) induced DILI (PM-DILI) have received much attention This study aimed to identify a simple and high-efficiency approach to PM-DILI diagnosis via metabolomics analysis.

Methods: Plasma metabolites in 13 PM-DILI patients were profiled by liquid chromatography along with high-resolution mass spectrometry. Meanwhile, the metabolic characteristics of the PM-DILI were compared with that of autoimmune hepatitis (AIH), hepatitis B (HBV), and healthy volunteers.

Results: Twenty-four metabolites were identified to present significantly different levels in PM-DILI patients compared with HBV and AIH groups. These metabolites were enriched into glucose, amino acids, and sphingolipids metabolisms. Among these essential metabolites, the ratios of P-cresol sulfate vs. phenylalanine and inosine vs. bilirubin were further selected using a stepwise decision tree to construct a classification model in order to differentiate PM-DILI from HBV and AIH. The model was highly effective with sensitivity of 92.3% and specificity of 88.9%.

Conclusions: This study presents an integrated view of the metabolic features of PM-DILI induced by herbal medicine, and the four-metabolite decision tree technique imparts a potent tool in clinical diagnosis.

Metabolic Alterations in the Outer Membrane Vesicles of Patients with Alzheimer's Disease: An LC-MS/MS-based Metabolomics Analysis

OBJECTIVE

To characterize the specific metabolomics profiles in the outer membrane vesicles (OMVs) of patients with Alzheimer's Disease (AD) and to explore potential metabolic biomarkers and their diagnostic roles.

METHODS

Nine AD patients and age- and sex-matched healthy controls were enrolled, and feces were collected. OMVs were extracted, purified, and then analyzed using liquid chromatography-tandem mass chromatography (LC-MS/MS) method coupled with a series of multivariate statistical analyses.

RESULTS

Remarkable differences were found between the OMVs from AD patients and those from healthy controls. A number of differential metabolites and several top-altered metabolic pathways were identified. The levels of aspartate, L-aspartate, imidazole-4-acetate and L-glutamate were confirmed to be highly upregulated in AD-OMVs. Other differential metabolites, such as arachidic acid, prostaglandin G2, and leukotriene B4, were also identified. Furthermore, the differential metabolites possessed higher areas under the ROC curve (AUCs).

CONCLUSION

Metabolic activity is significantly altered in the OMVs from AD patients. This data might be helpful for identifying novel biomarkers and their diagnostic roles in AD. Furthermore, OMVs metabolomics analysis combined with GWAS could enrich our understanding of the genetic spectrum of AD and lead to early predictions and diagnosis and clinical applications of better AD treatments.

Exploration of anti-inflammatory mechanism of forsythiaside A and forsythiaside B in CuSO4-induced inflammation in zebrafish by metabolomic and proteomic analyses

BACKGROUND

Inflammation is a general pathological phenomenon during severe disturbances to the homeostasis. Forsythiaside A (FA) and forsythiaside B (FB), isolated from the dried fruit of Forsythia suspensa (Thunb.) Vahl, are phenylethanoid compounds that show a significant anti-inflammatory effect. However, the properties and therapeutic mechanisms of this effect have not yet been systematically elucidated.

METHODS

In this study, the anti-inflammatory effects of FA and FB were investigated in CuSO₄-induced inflammation in zebrafish larvae. Intracellular generation of reactive oxygen species (ROS) and nitric oxide (NO) was investigated using fluorescence probes. Metabolomic and proteomic analyses using liquid chromatography-mass spectrometry were carried out to identify the expressions of metabolites and proteins associated with the anti-inflammatory mechanism of FA and FB. Quantitative polymerase chain reaction (PCR) was performed to detect the progressive changes in gene expression.

RESULTS

FA and FB inhibited neutrophils migration to the damaged neuromasts and remarkably reduced CuSO₄-induced ROS and NO generation in zebrafish larvae. Metabolomic analysis pointed to the involvement of nicotinate and nicotinamide metabolism, energy metabolism, pyrimidine metabolism, and purine metabolism. Proteomic analysis identified 146 differentially expressed proteins between the control and model groups. These included collagen [collagen type II alpha 1b precursor (col2a1b), collagen alpha-2(IX) chain precursor (col9a2), collagen type IX alpha I precursor (col9a1b)], nucleoside diphosphate kinase 3 isoform X1 (Nme3), WD repeat-containing protein 3 (Wdr3), and 28S ribosomal protein S7 mitochondrial precursor (Mrps7). FA and FB were shown to reverse the abnormal expressions of potential metabolite and protein biomarkers and alleviate CuSO₄-induced damage to the neuromasts in the zebrafish lateral line.

CONCLUSIONS

Our results indicate that FA and FB possess remarkable anti-inflammatory properties, protecting against CuSO₄-induced neuromasts damage in zebrafish larvae. The results also suggest a multi-component and multi-regulatory therapeutic mechanism for FA and FB.

Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats

Copper, an essential microelement, can still be harmful to health and has a significant impact on the gut microbiota, which is closely related to health when copper is ingested excessively. However, the effects of low dose exposure to copper early in life on health and the gut microbiota are not well understood. Here, the effects of early-life exposure of copper on the toxicity, gut microbiota and the metabolome were investigated in Sprague-Dawley (SD) rats. The results showed that 0.20 and 1.00 mg/kg BW copper early-life exposure in SD rats significantly increased ALT, AST, and ALP levels in the blood and caused liver damage. Copper exposure had a dose-dependent effect on the alpha and beta diversity and reduced the abundance of probiotics, the ratio of Firmicutes to Bacteroidetes (F/B), and changed the abundance of fat metabolism and intestinal inflammation-related bacteria. The results of the fecal metabolome also demonstrated the effects of early-life copper exposure on liver damage and intestinal inflammation-related metabolic pathways. Together, our findings demonstrated that copper exposure during early life induced liver damage and gut microbiota dysbiosis and affected the relevant metabolic pathways.

Serum Zinc Level and non-Protein Respiratory Quotient in Patients with Chronic Liver Diseases

We sought to clarify the correlation between non-protein respiratory quotient (npRQ) in indirect calorimetry and serum zinc (Zn) level in chronic liver diseases (CLDs, n = 586, 309 liver cirrhosis (LC) patients, median age = 63 years). Clinical parameters potentially linked to npRQ <0.85 (best cutoff point for the prognosis in LC patients) were also examined in receiver operating characteristic curve (ROC) analyses. The median npRQ was 0.86. The median serum Zn level was 64 μg/dL. The median npRQ in patients with non-LC, Child-Pugh A, Child-Pugh B and Child-Pugh C were 0.89, 0.85, 0.83 and 0.82 (overall p < 0.0001)). The median serum Zn level in patients with npRQ <0.85 (58 μg/dL) was significantly lower than that in patients with npRQ ≥ 0.85 (68 μg/dL) (p < 0.0001). The correlation coefficient (r) between npRQ level and serum Zn level for all cases was 0.40 (p < 0.0001). Similar tendencies were observed in all subgroup analyses. The highest correlation coefficient between serum Zn level and npRQ was found in patients with Child-Pugh C (n = 22, r = 0.69). In ROC analyses for npRQ <0.85, serum Zn level had the highest area under the ROC (AUC) among baseline laboratory parameters (AUC = 0.69). In conclusion, serum Zn level can be helpful for npRQ in patients with CLDs.

Metabolomics Analysis of the Deterioration Mechanism and Storage Time Limit of Tender Coconut Water during Storage

Tender coconut water tastes sweet and is enjoyed by consumers, but its commercial development is restricted by an extremely short shelf life, which cannot be explained by existing research. UPLC-MS/MS-based metabolomics methods were used to identify and statistically analyze metabolites in coconut water under refrigerated storage. A multivariate statistical analysis method was used to analyze the UPLC-MS/MS datasets from 35 tender coconut water samples stored for 0-6 weeks. In addition, we identified other differentially expressed metabolites by selecting p-values and fold changes. Hierarchical cluster analysis and association analysis were performed with the differentially expressed metabolites. Metabolic pathways were analyzed using the KEGG database and the MetPA module of MetaboAnalyst. A total of 72 differentially expressed metabolites were identified in all groups. The OPLS-DA score chart showed that all samples were well grouped. Thirty-one metabolic pathways were enriched in the week 0-1 samples. The results showed that after a tender coconut is peeled, the maximum storage time at 4 °C is 1 week. Analysis of metabolic pathways related to coconut water storage using the KEGG and MetPA databases revealed that amino acid metabolism is one of the main causes of coconut water quality deterioration.

Metabolomics profiles of patients with Wilson disease reveal a distinct metabolic signature

INTRODUCTION

Wilson disease (WD) is characterized by excessive intracellular copper accumulation in liver and brain due to defective copper biliary excretion. With highly varied phenotypes and a lack of biomarkers for the different clinical manifestations, diagnosis and treatment can be difficult.

OBJECTIVE

The aim of the present study was to analyze serum metabolomics profiles of patients with Wilson disease compared to healthy subjects, with the goal of identifying differentially abundant metabolites as potential biomarkers for this condition.

METHODS

Hydrophilic interaction liquid chromatography-quadrupole time of flight mass spectrometry was used to evaluate the untargeted serum metabolome of 61 patients with WD (26 hepatic and 25 neurologic subtypes, 10 preclinical) compared to 15 healthy subjects. We conducted analysis of covariance with potential confounders (body mass index, age, sex) as covariates and partial least-squares analysis.

RESULTS

After adjusting for clinical covariates and multiple testing, we identified 99 significantly different metabolites (FDR < 0.05) between WD and healthy subjects. Subtype comparisons also revealed significantly different metabolites compared to healthy subjects: WD hepatic subtype (67), WD neurologic subtype (57), WD hepatic-neurologic combined (77), and preclinical (36). Pathway analysis revealed these metabolites are involved in amino acid metabolism, the tricarboxylic acid cycle, choline metabolism, and oxidative stress.

CONCLUSIONS

Patients with WD are characterized by a distinct metabolomics profile providing new insights into WD pathogenesis and identifying new potential diagnostic biomarkers.

Emerging therapeutic biomarkers of autoimmune hepatitis and their impact on current and future management

Autoimmune hepatitis lacks a quantifiable biomarker that is close to its pathogenic mechanisms and that accurately reflects inflammatory activity, correlates with treatment response, and ensures inactive disease before treatment withdrawal. Areas covered: Micro-ribonucleic acids, programmed death-1 protein and its ligands, macrophage migration inhibitory factor, soluble CD163, B cell activating factor, and metabolite patterns in blood were considered the leading candidates as therapeutic biomarkers after search of PubMed from August 1981 to August 2017 using the search words 'biomarkers of autoimmune hepatitis'. Expert commentary: Each of the candidate biomarkers is close to the putative pathogenic mechanisms of autoimmune hepatitis, and each has attributes that support its potential role as a surrogate marker of inflammatory activity that can be monitored during treatment. Future studies must demonstrate the superiority of each biomarker to conventional indices of inflammatory activity and validate their correlation with treatment response and outcome. A reliable therapeutic biomarker would facilitate the individualization of current management algorithms, ensure that pathogenic mechanisms were disrupted or eliminated prior to treatment withdrawal, and reduce the frequency of relapse or unnecessary protracted therapy. The biomarker might also prove to be a target of next-generation therapies.