Mechanism-based identification of plasma metabolites associated with liver toxicity

Applications of genome-scale metabolic models to the study of human diseases: A systematic review

BACKGROUND AND OBJECTIVES

Genome-scale metabolic networks (GEMs) represent a valuable modeling and computational tool in the broad field of systems biology. Their ability to integrate constraints and high-throughput biological data enables the study of intricate metabolic aspects and processes of different cell types and conditions. The past decade has witnessed an increasing number and variety of applications of GEMs for the study of human diseases, along with a huge effort aimed at the reconstruction, integration and analysis of a high number of organisms. This paper presents a systematic review of the scientific literature, to pursue several important questions about the application of constraint-based modeling in the investigation of human diseases. Hopefully, this paper will provide a useful reference for researchers interested in the application of modeling and computational tools for the investigation of metabolic-related human diseases.

METHODS

This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Elsevier Scopus®, National Library of Medicine PubMed® and Clarivate Web of Science™ databases were enquired, resulting in 566 scientific articles. After applying exclusion and eligibility criteria, a total of 169 papers were selected and individually examined.

RESULTS

The reviewed papers offer a thorough and up-to-date picture of the latest modeling and computational approaches, based on genome-scale metabolic models, that can be leveraged for the investigation of a large variety of human diseases. The numerous studies have been categorized according to the clinical research area involved in the examined disease. Furthermore, the paper discusses the most typical approaches employed to derive clinically-relevant information using the computational models.

CONCLUSIONS

The number of scientific papers, utilizing GEM-based approaches for the investigation of human diseases, suggests an increasing interest in these types of approaches; hopefully, the present review will represent a useful reference for scientists interested in applying computational modeling approaches to investigate the aetiopathology of human diseases; we also hope that this work will foster the development of novel applications and methods for the discovery of clinically-relevant insights on metabolic-related diseases.

Hepatoprotective efficacy of quinoa seed extract against CCl4- induced acute liver toxicity in rat model

The current research explored the possible protective effect of chenopodium quinoa extract against CCl4 acute liver toxicity in Sprague Dawley rats. Thirty rats were divided into five groups with six rats in each group. CCl4 (Carbon tetrachloride) was administered at a dose rate of 2 mL/kg b.w. intra-peritoneally once a week for 3 weeks. The plant extract was given through oral gavage for a period of 21 days. Group I served as a normal group which was given with basal diet. Group II was referred to as a positive control group and received CCl4 2 mL/kg body weight (i.p.). Group III was the standard treatment group and received 2 mL/kg CCl4 (i.p.) and 16 mg/kg body weight (p.o.) silymarin. Group IV was the plant treatment group, which received 2 mL/kg CCl4 (i.p.) and 600 mg/kg body weight of quinoa seed extract (p.o.). Group V was the combined treatment group, which received 2 mL/kg CCl4 (i.p.) accompanied with a combination of silymarin (p.o.) 16 mg/kg body weight and quinoa seed extract (p.o.) 600 mg/kg body weight. The liver biomarkers were assessed along with histopathological analysis to observe the changes in the liver. The outcome suggested that the treatment, which was given with the combination of silymarin and quinoa seed extract, significantly enhanced the antioxidant levels, reduced the oxidative stress, and restored the liver function as evidenced by biochemical parameters histopathological studies. The hepatoprotective potential may be due to the antioxidant and anti-inflammatory properties of quinoa seed extract.

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism

Improvements in the diagnosis and treatment of cancer have revealed long-term side effects of chemotherapeutics, particularly cardiotoxicity. Here, we present paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches identify some commonly affected pathways and metabolites but are not able to readily identify metabolic adaptations in response to cardiotoxicity. The paired data was integrated with a genome-scale metabolic network reconstruction of the heart to identify shifted metabolic functions, unique metabolic reactions, and changes in flux in metabolic reactions in response to these compounds. Using this approach, we confirm previously seen changes in the p53 pathway by doxorubicin and RNA synthesis by 5-fluorouracil, we find evidence for an increase in phospholipid metabolism in response to acetaminophen, and we see a shift in central carbon metabolism suggesting an increase in metabolic demand after treatment with doxorubicin and 5-fluorouracil.

Gardenia extract protects against intrahepatic cholestasis by regulating bile acid enterohepatic circulation

ETHNOPHARMACOLOGICAL RELEVANCE

Cholestasis is the main manifestation of cholestatic liver disease, which has a risk of progression to end-stage liver disease. Gardeniae Fructus is the dried fruit of Gardeniae jasminoides Ellis, a plant of the Rubiaceae family. Gardeniae Fructus has shown therapeutic potential in cholestasis-related liver diseases and it is generally believed that Gardeniae Fructus ameliorates cholestasis, which could be related to its influence on bile acids (BAs) metabolism. However, the specific targets of Gardeniae Fructus and its impact on enterohepatic circulation of BAs have not yet been fully elucidated.

AIM OF THE STUDY

To systematically elucidate the mechanism by which Gardenia extract (GE, total iridoids in Gardeniae Fructus, which contains the predominant and characteristic phytoconstituents of Gardeniae Fructus) ameliorates alpha-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury.

MATERIALS AND METHODS

Sprague-Dawley rats were orally administered water, obeticholic acid (OCA, 2 mg/kg), or GE (21 and 42 mg/kg) once daily for five days. On the third day, the model was established by administration of a single dose of ANIT (40 mg/kg) by oral gavage. Biochemical and pathological analyses, BA metabolomics, transcriptomics, and qRT-PCR were performed.

RESULTS

The profile of BAs in serum and liver confirmed that GE attenuated ANIT-induced acute cholestasis by affecting BA metabolism in a dose-dependent manner. Liver transcriptomic analysis indicated that GE mainly influenced the primary bile acid (PBA) biosynthesis and bile secretion pathways. GE mainly affected PBA biosynthesis in liver by upregulating Cyp8b1 gene expression, thereby significantly reducing the level of total bile acids (TBA). GE mainly promoted PBA excretion from liver into duodenum by upregulating Fxr and Oatp1 gene expression, thereby increasing the excretion of PBA in feces, and inhibiting PBA in liver entering the blood by alternative routes to reduce TBA levels in serum and urine and improve the enterohepatic circulation of BAs.

CONCLUSION

GE attenuated ANIT-induced hepatotoxicity and cholestasis in rats by upregulating Cyp8b1 expression to inhibit BA synthesis in the liver, while also promoting BA excretion via the intestinal-fecal route, and improving enterohepatic circulation of BAs.

Ultra-performance chromatography-electrospray tandem mass spectrometry analysis of bile acid profiles in the enterohepatic circulation following geniposide and acetaminophen-induced liver injury

Bile acids (BAs) play an important role in pre-diagnosing drug-induced liver injury (DILI). However, in clinical practice, different types of liver injury are characterized by different pathogeneses and pathological manifestations. Therefore, whether BAs can be used as biomarkers across different DILIs remains unclear. In this study, an ultra-performance chromatography-mass spectrometry (MS)/MS-based technique was developed for the simultaneous quantitative analysis of 31 BAs in the serum, liver, feces, urine, and intestinal contents of rats treated with acetaminophen (APAP) and geniposide to induce liver injury. The total extraction recovery for representative analytes ranged between 80.60% and 99.23% in the serum, urine, liver, feces, and intestinal contents. The correlation coefficients for all standard curves of the different matrices were at least 0.99. Validation of the BA analytical method including selectivity, residue, lower limit of quantification, accuracy, precision, matrix effect, and stability conformed with the biospecimen quality control standards of the Chinese Pharmacopoeia (version 2020). Serum biochemical and pathohistological analyses revealed APAP- and geniposide-induced hepatocellular and cholestatic DILI, respectively, with different effects on BA profiles in the enterohepatic circulation. Metabolomics further revealed that the trends in BA changes in the serum, feces, urine, and intestinal tissues were consistent between the geniposide- and APAP-treated groups. However, in the liver, the total BAs (TBA) concentration increased by 1.70 fold in the geniposide group but decreased by 43% in the APAP group compared with the control group. Multivariate analysis revealed differentially expressed BAs, including TCA, CA, and GCA, which are potential biomarkers for DILI, in the serum, liver, and urine following treatment with geniposide. Interestingly, the differentially expressed BAs in the APAP group were similar to those in the control group. Additionally, the magnitude of changes in the TBA in the urine (3.3 fold and 15.5 fold in the APAP and geniposide groups, respectively) was higher than that in the blood (290 fold and 640 fold in the APAP and geniposide groups, respectively). However, given the BA profiles after geniposide- and APAP-induced liver injury, BAs were found to be more suitable as biomarkers for diagnosing cholestatic liver injury. Overall, the BA assay developed in this study is rapid, simple, accurate, validated, sensitive, and suitable for analyzing the levels and distribution of BAs in various parts of the enterohepatic circulation.

Understanding the hepatoxicity of inorganic mercury through guts: Perturbance to gut microbiota, alteration of gut-liver axis related metabolites and damage to gut integrity

Mercury (Hg) brings adverse effects to the environment and human beings and inorganic mercury (IHg) is a typical hepatic toxin. This work studied the impacts of IHg on gut microbes and metabolome together with its damage to liver and gut in rats through gut microbiome, metabolomics and metallomics. Sprague Dawley (SD) rats were orally exposed to 0.4 μg/mL IHg and sacrificed after 24 h. It was found that IHg perturbed greatly on the gut microbiota, such as increased pathogenic bacteria like G. bacillus. In addition, IHg also changed gut-liver axis related metabolites, which was confirmed by the secretion of a large number of inflammatory factors in both the gut and the liver. The changed gut-liver axis related metabolites correlated well to the changes of gut microbiome. In all, besides the direct deposition in liver of Hg, the perturbance to gut microbiome and alteration of gut-liver axis related metabolites by IHg also contributed to its hepatoxicity, which provides new insights about the hepatoxicity of chemicals. The strategy applied in this work may also be used to understand the hepatoxicity of other chemicals.

Genomics and metabolomics of early-stage thioacetamide-induced liver injury: An interspecies study between guinea pig and rat

To study the complex processes involved in liver injuries, researchers rely on animal investigations, using chemically or surgically induced liver injuries, to extrapolate findings and infer human health risks. However, this presents obvious challenges in performing a detailed comparison and validation between the highly controlled animal models and development of liver injuries in humans. Furthermore, it is not clear whether there are species-dependent and -independent molecular initiating events or processes that cause liver injury before they eventually lead to end-stage liver disease. Here, we present a side-by-side study of rats and guinea pigs using thioacetamide to examine the similarities between early molecular initiating events during an acute-phase liver injury. We exposed Sprague Dawley rats and Hartley guinea pigs to a single dose of 25 or 100 mg/kg thioacetamide and collected blood plasma for metabolomic analysis and liver tissue for RNA-sequencing. The subsequent toxicogenomic analysis identified consistent liver injury trends in both genomic and metabolomic data within 24 and 33 h after thioacetamide exposure in rats and guinea pigs, respectively. In particular, we found species similarities in the key injury phenotypes of inflammation and fibrogenesis in our gene module analysis for liver injury phenotypes. We identified expression of several common genes (e.g., SPP1, TNSF18, SERPINE1, CLDN4, TIMP1, CD44, and LGALS3), activation of injury-specific KEGG pathways, and alteration of plasma metabolites involved in amino acid and bile acid metabolism as some of the key molecular processes that changed early upon thioacetamide exposure and could play a major role in the initiation of acute liver injury.

A metabolomic analysis of thiol response for standard and modified N-acetyl cysteine treatment regimens in patients with acetaminophen overdose

N-acetylcysteine (NAC) is an antidote to prevent acetaminophen (paracetamol-APAP)-induced acute liver injury (ALI). The 3-bag licensed 20.25 h standard regimen, and a 12 h modified regimen, are used to treat APAP overdose. This study evaluated the redox thiol response and APAP metabolites, in patients with a single APAP overdose treated with either the 20.25 h standard or 12 h modified regimen. We used liquid chromatography tandem mass spectrometry to quantify clinically important oxidative stress biomarkers and APAP metabolites in plasma samples from 45 patients who participated in a randomized controlled trial (SNAP trial). We investigated the time course response of plasma metabolites at predose, 12 h, and 20.25 h post-start of NAC infusion. The results showed that the 12 h modified regimen resulted in a significant elevation of plasma NAC and cysteine concentrations at 12 h post-infusion. We found no significant alteration in the metabolism of APAP, mitochondrial, amino acids, and other thiol biomarkers with the two regimens. We examined APAP and purine metabolism in overdose patients who developed ALI. We showed the major APAP-metabolites and xanthine were significantly higher in patients with ALI. These biomarkers correlated well with alanine aminotransferase activity at admission. Receiver operating characteristic analysis showed that at admission, plasma APAP-metabolites and xanthine concentrations were predictive for ALI. In conclusion, a significantly higher redox thiol response with the modified NAC regimen at 12 h postdose suggests this regimen may produce greater antioxidant efficacy. At baseline, plasma APAP and purine metabolites may be useful biomarkers for early prediction of APAP-induced ALI.

In vivo2H/13C flux analysis in metabolism research

Identifying the factors and mechanisms that regulate metabolism under normal and diseased states requires methods to quantify metabolic fluxes of live tissues within their physiological milieu. A number of recent developments have expanded the reach and depth of isotope-based in vivo flux analysis, which have in turn challenged existing dogmas in metabolism research. First, minimally invasive techniques of intravenous isotope infusion and sampling have advanced in vivo metabolic tracer studies in animal models and human subjects. Second, recent breakthroughs in analytical instrumentation have expanded the scope of isotope labeling measurements and reduced sample volume requirements. Third, innovative modeling approaches and publicly available software tools have facilitated rigorous analysis of sophisticated experimental designs involving multiple tracers and expansive metabolomics datasets. These developments have enabled comprehensive in vivo quantification of metabolic fluxes in specific tissues and have set the stage for integrated multi-tissue flux assays.

Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats

Liver disease and disorders associated with aberrant hepatocyte metabolism can be initiated via drug and environmental toxicant exposures. In this study, we tested the hypothesis that gene and metabolic profiling can reveal commonalities in liver response to different toxicants and provide the capability to identify early signatures of acute liver toxicity. We used Sprague Dawley rats and three classical hepatotoxicants: acetaminophen (2 g/kg), bromobenzene (0.4 g/kg), and carbon tetrachloride (0.3 g/kg), to identify early perturbations in liver metabolism after a single acute exposure dose. We measured changes in liver genes and plasma metabolites at two time points (5 and 10 h) and used genome-scale metabolic models to identify commonalities in liver responses across the three toxicants. We found strong correlations for gene and metabolic profiles between the toxicants, indicative of similarities in the liver response to toxicity. We identified several injury-specific pathways in lipid and amino acid metabolism that changed similarly across the three toxicants. Our findings suggest that several plasma metabolites in lipid and amino acid metabolism are strongly associated with the progression of liver toxicity, and as such, could be targeted and clinically assessed for their potential as early predictors of acute liver toxicity.