Quantitative 13C Traces of Glucose Fate in Hepatitis B Virus-Infected Hepatocytes

In vivo Hyperpolarized Metabolic Imaging to Monitor the Progression of Hepatitis B Virus (HBV)-Related Hepatitis to Liver Fibrosis

PURPOSE

This study aimed to assess metabolic changes to monitor the progression from normal liver to hepatitis B virus (HBV)-related hepatitis and liver fibrosis using hyperpolarized 13C magnetic resonance imaging (MRI).

PROCEDURES

Hepatitis was induced in mice (n = 16) via hydrodynamic injection of HBV 1.2 plasmid (25 μg). Among them, liver fibrosis was induced in the mice (n = 8) through weight-adapted administration of thioacetamide with ethanol. Normal control mice (n = 8) were injected with a phosphate buffer solution. Subsequently, a hyperpolarized 13C MRI was performed on the mouse liver in vivo. The level of hepatitis B surface antigen (HBsAg) in blood serum was measured. Statistical analysis involved comparing the differential metabolite ratios, blood biochemistry values, and body weight among the three groups using the Kruskal-Wallis one-way analysis of variance.

RESULTS

HBsAg was absent in the normal and fibrosis groups, while it was detected in the hepatitis group. The ratios of [1-13C] lactate/pyruvate, [1-13C] alanine/pyruvate, [1-13C] lactate/total carbon, and [1-13C] alanine/total carbon were significantly lower in the normal control group than in the hepatitis and fibrosis groups (p < 0.05). Moreover, these ratios were significantly higher in the fibrosis group than in the hepatitis group (p < 0.05). However, no significant differences were observed in either [1-13C] pyruvate-hydrate/pyruvate or [1-13C] pyruvate-hydrate/total carbon among the three groups.

CONCLUSIONS

The levels of [1-13C] lactate and [1-13C] alanine in vivo may serve as valuable indicators for differentiating between HBV-related hepatitis, liver fibrosis, and normal liver.

Metabolomics analysis of CEF cells infected with avian leukosis virus subgroup J based on UHPLC-QE-MS

Avian leukosis virus subgroup J (ALV-J) is a retrovirus that can cause immunosuppression and tumors in chicken. However, relative pathogenesis is still not clear. At present, metabolomics has shown great potential in the screening of tumor metabolic markers, prognostic evaluation, and drug target design. In this study, we utilize an untargeted metabolomics approach based on ultrahigh-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS) to analyze the metabolic changes in chicken embryo fibroblast (CEF) cells infected by ALV-J. We found that ALV-J infection significantly altered a wealth of metabolites compared with control group. Additionally, most of the differentially expressed metabolites belonged to lipid metabolism, purine nucleotide metabolism and amino acid metabolism. Among them, the proportion of lipid metabolites account for the highest proportion (around 31%). Results suggest that these changes may be conductive to the formation of virion, thereby promoting the replication of ALV-J. These data provided metabolic evidence and potential biomarkers for the cellular metabolic changes induced by ALV-J, and provided important insight for further understanding the replication needs and pathogenesis of ALV-J.

Metabolomics in viral hepatitis: advances and review

Viral hepatitis is a major worldwide public health issue, affecting hundreds of millions of people and causing substantial morbidity and mortality. The majority of the worldwide burden of viral hepatitis is caused by five biologically unrelated hepatotropic viruses: hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). Metabolomics is an emerging technology that uses qualitative and quantitative analysis of easily accessible samples to provide information of the metabolic levels of biological systems and changes in metabolic and related regulatory pathways. Alterations in glucose, lipid, and amino acid levels are involved in glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, and amino acid metabolism. These changes in metabolites and metabolic pathways are associated with the pathogenesis and medication mechanism of viral hepatitis and related diseases. Additionally, differential metabolites can be utilized as biomarkers for diagnosis, prognosis, and therapeutic responses. In this review, we present a thorough overview of developments in metabolomics for viral hepatitis.

Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry

Direct observation of metabolites in living cells by mass spectrometry offers a bright future for biological studies but also suffers a severe challenge to untargeted peak assignment to tentative metabolite candidates. In this study, we developed a method combining stable isotope tracing and induced electrospray mass spectrometry for living-cells metabolite measurement and identification. By using ¹³C₆-glucose and ammonium chloride-¹⁵N as the sole carbon and nitrogen sources for cell culture, Escherichia coli synthesized metabolites with ¹⁵N and ¹³C elements. Tracing the number of carbon and nitrogen atoms could offer a complementary dimension for candidate peak searching. As a result, the identification confidence of metabolites achieved a universal improvement based on carbon/nitrogen labelling and filtration.

Metabolomics in Cell Biology

Metabolomics has long been used in a biomedical context. The most typical samples are body fluids in which small molecules can be detected and quantified using technologies such as Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). Many studies, in particular in the wider field of cancer research, are based on cellular models. Different cancer cells can have vastly different ways of regulating metabolism and responses to drug treatments depend on specific metabolic mechanisms which are often cell type specific. This has led to a series of publications using metabolomics to study metabolic mechanisms. Cell-based metabolomics has specific requirements and allows for interesting approaches where metabolism is followed in real-time. Here applications of metabolomics in cell biology have been reviewed, providing insight into specific technologies used and showing exemplary case studies with an emphasis towards applications which help to understand drug mechanisms.

What role for cellular metabolism in the control of hepatitis viruses?

Hepatitis B, C and D viruses (HBV, HCV, HDV, respectively) specifically infect human hepatocytes and often establish chronic viral infections of the liver, thus escaping antiviral immunity for years. Like other viruses, hepatitis viruses rely on the cellular machinery to meet their energy and metabolite requirements for replication. Although this was initially considered passive parasitism, studies have shown that hepatitis viruses actively rewire cellular metabolism through molecular interactions with specific enzymes such as glucokinase, the first rate-limiting enzyme of glycolysis. As part of research efforts in the field of immunometabolism, it has also been shown that metabolic changes induced by viruses could have a direct impact on the innate antiviral response. Conversely, detection of viral components by innate immunity receptors not only triggers the activation of the antiviral defense but also induces in-depth metabolic reprogramming that is essential to support immunological functions. Altogether, these complex triangular interactions between viral components, innate immunity and hepatocyte metabolism may explain why chronic hepatitis infections progressively lead to liver inflammation and progression to cirrhosis, fibrosis and hepatocellular carcinoma (HCC). In this manuscript, we first present a global overview of known connections between the innate antiviral response and cellular metabolism. We then report known molecular mechanisms by which hepatitis viruses interfere with cellular metabolism in hepatocytes and discuss potential consequences on the innate immune response. Finally, we present evidence that drugs targeting hepatocyte metabolism could be used as an innovative strategy not only to deprive viruses of key metabolites, but also to restore the innate antiviral response that is necessary to clear infection.

Improved pharmacokinetics of tenofovir ester prodrugs strengthened the inhibition of HBV replication and the rebalance of hepatocellular metabolism in preclinical models

Tenofovir (TFV) ester prodrugs, a class of nucleotide analogs (NAs), are the first-line clinical anti-hepatitis B virus (HBV) drugs with potent antiviral efficacy, low resistance rate and high safety. In this work, three marketed TFV ester drugs, tenofovir disoproxil fumarate (TDF), tenofovir alafenamide fumarate (TAF) and tenofovir amibufenamide fumarate (TMF), were used as probes to investigate the relationships among prodrug structures, pharmacokinetic characteristics, metabolic activations, pharmacological responses and to reveal the key factors of TFV ester prodrug design. The results indicated that TMF and TAF exhibited significantly stronger inhibition of HBV DNA replication than did TDF in HBV-positive HepG2.2.15 cells. The anti-HBV activity of TMF was slightly stronger than TAF after 9 days of treatment (EC₅₀ 7.29 ± 0.71 nM vs. 12.17 ± 0.56 nM). Similar results were observed in the HBV decline period post drug administration to the HBV transgenic mouse model, although these three TFV prodrugs finally achieved the same anti-HBV effect after 42 days treatments. Furthermore, TFV ester prodrugs showed a correcting effect on disordered host hepatic biochemical metabolism, including TCA cycle, glycolysis, pentose phosphate pathway, purine/pyrimidine metabolism, amino acid metabolism, ketone body metabolism and phospholipid metabolism. The callback effects of the three TFV ester prodrugs were ranked as TMF > TAF > TDF. These advantages of TMF were believed to be attributed to its greater bioavailability in preclinical animals (SD rats, C57BL/6 mice and beagle dogs) and better target loading, especially in terms of the higher hepatic level of the pharmacologically active metabolite TFV-DP, which was tightly related to anti-HBV efficacy. Further analysis indicated that stability in intestinal fluid determined the actual amount of TFV prodrug at the absorption site, and hepatic/intestinal stability determined the maintenance amount of prodrug in circulation, both of which influenced the oral bioavailability of TFV prodrugs. In conclusion, our research revealed that improved pharmacokinetics of TFV ester prodrugs (especially intestinal stability) strengthened the inhibition of HBV replication and the rebalance of hepatocellular metabolism, which provides new insights and a basis for the design, modification and evaluation of new TFV prodrugs in the future.

White Spot Syndrome Virus Triggers a Glycolytic Pathway in Shrimp Immune Cells (Hemocytes) to Benefit Its Replication

White spot syndrome virus (WSSV) is the causative agent of a shrimp disease that inflicts in huge economic losses in shrimp-farming industry. WSSV triggers aerobic glycolysis in shrimp immune cells (hemocytes), but how this virus regulates glycolytic enzymes or pathway is yet to be characterized. Therefore, mRNA levels and activity of four important glycolytic enzymes, Hexokinase (HK), Phosphofructokinase (PFK), Pyruvate kinase (PK), and Lactate dehydrogenase (LDH), were measured in WSSV-infected shrimp hemocytes. Gene expression of HK and PFK, but not LDH or PK, was increased at the viral genome replication stage (12 hpi); furthermore, activity of these enzymes, except HK, was concurrently increased. However, there was no increased enzyme activity at the viral late stage (24 hpi). In vivo dsRNA silencing and glycolysis disruption by 2-DG further confirmed the role of glycolysis in virus replication. Based on tracing studies using stable isotope labeled glucose, glycolysis was activated at the viral genome replication stage, but not at the viral late stage. This study demonstrated that WSSV enhanced glycolysis by activating glycolytic enzyme at the viral genome replication stage, providing energy and biomolecules for virus replication.

Proteomic characterization of the natural history of chronic HBV infection revealed by tandem mass tag-based quantitative proteomics approach

Currently, determining when to start antiviral therapy in patients with chronic HBV infection is a controversial issue. One crucial reason is that biomarkers for distinguishing the natural history of chronic HBV infection are unmet needs. In this study, we aimed to explore novel biomarkers and therapeutic targets for the diagnosis and treatment of chronic HBV infection by using tandem mass tag (TMT)-based quantitative proteomics approach. Here, we firstly revealed the serum proteomic characterization of the natural history of chronic HBV infection using multiplex TMT labeling coupled with liquid chromatography-mass spectrometry. Then, we verified the levels of differentially expressed proteins (DEPs) across a large number of clinical samples by enzyme-linked immunosorbent assay (ELISA). We found that DEPs over the different phases of chronic HBV infection were primarily involved in the biological process of leukocyte-mediated immunity. Patients with chronic hepatitis were characterized as having an up-regulated proteasome pathway, including upregulation of proteasome activator subunit 1 (PSME1) and proteasome subunit alpha type 7 (PSMA7) levels. In addition, immune tolerant phase patients were characterized by having the lowest ephrin-B2 (EFNB2) levels and highest heat responsive protein 12 (HRSP12) levels. Moreover, inactive HBV carrier state patients were characterized by having a down-regulated glycolysis/gluconeogenesis pathway, with especially low expression of related enzymes alpha-enolase (ENO1) and fructose-1,6-bisphosphatase 1 (FBP1). What's more, HBeAg-negative chronic hepatitis patients were characterized as having the highest interleukin 18 binding protein (IL-18BP) levels. Thus, our results provide several potential diagnostic biomarkers for distinguishing the natural history of chronic HBV infection, such as PSME1, PSMA7, EFNB2, ENO1, and IL-18BP, and also present potential therapeutic interventions for chronic hepatitis B patients, such as targeting the proteasome or glycolysis/gluconeogenesis pathways. Our findings shed new light on the development of novel diagnostic biomarkers and therapeutic targets for the diagnosis and treatment of chronic HBV infection.

The thermogenic activity of adjacent adipocytes fuels the progression of ccRCC and compromises anti-tumor therapeutic efficacy

Clear cell renal cell carcinoma (ccRCC) preferentially invades into perinephric adipose tissue (PAT), a process associated with poor prognosis. However, the detailed mechanisms underlying this interaction remain elusive. Here, we describe a bi-directional communication between ccRCC cells and the PAT. We found that ccRCC cells secrete parathyroid-hormone-related protein (PTHrP) to promote the browning of PAT by PKA activation, while PAT-mediated thermogenesis results in the release of excess lactate to enhance ccRCC growth, invasion, and metastasis. Further, tyrosine kinase inhibitors (TKIs) extensively used in the treatment of ccRCC enhanced this vicious cycle of ccRCC-PAT communication by promoting the browning of PAT. However, if this cross-communication was short circuited by the pharmacological suppression of adipocyte browning via H89 or KT5720, the anti-tumor efficacy of the TKI, sunitinib, was enhanced. These results suggest that ccRCC-PAT cross-communication has important clinical relevance, and use of combined therapy holds great promise in enhancing the efficacy of TKIs.

NMR-Based Metabolomics in Cancer Research

Nuclear magnetic resonance (NMR) spectroscopy offers reproducible quantitative analysis and structural identification of metabolites in various complex biological samples, such as biofluids (plasma, serum, and urine), cells, tissue extracts, and even intact organs. Therefore, NMR-based metabolomics, a mainstream metabolomic platform, has been extensively applied in many research fields, including pharmacology, toxicology, pathophysiology, nutritional intervention, disease diagnosis/prognosis, and microbiology. In particular, NMR-based metabolomics has been successfully used for cancer research to investigate cancer metabolism and identify biomarker and therapeutic targets. This chapter highlights the innovations and challenges of NMR-based metabolomics platform and its applications in cancer research.

Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures

Biological organisms are constantly exposed to an immense repertoire of molecules that cover environmental or food-derived molecules and drugs, triggering a continuous flow of stimuli-dependent adaptations. The diversity of these chemicals as well as their concentrations contribute to the multiplicity of induced effects, including activation, stimulation, or inhibition of physiological processes and toxicity. Metabolism, as the foremost phenotype and manifestation of life, has proven to be immensely sensitive and highly adaptive to chemical stimuli. Therefore, studying the effect of endo- or xenobiotics over cellular metabolism delivers valuable knowledge to apprehend potential cellular activity of individual molecules and evaluate their acute or chronic benefits and toxicity. The development of modern metabolomics technologies such as mass spectrometry or nuclear magnetic resonance spectroscopy now offers unprecedented solutions for the rapid and efficient determination of metabolic profiles of cells and more complex biological systems. Combined with the availability of well-established cell culture techniques, these analytical methods appear perfectly suited to determine the biological activity and estimate the positive and negative effects of chemicals in a variety of cell types and models, even at hardly detectable concentrations. Metabolic phenotypes can be estimated from studying intracellular metabolites at homeostasis in vivo, while in vitro cell cultures provide additional access to metabolites exchanged with growth media. This article discusses analytical solutions available for metabolic phenotyping of cell culture metabolism as well as the general metabolomics workflow suitable for testing the biological activity of molecular compounds. We emphasize how metabolic profiling of cell supernatants and intracellular extracts can deliver valuable and complementary insights for evaluating the effects of xenobiotics on cellular metabolism. We note that the concepts and methods discussed primarily for xenobiotics exposure are widely applicable to drug testing in general, including endobiotics that cover active metabolites, nutrients, peptides and proteins, cytokines, hormones, vitamins, etc.

Quantitative Isotopomer Rates in Real-Time Metabolism of Cells Determined by NMR Methods

Tracer-based metabolism is becoming increasingly important for studying metabolic mechanisms in cells. NMR spectroscopy offers several approaches to measure label incorporation in metabolites, including ¹³ C- and ¹ H-detected spectra. The latter are generally more sensitive, but quantification depends on the proton-carbon ¹ J_CH coupling constant, which varies significantly between different metabolites. It is therefore not possible to have one experiment optimised for all metabolites, and quantification of ¹ H-edited spectra such as HSQCs requires precise knowledge of coupling constants. Increasing interest in tracer-based and metabolic flux analysis requires robust analyses with reasonably small acquisition times. Herein, we compare ¹³ C-filtered and ¹³ C-edited methods for quantification and show the applicability of the methods for real-time NMR spectroscopy of cancer-cell metabolism, in which label incorporations are subject to constant flux. We find an approach using a double filter to be most suitable and sufficiently robust to reliably obtain ¹³ C incorporations from difference spectra. This is demonstrated for JJN3 multiple myeloma cells processing glucose over 24 h. The proposed method is equally well suited for calculating the level of label incorporation in labelled cell extracts in the context of metabolic flux analysis.

A framework for tracer-based metabolism in mammalian cells by NMR

Metabolism changes extensively during the normal proliferation and differentiation of mammalian cells, and in cancer and inflammatory diseases. Since changes in the metabolic network reflect interactions between genetic, epigenetic and environmental changes, it is helpful to study the flow of label from isotopically labelled precursors into other metabolites rather than static metabolite levels. For this Nuclear Magnetic Resonance (NMR) spectroscopy is an attractive technique as it can quantify site-specific label incorporation. However, for applications using human cells and cell lines, the challenge is to optimize the process to maximize sensitivity and reproducibility. Here we present a new framework to analyze metabolism in mammalian cell lines and primary cells, covering the workflow from the preparation of cells to the acquisition and analysis of NMR spectra. We have applied this new approach in hematological and liver cancer cell lines and confirm the feasibility of tracer-based metabolism in primary liver cells.

Isotope tracing assisted metabolic profiling: Application to understanding HSP60 silencing mediated tumor progression

Isotope-tracing facilitates the understanding of metabolic regulation in biological systems. Depending on the selection of tracers, some essential metabolites cannot be traced. A comprehensive understanding of the regulated pathways can only be achieved with focus beyond labeled metabolites. The isotope tracing assisted metabolic profiling described here is a platform for high throughput mapping of isotope labeled metabolites with simultaneous metabolomics profiling. This approach incorporates an in-house MS/MS library for metabolite identification and ID-based quantitation. An "Isotopic" software was developed to generate potential labeled isotopomers. Using this platform, a total of 394 metabolites were reliably identified based on MS/MS confirmation in 3 million 293 T cells, among which 54 and 43 metabolites were discovered to carry extensive labels (>2%) from ¹³C₆-glucose and ¹³C₅-glutamine respectively. Citrate flowing into malate shuttle was also observed. More interestingly, the rate-limiting step in NAD and UDP-GlcNAc biosynthesis was clearly observed according to time course labeling. In HSP60 knockdown cell lines, enhanced purine and pyrimidine biosynthesis were confirmed by the abundance and labeling percentages of intermediate metabolites.

Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration

Metabolomics aims to quantitatively measure small-molecule metabolites in biological samples, such as bodily fluids (e.g., urine, blood, and saliva), tissues, and breathe exhalation, which reflects metabolic responses of a living system to pathophysiological stimuli or genetic modification. In the past decade, metabolomics has made notable progresses in providing useful systematic insights into the underlying mechanisms and offering potential biomarkers of many diseases. Metabolomics is a complementary manner of genomics and transcriptomics, and bridges the gap between genotype and phenotype, which reflects the functional output of a biological system interplaying with environmental factors. Recently, the technology of metabolomics study has been developed quickly. This review will discuss the whole pipeline of metabolomics study, including experimental design, sample collection and preparation, sample detection and data analysis, as well as mechanism interpretation, which can help understand metabolic effects and metabolite function for living organism in system level.

Integrated semi-targeted metabolomics analysis reveals distinct metabolic dysregulation in pleural effusion caused by tuberculosis and malignancy

BACKGROUND

Tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE) are the 2 most frequent causes of exudative pleural effusions (PEs). However, the clinical differentiation is challenging.

METHODS

Metabolic signatures in pleural effusion from 156 patients were profiled. An integrated semi-targeted metabolomics platform was incorporated for high throughput metabolite identification and quantitation. In this platform, orbitrap based mass spectrometry with data dependent MS/MS acquisition was applied in the analysis. In-house database containing ~1000MS/MS spectra were established and "MetaInt" was developed for metabolite alignment.

RESULTS

Using this strategy, lower levels of amino acids, citric acid cycle intermediates and free fatty acids accompanied with elevated acyl-carnitines and bile acids were observed, demonstrating increased energy expenditure caused by TPE. Kynurenine pathway from tryptophan was significantly enhanced in TPE. The ratio of tryptophan/kynurenine exhibited decent performance in differentiating TPE from MPE with sensitivity of 92.7% and specificity of 86.1%. After two further independent validations, it turns out that the ratio of tryptophan/kynurenine can be applied confidently as a potential biomarker together with adenosine deaminase (ADA) for clinical diagnosis of TPE.

CONCLUSIONS

Conclusively, the integrated in-house platform for high throughput semi-targeted metabolomics analysis reliably identified great potential of tryptophan/kynurenine ratio as a novel diagnostic biomarker to distinguish pleural effusion caused by tuberculosis and malignancy.