Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases.

The rising prevalence of liver diseases related to obesity and excessive use of alcohol is fuelling an increasing demand for accurate biomarkers aimed at community screening, diagnosis of steatohepatitis and significant fibrosis, monitoring, prognostication and prediction of treatment efficacy. Breakthroughs in omics methodologies and the power of bioinformatics have created an excellent opportunity to apply technological advances to clinical needs, for instance in the development of precision biomarkers for personalised medicine. Via omics technologies, biological processes from the genes to circulating protein, as well as the microbiome - including bacteria, viruses and fungi, can be investigated on an axis. However, there are important barriers to omics-based biomarker discovery and validation, including the use of semi-quantitative measurements from untargeted platforms, which may exhibit high analytical, inter- and intra-individual variance. Standardising methods and the need to validate them across diverse populations presents a challenge, partly due to disease complexity and the dynamic nature of biomarker expression at different disease stages. Lack of validity causes lost opportunities when studies fail to provide the knowledge needed for regulatory approvals, all of which contributes to a delayed translation of these discoveries into clinical practice. While no omics-based biomarkers have matured to clinical implementation, the extent of data generated has enabled the hypothesis-free discovery of a plethora of candidate biomarkers that warrant further validation. To explore the many opportunities of omics technologies, hepatologists need detailed knowledge of commonalities and differences between the various omics layers, and both the barriers to and advantages of these approaches.

Human Cerebrospinal Fluid Sample Preparation and Annotation for Integrated Lipidomics and Metabolomics Profiling Studies.

Cerebrospinal fluid (CSF) is a metabolically diverse biofluid and a key specimen for exploring biochemical changes in neurodegenerative diseases. Detecting lipid species in CSF using mass spectrometry (MS)-based techniques remains challenging because lipids are highly complex in structure, and their concentrations span over a broad dynamic range. This work aimed to develop a robust lipidomics and metabolomics method based on commonly used two-phase extraction systems from human CSF samples. Prioritizing lipid detection, biphasic extraction methods, Folch, Bligh and Dyer (B&D), Matyash, and acidified Folch and B&D (aFolch and aB&D) were compared using 150 µL of human CSF samples for the simultaneous extraction of lipids and metabolites with a wide range of polarity. Multiple chromatographical separation approaches, including reversed-phase liquid chromatography (RPLC), hydrophilic interaction liquid chromatography (HILIC), and gas chromatography (GC), were utilized to characterize human CSF metabolome. The aB&D method was found as the most reproducible technique (RSD < 15%) for lipid extraction. The aB&D and B&D yielded the highest peak intensities for targeted lipid internal standards and displayed superior extracting power for major endogenous lipid classes. A total of 674 unique metabolites with a wide polarity range were annotated in CSF using, combining RPLC-MS/MS lipidomics (n = 219), HILIC-MS/MS (n = 304), and GC-quadrupole time of flight (QTOF) MS (n = 151). Overall, our findings show that the aB&D extraction method provided suitable lipid coverage, reproducibility, and extraction efficiency for global lipidomics profiling of human CSF samples. In combination with RPLC-MS/MS lipidomics, complementary screening approaches enabled a comprehensive metabolite signature that can be employed in an array of clinical studies.

Ceramides are decreased after liraglutide treatment in people with type 2 diabetes: a post hoc analysis of two randomized clinical trials.

BACKGROUND: Specific ceramides have been identified as risk markers for cardiovascular disease (CVD) years before onset of disease. Treatment with the glucagon-like peptide-1 receptor agonist (GLP-1RA) liraglutide has been shown to induce beneficial changes in the lipid profile and reduce the risk of CVD. Reducing lipotoxic lipids with an antidiabetic drug therapy could be a path towards precision medicine approaches for the treatment of complications to diabetes. In this post-hoc study, an investigation was carried out on the effect of liraglutide on CVD-risk associated ceramides in two randomized clinical trials including participants with type 2 diabetes (T2D). METHODS: This study analyzed plasma samples from two independent randomized placebo-controlled clinical trials. The first trial, Antiproteinuric Effects of Liraglutide Treatment (LirAlbu12) followed a crossover design where 27 participants were treated for 12 weeks with either liraglutide (1.8 mg/d) or placebo, followed by a four-week washout period, and then another 12 weeks of the other treatment. The second clinical trial, Effect of Liraglutide on Vascular Inflammation in Type-2 Diabetes (LiraFlame26), lasted for 26 weeks and followed a parallel design, where 102 participants were randomized 1:1 to either liraglutide or placebo. Heresix prespecified plasma ceramides were measured using liquid chromatography mass spectrometry and assessed their changes using linear mixed models. Possible confounders were assessed with mediation analyses. RESULTS: In the LiraFlame26 trial, 26-week treatment with liraglutide resulted in a significant reduction of two ceramides associated with CVD risk, C16 Cer and C24:1 Cer (p < 0.05) compared to placebo. None of the remaining ceramides showed statistically significant changes in response to liraglutide treatment compared to placebo. Significant changes in ceramides were not found after 12-weeks of liraglutide treatment in the LirAlbu12 trial. Mediation analyses showed that weight loss did not affect ceramide reduction. CONCLUSIONS: It was demonstrated that treatment with liraglutide resulted in a reduction in C16 Cer and C24:1 Cer after 26 weeks of treatment. These findings suggest the GLP-1RA can be used to modulate ceramides in addition to its other properties. TRIAL REGISTRATION: Clinicaltrial.gov identifier: NCT02545738 and NCT03449654.

Sphingolipids Are Depleted in Alcohol-Related Liver Fibrosis.

BACKGROUND & AIMS: Alcohol disturbs hepatic lipid synthesis and transport, but the role of lipid dysfunction in alcohol-related liver disease (ALD) is unclear. In this biopsy-controlled, prospective, observational study, we characterized the liver and plasma lipidomes in patients with early ALD. METHODS: We performed mass spectrometry-based lipidomics of paired liver and plasma samples from 315 patients with ALD and of plasma from 51 matched healthy controls. We associated lipid levels with histologic fibrosis, inflammation, and steatosis with correction for multiple testing and adjustment for confounders. We further investigated sphingolipid regulation by means of quantitative real-time polymerase chain reaction sequencing of microRNA, prediction of liver-related events, and tested causality with Mendelian randomization. RESULTS: We detected 198 lipids in the liver and 236 lipids in the circulation from 18 lipid classes. Most sphingolipids (sphingomyelins and ceramides) and phosphocholines were co-down-regulated in both liver and plasma, where lower abundance correlated with higher fibrosis stage. Sphingomyelins showed the most pronounced negative correlation to fibrosis, mirrored by negative correlations in both liver and plasma with hepatic inflammation. Reduced sphingomyelins predicted future liver-related events. This seemed to be characteristic of "pure ALD," as sphingomyelin levels were higher in patients with concomitant metabolic syndrome and ALD/nonalcoholic fatty liver disease overlap. Mendelian randomization in FinnGen and UK Biobanks indicated ALD as the cause of low sphingomyelins, and alcohol use disorder did not correlate with genetic susceptibility to low sphingomyelin levels. CONCLUSIONS: Alcohol-related liver fibrosis is characterized by selective and progressive lipid depletion in liver and blood, particularly sphingomyelins, which also associates with progression to liver-related events.

Effects of Butyrate Supplementation on Inflammation and Kidney Parameters in Type 1 Diabetes: A Randomized, Double-Blind, Placebo-Controlled Trial.

Type 1 diabetes is associated with increased intestinal inflammation and decreased abundance of butyrate-producing bacteria. We investigated the effect of butyrate on inflammation, kidney parameters, HbA1c, serum metabolites and gastrointestinal symptoms in persons with type 1 diabetes, albuminuria and intestinal inflammation. We conducted a randomized placebo-controlled, double-blind, parallel clinical study involving 53 participants randomized to 3.6 g sodium butyrate daily or placebo for 12 weeks. The primary endpoint was the change in fecal calprotectin. Additional endpoints were the change in fecal short chain fatty acids, intestinal alkaline phosphatase activity and immunoglobulins, serum lipopolysaccharide, CRP, albuminuria, kidney function, HbA1c, metabolites and gastrointestinal symptoms. The mean age was 54 ± 13 years, and the median [Q1:Q3] urinary albumin excretion was 46 [14:121] mg/g. The median fecal calprotectin in the butyrate group was 48 [26:100] µg/g at baseline, and the change was -1.0 [-20:10] µg/g; the median in the placebo group was 61 [25:139] µg/g at baseline, and the change was -12 [-95:1] µg/g. The difference between the groups was not significant (p = 0.24); neither did we find an effect of butyrate compared to placebo on the other inflammatory markers, kidney parameters, HbA1c, metabolites nor gastrointestinal symptoms. Twelve weeks of butyrate supplementation did not reduce intestinal inflammation in persons with type 1 diabetes, albuminuria and intestinal inflammation.

High-Throughput UHPLC-MS to Screen Metabolites in Feces for Gut Metabolic Health.

Feces are the product of our diets and have been linked to diseases of the gut, including Chron's disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n = 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. MS analyses of the prepared fecal samples have shown reproducibility and coverage of n = 28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD (limit of detection), LOQ (limit of quantification), range of linearity and method recovery. The average concentrations for 135 healthy participants are reported here for clinical applications. Our high-throughput method provides a novel tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.

Liraglutide Lowers Palmitoleate Levels in Type 2 Diabetes. A Post Hoc Analysis of the LIRAFLAME Randomized Placebo-Controlled Trial.

Background: Liraglutide is a glucose-lowering medication used to treat type 2 diabetes and obesity. It is a GLP-1 receptor agonist with downstream metabolic changes beyond the incretin system, such as reducing the risk of cardiovascular complications. The understanding of these changes is critical for improving treatment outcomes. Herein, we present a post hoc experimental analysis using metabolomic phenotyping to discover molecular mecphanisms in response to liraglutide. Method: Plasma samples were obtained from The LiraFlame Study (ClinicalTrials.gov identifier: NCT03449654), a randomized double-blinded placebo-controlled clinical trial, including 102 participants with type 2 diabetes randomized to either liraglutide or placebo treatment for 26 weeks. Mass spectrometry-based metabolomics analyses were carried out on samples from baseline and the end of the trial. Metabolites (n=114) were categorized into pathways and linear mixed models were constructed to evaluate the association between changes in metabolites and liraglutide treatment. Results: We found the free fatty acid palmitoleate was significantly reduced in the liraglutide group compared to placebo (adjusted for multiple testing p-value = 0.04). The activity of stearoyl-CoA desaturase-1 (SCD1), the rate limiting enzyme for converting palmitate into palmitoleate, was found significantly downregulated by liraglutide treatment compared to placebo (p-value = 0.01). These metabolic changes have demonstrated to be linked to insulin sensitivity and cardiovascular health.

Increasing calcium phosphate aqueous solubility and spontaneous supersaturation combining citrate and gluconate with perspectives for functional foods.

Uptake of calcium from food depends on solubility of calcium salts in the intestines, and precipitation of calcium phosphates decreases bioaccessibility of food calcium. Citrate as a high affinity complex binder for calcium was found spontaneously to create strongly supersaturated solutions by rapid dissolution of calcium hydrogen phosphate characterized by short lag phases for precipitation. Gluconate with weaker affinity for calcium binding showed longer lag phases for precipitation from supersaturated solutions. For citrate/gluconate combinations, the highest degree of supersaturation with longest lag phases for precipitation were found by trial-and-error experiments for a citrate/gluconate ratio of 1:10 for dissolution of calcium hydrogen phosphate resulting in supersaturation factors around three and without precipitation for more than a month. The aim of the present study was to provide a physicochemical explanation of this robust supersaturation. Calcium speciation based on electrochemical calcium activity measurement identified a low [Ca2+]·[HCitr2-] product as critical for supersaturation.

Calcium availability from whey mineral residues increased by hydrogen citrate.

Insoluble mineral residues from whey processing dominated by hydroxyapatite and calcium hydrogen phosphate were found to dissolve isothermally in aqueous sodium hydrogen citrate. Dissolution occurred spontaneously and the resultant homogeneous solutions were found to be supersaturated solutions in both calcium citrate and calcium hydrogen phosphate. Supersaturation was investigated by visual inspection combined with turbidity measurements and analyses of calcium and phosphorous by ICP. The maximal supersaturation was found to be proportional to total hydrogen citrate concentration. For 0.2 M hydrogen citrate, maximum calcium concentration was achieved in the first hours of dissolution resulting in the supersaturation of calcium hydrogen phosphate with a factor of 10. Calcium citrate rather than calcium hydrogen phosphate precipitated from the supersaturated solutions and the time elapsing before precipitation began, increased with increasing concentrations of excess of hydrogen citrate. This lag phase for precipitation ranged from several hours for 0.2 M hydrogen citrate to more than a day for higher hydrogen citrate concentrations, for which the solutions were saturated in calcium hydrogen phosphate and became supersaturated only in calcium citrate due to the strong binding of calcium by citrate. The appearance and decay of supersaturation was kinetically studied in order to provide the background for future exploration of whey minerals in functional foods for improved calcium nutrition.

Hydroxycarboxylate combinations for increasing solubility and robustness of supersaturated solutions of whey mineral residues.

Calcium phosphates present in whey mineral residue is a potential source of calcium for dietary purposes. Combinations of aqueous isocitrate and citrate were found more efficient than each of the isomers in dissolving dried insoluble whey processing mineral residues spontaneously forming supersaturated solutions. Hydrogen isocitrate was found around 30% less efficient in these non thermal dissolution processes compared to hydrogen citrate based on amount of dissolved calcium. In contrast, the lag phase of up to 4 h for precipitation of calcium citrate from the supersaturated solutions was significantly longer when calcium isocitrate was present. Highest degree of supersaturation with longest lag phase for precipitation was found for citrate/isocitrate combinations in a 1:1 ratio. Addition of calcium saccharate during dissolution further prolonged the lag phase simultaneously preserving the higher supersaturation degrees. Combinations of the three hydroxycarboxylates seem accordingly to provide a basis for increasing calcium availability from dried whey mineral fractions consisting mainly of calcium hydrogen phosphate and hydroxyapatite of low solubility with the perspective of transforming a side stream from cheese production into valuable functional foods.

Selection for Growth and Precocity Alters Muscle Metabolism in Nellore Cattle.

To clarify the relationship between beef genetic selection for growth and precocity with muscle metabolism and metabolites, we performed metabolomic analysis using Longissimus lumborum (LL) muscle from Nellore cattle with divergent selection for these traits (high growth, HG; low growth, LG; high precocity, HP; low precocity, LP). Genetic potential for growth affected muscle protein and energetic metabolism. HG animals had a high concentration of arginine, carnosine, and leucine compared to LG animals. HP animals presented a high concentration of glutamine, betaine, creatinine, isoleucine, carnitine, acetyl carnitine, and lower levels of glucose compared to LP animals, affecting protein and fatty acid metabolism. Intensity of selection (high or low) was correlated with changes in protein metabolism, and the type of selection (growth or precocity) affected fat metabolism. In conclusion, both HG and HP appear to be correlated with a high concentration of protein metabolites and changes in protein metabolic pathways, while selection for precocity is more correlated with changes in fat metabolism compared to animals selected for growth.

Mate extract as feed additive for improvement of beef quality.

Mate (Ilex paraguariensis A.St.-Hil.) is generally recognized as safe (GRAS status) and has a high content of alkaloids, saponins, and phenolic acids. Addition of mate extract to broilers feed has been shown to increase the oxidative stability of chicken meat, however, its effect on beef quality from animals supplemented with mate extract has not been investigated so far. Addition of extract of mate to a standard maize/soy feed at a level of 0.5, 1.0 or 1.5% w/w to the diet of feedlot for cattle resulted in increased levels of inosine monophosphate, creatine and carnosine in the fresh meat. The content of total conjugated linoleic acid increased in the meat as mate extract concentration was increased in the feed. The tendency to radical formation in meat slurries as quantified by EPR spin-trapping decreased as increasing mate extract addition to feed, especially after storage of the meat, indicating higher oxidative stability. Mate supplementation in the diet did not affect animal performance and carcass characteristics, but meat from these animals was more tender and consequently more accepted by consumers. Mate extract is shown to be a promising additive to feedlot diets for cattle to improve the oxidative stability, nutritive value and sensory quality of beef.

Kinetics and thermodynamics of 1-hydroxyethyl radical reaction with unsaturated lipids and prenylflavonoids.

Hydroxyalkyl radicals have been reported to induce lipid oxidation as the key aspect of the pathogenesis of alcoholic fatty liver disease and are responsible for the alkylation and cleavage of DNA during the metabolism of a wide range of genotoxic compounds. However, relevant kinetic data for the oxidation of unsaturated lipids by 1-hydroxyethyl radical (HER) has not been reported. In this study, the rate constants for the reaction of unsaturated fatty acid methyl esters and sterols with HER have been determined using a competitive kinetic approach employing the spin-trap α-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN) as the competitive substrate. Polyunsaturated fatty acid methyl ester is shown to react with HER with an apparent second-order rate constant ranging from (3.7 ± 0.1) × 10(6) L mol(-1) s(-1) for methyl linoleate to (2.7 ± 0.2) × 10(7) L mol(-1) s(-1) for methyl docosahexanoate at 25.0 ± 0.2 °C in ethanol. The apparent second-order rate constant for polyunsaturated fatty acid methyl ester oxidation by HER is dependent on the number of bisallylic hydrogen atoms rather than on the bond dissociation energy value for the weakest C-H bond as determined by ab initio density functional theory calculations. Sterols displayed higher reactivity compared to unsaturated fatty acid methyl esters with apparent second-order rate constants of (2.7 ± 0.1) × 10(6) and (5.2 ± 0.1) × 10(7) L mol(-1) s(-1) at 25.0 ± 0.2 °C in ethanol for cholesterol and ergosterol, respectively. Similar experiments with prenylflavonoids as potential herbal chemopreventive agents for preventing alcoholic liver diseases yield apparent second-order rate constants close to the diffusion control with kapp values of (1.5 ± 0.2) and (3.6 ± 0.1) × 10(9) L mol(-1)s(-1) for 6-prenylnarigerin and xanthohumol at 25.0 ± 0.2 °C in ethanol solution, respectively. Polyunsaturated lipids were revealed to be highly reactive oxidizable substrates toward HER-induced oxidation in biological systems leading to damage of membranes and sensitive structures.

Riboflavin photosensitized oxidation of myoglobin.

The reaction of the fresh meat pigment oxymyoglobin, MbFe(II)O2, and its oxidized form metmyoglobin, MbFe(III), with triplet-state riboflavin involves the pigment protein, which is oxidatively cleaved or dimerized as shown by SDS-PAGE and Western blotting. The overall rate constant for oxidation of MbFe(II)O2 by ³Rib is (3.0 ± 0.5) × 109 L·mol⁻¹·s⁻¹ and (3.1 ± 0.4) × 109 L·mol⁻¹·s⁻¹ for MbFe(III) in phosphate buffer of pH 7.4 at 25 °C as determined by laser flash photolysis. The high rates are rationalized by ground state hydrophobic interactions as detected as static quenching of fluorescence from singlet-excited state riboflavin by myoglobins using time-resolved fluorescence spectroscopy and a Stern-Volmer approach. Binding of riboflavin to MbFe(III) has K(a) = (1.2 ± 0.2) × 104 mol·L⁻¹ with ΔH° = -112 ± 22 kJ·mol⁻¹ and ΔS° = -296 ± 75 J·mol⁻¹·K⁻¹. For meat, riboflavin is concluded to be a photosensitizer for protein oxidation but not for discoloration.