Search Results (68)

Background: Metabolomics is recognized as crucial technology for advancing our ability to diagnose, characterize, and monitor treatment of disease. Yet, metabolomics-based diagnostic testing has not been widely adapted into clinical practice because its technical requirements make it generally incompatible with operation at the point of care. One way to expand the reach of metabolomics-based testing, and its clinical benefits, is to utilize dried blood spots (DBS) as a testing sample type. Their easy collection, ambient storage capability, and cost-effective shipment make DBSs ideal for diagnostic tests that require the use of a centralized technology. Methods: To date, relatively few studies have investigated the performance of DBSs at capturing the global metabolome and reporting changes associated with physiological processes. In this study, we investigated those factors by performing global metabolomic profiling on DBSs collected from study volunteers under fasted and postprandial states, with and without dietary fish oil supplementation. Results: DBSs demonstrated broad coverage of metabolic pathways and captured numerous metabolic changes associated with feeding, fasting, and fish oil supplementation that have been reported in plasma and serum. Conclusions: Our findings support the hypothesis that DBSs are a viable sample type for metabolomics-based diagnostic testing and justify follow-up validation studies. Full article

Background: High-risk prostate cancer is often treated with combined androgen deprivation therapy (ADT) and radiotherapy (RT). Blood biomarkers may enable treatments to be tailored to individual patients. Metabolomics, the study of small-molecule alterations in blood, is promising, and lipids are emerging as potential markers of poor prognosis. This study aims to investigate metabolic changes during prostate cancer treatment and their correlation to disease outcome. Methods: This study included 136 blood plasma samples from 35 patients with high-risk prostate cancer treated with RT and ADT, recruited from the Uppsala/Umeå Comprehensive Cancer Consortium (U-CAN) project. Blood samples were collected before, during, and after treatment and analyzed at Metabolon Inc. (Durham, NC, USA). To study differences in metabolic levels during treatment, three different sampling time points were considered: before ADT, in-between ADT and RT, and after RT. Both multivariate (orthogonal projections to latent structures, OPLS) and univariate analyses were performed, where statistical significance in combination with a large fold change was considered indicative of a substantial change. Results: Significant changes in metabolite levels were observed. Many of the significant metabolites for the whole course of treatment were also significant during ADT but not during RT, indicating that changes during ADT dominated the overall treatment. Changes were found to be especially common in steroids and fatty acids. Multivariate analysis revealed significant differences in metabolites between relapsing and non-relapsing patients. Among the significant metabolites were cholesterol and epiandrosterone. Conclusions: Metabolomics can identify biomarkers for prostate cancer treatment response and relapse. Further studies are needed to identify patterns and individual metabolites to personalize treatment strategies for prostate cancer. Full article

Background/Objectives: Despite the growing popularity of fresh food for dogs, there is an extremely small amount of literature evaluating the potential health benefits of fresh food and reduced processing compared to traditionally processed shelf stable cans, extruded kibble, or other food formats. Additionally, aging dogs have been previously documented to have altered metabolism and nutritional needs compared to a healthy adult dog population, but these differences are not well defined. The objective of the study was to compare the effects of feeding a fresh, human-grade food versus a standard extruded kibble diet in a year-long longitudinal study on serum metabolomic profiles in senior dogs. Methods: Twenty-two healthy mixed-breed geriatric Alaskan sled dogs were age- and sex matched into two feeding groups. All dogs were fed the extruded diet (control) for a 4-month washout period prior to being transitioned into their respective treatment group. Group 1 continued to be fed the control diet, while Group 2 was transitioned to a fresh, human-grade food (treatment). Body weight and body condition were assessed monthly, and calorie intake was adjusted to maintain body weight. Individual serum samples were collected at day 0 and months 1, 3, 6, and 12. Metabolomic profiling of serum samples was performed by Metabolon, Inc. (Durham, NC, USA). Data was analyzed using two-way analysis of variance with repeated measures to determine treatment differences. Results: Dogs fed the treatment food had an increase in branched-chain amino acid metabolism, creatine, carnosine, anserine, fatty acid metabolism, long-chain n-3 fatty acids, lipolysis, and ketogenesis. The treatment group had decreased advanced glycation end products, fatty acid synthesis, and creatinine. Conclusions: This study is the first long-term feeding study evaluating serum metabolomics in dogs that demonstrates the dramatic and sustained impact that diet can have on canine metabolism. Full article

Pontocerebellar hypoplasia (PCH) encompasses a group of autosomal recessive neurodegenerative disorders marked by cerebellar and pontine atrophy. Multiple subtypes of PCH have been identified, among which the rare subtype PCH type 16 is caused by MINPP1 genetic variants. MINPPI encodes an enzyme essential for inositol polyphosphate dephosphorylation, regulating calcium and iron homeostasis. We conducted genome sequencing on a proband from the consanguineous family, who presented with a severe neurodegenerative disorder, to identify the underlying cause of disease. A comprehensive clinical assessment in addition to neuroradiological findings are described. We performed the functional validation of the identified variant and conducted untargeted metabolomic analyses. The clinical and radiological assessment of the patient showed a congenital brain anomaly and neurodegenerative symptoms. Further genetic analysis identified a homozygous loss-of-function variant (c.1401del, p.Ser468Valfs10*) in MINPP1, providing molecular confirmation of a clinical PCH diagnosis. While real-time quantitative PCR (RT-qPCR) showed that MINPP1 gene expression was unaffected in the proband, Western blot analysis demonstrated reduced protein abundance, supporting a pathogenic role of the variant. Metabolomic profiling revealed elevated lipid levels and disrupted inositol metabolism, providing further insights into the disease mechanism. These findings establish the pathogenicity of the p.Ser468Valfs10* variant in MINPP1 and highlight inositol metabolism as a potential pathway involved in PCH16, advancing the understanding of the pathophysiology of the disease. Full article

Background: This study aims to explore metabolic biomarkers and pathways in breast cancer prognosis. Methods: We performed a global post-radiotherapy (RT) urinary metabolomic analysis of 120 breast cancer patients: 60 progression-free (PF) patients as the reference and 60 with progressive disease (PD: recurrence, second primary, metastasis, or death). UPLC-MS/MS (Metabolon Inc.) identified 1742 biochemicals (1258 known and 484 unknown structures). Following normalization to osmolality, log transformation, and imputation of missing values, a Welch’s two-sample t-test was used to identify biochemicals and metabolic pathways that differed between PF and PD groups. Data analysis and visualization were performed with MetaboAnalyst. Results: Metabolic biomarkers and pathways that significantly differed between the PD and PF groups were the following: amino acid metabolism, including phenylalanine, tyrosine, and tryptophan biosynthesis (impact value (IV) = 1.00; p = 0.0007); histidine metabolism (IV = 0.60; p < 0.0001); and arginine and proline metabolism (IV = 0.70; p = 0.0035). Metabolites of carbohydrate metabolism, including glucose (p = 0.0197), sedoheptulose (p = 0.0115), and carboxymethyl lysine (p = 0.0098), were elevated in patients with PD. Gamma-glutamyl amino acids, myo-inositol, and oxidative stress biomarkers, including 7-Hydroxyindole Sulfate and sulfate, were elevated in patients who died (p ≤ 0.05). Conclusions: Amino acid metabolism emerged as a key pathway in breast cancer progression, while carbohydrate and oxidative stress metabolites also showed potential utility as biomarkers for breast cancer progression. These findings demonstrate applications of metabolomics in identifying metabolic biomarkers and pathways as potential targets for predicting breast cancer progression. Full article

Background/Objectives: Irritable bowel syndrome (IBS) is a complex disorder affecting 10% of the global population, but the underlying mechanisms remain poorly understood. By integrating multifluid metabolomics, we aimed to identify metabolite markers of IBS in a large population-based cohort. Methods: We included individuals from TwinsUK with and without IBS, ascertained using the Rome III criteria, and analysed serum (232 cases, 1707 controls), urine (185 cases, 1341 controls), and stool (186 cases, 1284 controls) metabolites (Metabolon Inc.). Results: After adjusting for covariates, and multiple testing, 44 unique metabolites (25 novel) were associated with IBS, including lipids, amino acids, and xenobiotics. Androsterone sulphate, a sulfated steroid hormone precursor, was associated with lower odds of IBS in both urine (0.69 [95% confidence interval = 0.56–0.85], p = 2.34 × 10⁻⁴) and serum (0.75 [0.63–0.90], p = 1.54 × 10⁻³. Moreover, suberate (C8-DC) was associated with higher odds of IBS in serum (1.36 [1.15–1.61]; p = 1.84 × 10⁻⁴) and lower odds of IBS in stool (0.76 [0.63–0.91]; p = 2.30 × 10⁻³). On the contrary, 32 metabolites appeared to be fluid-specific, including indole, 13-HODE + 9-HODE, pterin, bilirubin (E,Z or Z,Z), and urolithin. The remaining 10 metabolites were associated with IBS in one fluid with suggestive evidence (p < 0.05) in another fluid. Finally, we identified androgenic signalling, dicarboxylates, haemoglobin, and porphyrin metabolism to be significantly over-represented in individuals with IBS compared to controls. Conclusions: Our results highlight the utility of a multi-fluid approach in IBS research, revealing distinct metabolic signatures across biofluids. Full article

Abdominal aortic aneurysm represents a significant public health concern, particularly in men aged 55 to 64, where it occurs in about 1%. We investigated the metabolomics and genetics of AAA by analyzing a cohort including 76 patients with AAA and randomly selected 228 controls. Utilizing the Metabolon DiscoveryHD4 platform for non-targeted metabolomics profiling, we identified several novel metabolites significantly associated with AAA. These metabolites were primarily related to environmental and lifestyle factors, notably smoking and pesticide exposure, which underscores the influence of external factors on the progression of AAA. Additionally, several genetic variants were associated with xenobiotics, highlighting a genetic predisposition that may exacerbate the effects of these environmental exposures. The integration of metabolomic and genetic data provides compelling evidence that lifestyle, environmental, and genetic factors are intricately linked to the etiology of AAA. The results of our study not only deepen the understanding of the complex pathophysiology of AAA but also pave the way for the development of targeted therapeutic strategies. Full article

Background: Oxycodone has an elevated abuse liability profile compared to other prescription opioid medications. However, many human and rodent metabolomics studies have not been specifically focused on oxycodone. Objectives: Investigating metabolomics changes associated with oxycodone exposure can provide insights into biochemical mechanisms of the addiction cycle and prognosis prediction. Methods: Plasma samples from 16 rats at pre-exposure and intoxication time points were profiled on the Metabolon platform. A total of 941 metabolites were characterized. We employed a k-Nearest Neighbor imputation to impute metabolites with low levels of missingness and binarized metabolites with moderate levels of missingness, respectively. Results: Of the 136 binarized metabolites, 6 showed differential abundance (FDR < 0.05), including 5 that were present at pre-exposure but absent at intoxication (e.g., adenine), while linoleamide (18:2n6) exhibited the opposite behavior. Among the 798 metabolites with low levels of missingness, 364 showed significant changes between pre-exposure and intoxication (FDR < 0.01), including succinate, oleamide, and sarcosine. We identified four pathways, including tryptophan metabolism, that were nominally enriched among the metabolites that change with oxycodone exposure (p < 0.05). Furthermore, we identified several metabolites that showed nominal correlations with the Addiction Index (composite of oxycodone behaviors): 17 at pre-exposure and 8 at intoxication. In addition, the changes in abundance between pre-exposure and intoxication time points of 9 metabolites were nominally correlated with the Addiction Index, including sphingomyelins, methylhistidines, and glycerols. Conclusions: In summary, not only were we able to capture oxy-induced changes in metabolic pathways using easily accessible blood samples, but we also demonstrated the potential of blood metabolomics to better understand addiction liability. Full article

Background/Objectives: Both aging and chronic obstructive pulmonary disease (COPD) are strongly associated with changes in the metabolome; however, it is unknown whether there are common aging/COPD metabolomic signatures and if accelerated aging is associated with COPD. Methods: Plasma from 5704 subjects from the Genetic Epidemiology of COPD study (COPDGene) and 2449 subjects from Subpopulations and intermediate outcome measures in COPD study (SPIROMICS) were profiled using the Metabolon global metabolomics platform (1013 annotated metabolites). Post-bronchodilator spirometry measures of airflow obstruction (forced expiratory volume at one second (FEV₁)/forced vital capacity (FVC) < 0.7) were used to define COPD. Elastic net regression was trained on never and former smokers with normal spirometry and no emphysema to create a metabolomic age score which was validated in SPIROMICS subjects. Results: Our metabolic age score was strongly associated with chronic age in the validation cohort (correlation coefficient = 0.8). COPD subjects with accelerated aging (>7 years difference between metabolic and actual age) had more severe disease compared with those who had decelerated aging (<−7 years difference between metabolic and actual age). COPD and aging metabolites were shared more than expected (p < 0.001), with amino acid and glutathione metabolism among pathways overrepresented. Conclusions: These findings suggest a common mechanism between aging and COPD and that COPD is associated with accelerated metabolic aging. Full article

It has been previously established that breast cancer cells exhibit high expression of the monocarboxylate (lactate) transporters (MCT1 and/or MCT4) and carbonic anhydrase IX (CAIX) and form a functional metabolon for proton-coupled lactate export, thereby stabilizing intracellular pH. CD147 is the MCT accessory protein that facilitates the creation of the MCT/CAIX complex. This study describes how the small molecule Beta-Galactose 2C (BGal2C) blocks the physical and functional interaction between CAIX and either MCT1 or MCT4 in Xenopus oocytes, which reduces the rate of proton and lactate flux with an IC₅₀ of ~90 nM. This value is similar to the K_i for inhibition of CAIX activity. Furthermore, it is shown that BGal2C blocks hypoxia-induced lactate transport in MDA-MB-231 and MCF-7 breast cancer cells, both of which express CAIX. As in oocytes, BGal2C interferes with the physical interaction between CAIX and MCTs in both cell types. Finally, X-ray crystallographic studies highlight unique interactions between BGal2C and a CAIX-mimic that are not observed within the CAII active site and which may underlie the strong specificity of BGal2C for CAIX. These studies demonstrate the utility of a novel sulfonamide in interfering with elevated proton and lactate flux, a hallmark of many solid tumors. Full article

Identification of the individuals having impaired kidney function is essential in preventing the complications of this disease. We measured 1009 metabolites at the baseline study in 10,159 Finnish men of the METSIM cohort and associated the metabolites with an estimated glomerular filtration rate (eGFR). A total of 7090 men participated in the 12-year follow-up study. Non-targeted metabolomics profiling was performed at Metabolon, Inc. (Morrisville, NC, USA) on EDTA plasma samples obtained after overnight fasting. We applied liquid chromatography mass spectrometry (LC-MS/MS) to identify the metabolites (the Metabolon DiscoveryHD4 platform). We performed association analyses between the eGFR and metabolites using linear regression adjusted for confounding factors. We found 108 metabolites significantly associated with a decrease in eGFR, and 28 of them were novel, including 12 amino acids, 8 xenobiotics, 5 lipids, 1 nucleotide, 1 peptide, and 1 partially characterized molecule. The most significant associations were with five amino acids, N-acetylmethionine, N-acetylvaline, gamma-carboxyglutamate, 3-methylglutaryl-carnitine, and pro-line. We identified 28 novel metabolites associated with decreased eGFR in the 12-year follow-up study of the METSIM cohort. These findings provide novel insights into the role of metabolites and metabolic pathways involved in the decline of kidney function. Full article

An application of CO₂/HCO₃⁻-free solution (Zero-CO₂) did not increase intracellular pH (pH_i) in ciliated human nasal epithelial cells (c-hNECs), leading to no increase in frequency (CBF) or amplitude (CBA) of the ciliary beating. This study demonstrated that the pH_i of c-hNECs expressing carbonic anhydrase IV (CAIV) is high (7.64), while the pH_i of ciliated human bronchial epithelial cells (c-hBECs) expressing no CAIV is low (7.10). An extremely high pH_i of c-hNECs caused pH_i, CBF and CBA to decrease upon Zero-CO₂ application, while a low pH_i of c-hBECs caused them to increase. An extremely high pH_i was generated by a high rate of HCO₃⁻ influx via interactions between CAIV and Na⁺/HCO₃⁻ cotransport (NBC) in c-hNECs. An NBC inhibitor (S0859) decreased pH_i, CBF and CBA and increased CBF and CBA in c-hNECs upon Zero-CO₂ application. In conclusion, the interactions of CAIV and NBC maximize HCO₃⁻ influx to increase pH_i in c-hNECs. This novel mechanism causes pH_i to decrease, leading to no increase in CBF and CBA in c-hNECs upon Zero-CO₂ application, and appears to play a crucial role in maintaining pH_i, CBF and CBA in c-hNECs periodically exposed to air (0.04% CO₂) with respiration. Full article

Metabolomics can uncover physiological responses to prebiotic fibre and omega-3 fatty acid supplements with known health benefits and identify response-specific metabolites. We profiled 534 stool and 799 serum metabolites in 64 healthy adults following a 6-week randomised trial comparing daily omega-3 versus inulin supplementation. Elastic net regressions were used to separately identify the serum and stool metabolites whose change in concentration discriminated between the two types of supplementations. Random forest was used to explore the gut microbiome’s contribution to the levels of the identified metabolites from matching stool samples. Changes in serum 3-carboxy-4-methyl-5-propyl-2-furanpropanoate and indoleproprionate levels accurately discriminated between fibre and omega-3 (area under the curve (AUC) = 0.87 [95% confidence interval (CI): 0.63–0.99]), while stool eicosapentaenoate indicated omega-3 supplementation (AUC = 0.86 [95% CI: 0.64–0.98]). Univariate analysis also showed significant increases in indoleproprionate with fibre, 3-carboxy-4-methyl-5-propyl-2-furanpropanoate, and eicosapentaenoate with omega-3. Out of these, only the change in indoleproprionate was partly explained by changes in the gut microbiome composition (AUC = 0.61 [95% CI: 0.58–0.64] and Rho = 0.21 [95% CI: 0.08–0.34]) and positively correlated with the increase in the abundance of the genus Coprococcus (p = 0.005). Changes in three metabolites discriminated between fibre and omega-3 supplementation. The increase in indoleproprionate with fibre was partly explained by shifts in the gut microbiome, particularly Coprococcus, previously linked to better health. Full article

Chalcone synthase (CHS) and chalcone isomerase (CHI) catalyze the first two committed steps of the flavonoid pathway that plays a pivotal role in the growth and reproduction of land plants, including UV protection, pigmentation, symbiotic nitrogen fixation, and pathogen resistance. Based on the obtained X-ray crystal structures of CHS, CHI, and chalcone isomerase-like protein (CHIL) from the same monocotyledon, Panicum virgatum, along with the results of the steady-state kinetics, spectroscopic/thermodynamic analyses, intermolecular interactions, and their effect on each catalytic step are proposed. In addition, PvCHI’s unique activity for both naringenin chalcone and isoliquiritigenin was analyzed, and the observed hierarchical activity for those type-I and -II substrates was explained with the intrinsic characteristics of the enzyme and two substrates. The structure of PvCHS complexed with naringenin supports uncompetitive inhibition. PvCHS displays intrinsic catalytic promiscuity, evident from the formation of p-coumaroyltriacetic acid lactone (CTAL) in addition to naringenin chalcone. In the presence of PvCHIL, conversion of p-coumaroyl-CoA to naringenin through PvCHS and PvCHI displayed ~400-fold increased V_max with reduced formation of CTAL by 70%. Supporting this model, molecular docking, ITC (Isothermal Titration Calorimetry), and FRET (Fluorescence Resonance Energy Transfer) indicated that both PvCHI and PvCHIL interact with PvCHS in a non-competitive manner, indicating the plausible allosteric effect of naringenin on CHS. Significantly, the presence of naringenin increased the affinity between PvCHS and PvCHIL, whereas naringenin chalcone decreased the affinity, indicating a plausible feedback mechanism to minimize spontaneous incorrect stereoisomers. These are the first findings from a three-body system from the same species, indicating the importance of the macromolecular assembly of CHS-CHI-CHIL in determining the amount and type of flavonoids produced in plant cells. Full article

Serotonin transporter (SERT) deficiency has been implicated in metabolic syndrome, intestinal inflammation, and microbial dysbiosis. Interestingly, changes in microbiome metabolic capacity and several alterations in host gene expression, including lipid metabolism, were previously observed in SERT^−/− mice ileal mucosa. However, the precise host or microbial metabolites altered by SERT deficiency that may contribute to the pleiotropic phenotype of SERT KO mice are not yet understood. This study investigated the hypothesis that SERT deficiency impacts lipid and microbial metabolite abundances in the ileal mucosa, where SERT is highly expressed. Ileal mucosal metabolomics was performed by Metabolon on wild-type (WT) and homozygous SERT knockout (KO) mice. Fluorescent-activated cell sorting (FACS) was utilized to measure immune cell populations in ileal lamina propria to assess immunomodulatory effects caused by SERT deficiency. SERT KO mice exhibited a unique ileal mucosal metabolomic signature, with the most differentially altered metabolites being lipids. Such changes included increased diacylglycerols and decreased monoacylglycerols in the ileal mucosa of SERT KO mice compared to WT mice. Further, the ileal mucosa of SERT KO mice exhibited several changes in microbial-related metabolites known to play roles in intestinal inflammation and insulin resistance. SERT KO mice also had a significant reduction in the abundance of ileal group 3 innate lymphoid cells (ILC3). In conclusion, SERT deficiency induces complex alterations in the ileal mucosal environment, indicating potential links between serotonergic signaling, gut microbiota, mucosal immunity, intestinal inflammation, and metabolic syndrome. Full article