Mass Spectrometry-based Metabolomics Research Articles

Multi-Omics Analysis of the Impact of Long Distance Trail Running on Red Blood Cells Highlights Acylcarnitine Mediated Lipid Damage Repair Mechanisms

Red blood cells (RBC) play critical roles in the maintenance of vascular tone and metabolite transfer in addition to their well characterized role in gas exchange. In this capacity, they play a central role in maintaining systemic activity during stressful physiological situations such as exercise. At the far end of the spectrum for endurance sports, the popularity of long-distance running has been increasing in recent years. However, literature on the impact of marathon and ultramarathon running on red blood cell physiology is limited. To characterize molecular responses in RBC to long-distance running, blood was sampled from 11 runners before and after the Martigny-Combes à Chamonix (MCC, distance: 40 km, elevation gain: 2300 m) or 12 runners before and after the Ultra - Trail du Mont Blanc (UTMB, distance: 171 km, elevation gain: 10,000 m) and separated into plasma and RBC components. Hematological parameters and RBC deformability were assessed before and after each race. 1 Here, the same samples were analyzed using mass spectrometry-based metabolomics, lipidomics, proteomics, and elemental analysis ( Figure 1A). While RBC after both races had decreased mean cell volume (MCV), RBC exhibited higher amounts of exposed phosphatidylserine (PS) on the outer membrane only after the MCC, which serves as a signal for eryptosis. However, hematocrit (Hct) remained unchanged after this race, but was significantly lower after the UTMB. 1 Although decreased Hct can result from hemodilution, the plasma levels of albumin, sodium, and potassium were not significantly altered in either race. In addition, RBC microparticles increased after the UTMB with concomitant decreases in the deformability of intact RBC at high shear stresses, effects of which were not observed after the MCC. Intracellular metabolic correlates with deformability were enriched with acylcarnitines (AC - Figure 1A), which inversely correlated with RBC deformability at 30 Pa. This compound class was also positively associated with the level of IL-6 in addition to kynurenine, an immunomodulatory metabolite which has also been linked to IL-6 level and RBC damage in COVID19. 2 Within RBC, that are largely devoid of mitochondria, AC play an intermediary role in membrane lipid repair ( Figure 1A). While AC and fatty acids were significantly higher after both races, the magnitude of increase was higher after the MCC ( Figure 1B). However, the ratios of lysophosphatidylcholines or lysophosphatidylethanolamines to their respective intact lipid counterparts were predominantly lower after the UTMB, indicating more active membrane lipid repair in these cells ( Figure 1B). In support, the coenzyme A precursor pantothenate was consumed after both races, though carnitine accumulated only after the UTMB possibly due to increased acyl-CoA utilization for lipid repair rather than interconversion into AC. Increased oxidative stress was also apparent in the proteome, which demonstrated that the proportion of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with irreversibly oxidized active site cysteine was significantly higher after the UTMB. As this protein plays a key regulatory role in glucose oxidation by mediating fluxes through glycolysis or the pentose phosphate pathway (PPP) in an oxidative stress-dependent fashion, 3 increased damage to its active site may partially explain a shift in glucose catabolism away from glycolysis and towards the PPP to generate NADPH reducing equivalents to cope with accumulating oxidative stress. In consideration of the varying temporal exposures to physiological stress between the MCC and UTMB, these results provide an in vivo snapshot into the accumulation of damage, repair, and removal of RBC as they circulate throughout the body during exercise. 1. Robert M, Stauffer E, Nader E, et al. Impact of Trail Running Races on Blood Viscosity and Its Determinants: Effects of Distance. Int. J. Mol. Sci. 2020;21(22):8531. 2. Thomas T, Stefanoni D, Dzieciatkowska M, et al. Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients. J. Proteome Res. 2020;19(11):4455-4469. 3. Reisz JA, Wither MJ, Dzieciatkowska M, et al. Oxidative modifications of glyceraldehyde 3-phosphate dehydrogenase regulate metabolic reprogramming of stored red blood cells. Blood. 2016;128(12):e32-e42.

Results from a Phase (Ph) 1 Clinical Study of the All-Oral Regimen of CC-486 and Venetoclax for Relapsed and Refractory Acute Myeloid Leukemia

Background: Venetoclax (Ven) with azacitidine (Aza) is the standard of care for newly diagnosed AML patients who are unfit for intensive induction chemotherapy. It is well known that this treatment also has activity in the relapsed and refractory (R/R) setting. However, this regimen requires 7 consecutive daily subcutaneous or intravenous doses of Aza each month, which continues indefinitely. The relative inconvenience of this, and its negative impact on quality of life, may lead to its early discontinuation, which may decrease the efficacy or durability of this regimen. A more convenient all-oral regimen may decrease visits to an infusion center, improve quality of life, and potentially increase the efficacy of the regimen due to improved compliance. CC-486 is the oral formulation of Aza that is currently approved for post-induction chemotherapy maintenance in AML. Methods: This is a single center open label, Ph I study investigating CC-486 and Ven in R/R AML patients. In the dose escalation phase, subjects received CC-486 at one of two cohorts (200 mg PO days 1-14 and 300 mg PO days 1-14). Ven was given at the 400 mg/day PO regimen, for 28 days, after an initial intra-patient dose escalation per the standard of care. Using a 3+3 study design for these two cohorts, we aimed to determine the maximum tolerated dose (MTD) of CC-486 in combination with Ven. An expansion cohort is planned for 10 additional patients treated at the MTD. To assess whether CC-486 exerts similar effects in the leukemia stem cell population (LSCs) compared to conventional IV Aza, we retrospectively analyzed patient samples from cohort 1 with a patient sample treated with Ven/IV Aza outside of the study. We performed mass spectrometry-based metabolomics analyses in LSCs isolated from patient samples as well as single-cell RNA sequencing. Results: A total of 9 patients were accrued for this Ph I study (Figure 1A). The average age at the time of enrolment was 66, and median prior treatment regimens was 1 (range 1-3). Five patients had received Ven/Aza in prior treatments. There were no dose-limiting toxicity (DLT) events and the MTD was determined to be 300mg. The most common hematologic toxicities were Gr 3-4 neutropenia (n = 8, 89%), Gr 3-4 anemia (n = 7, 78%), and Gr 3-4 thrombocytopenia (n = 5, 56%). The most common non-hematologic toxicities were Gr 1-2 nausea (n = 5, 56%), fatigue (n = 2, 22%), and diarrhea (n = 2, 22%). Febrile neutropenia was also seen in two subjects (Gr 1-2 n = 1, 11%, Gr 3-4 n= 1, 11%). Best responses were complete remission (CR) (n = 2, 22%) partial remission (PR) (n = 1, 11%), and stable disease (SD) (n= 3, 33%). Three patients proceeded to an allogeneic stem cell transplant. Overall survival was 288 days, 95% CI: (39 days, 424 days). To determine whether CC-486/Ven exerts similar effects on the LSC population compared to conventional IV Aza/Ven, LSCs were isolated from the bone marrow of a responder and non-responder, and these were compared to LSCs from a patient who underwent treatment and responded to conventional IV Aza/Ven. Given subjects who achieved a CR in the study cleared their blasts by day 4 rendering no leukemia cells for analyses, samples used were from Subject 1 (stable disease with unchanged blasts), and Subject 2 (stable disease with significant blast reduction). Metabolomics assays performed in LSCs at day 4 and day 28 suggested mitochondrial dysfunction, decreased electron transport chain complex II activity and decreased glutathione levels in Subject 2 and conventional IV Aza/Ven but not on Subject 1. These findings are consistent with Pollyea et al. 2018 suggesting CC-486/Ven targets LSCs by perturbing complex II activity and OXPHOS in LSCs. Further, scRNA seq performed in Subject 1 and 2 showed gene expression patterns similar to those seen in patients who respond to Aza/Ven vs not, including a significant shift of BCL-2 to MCL-1 expression in the cell population harboring LSCs (Figure 1B). Conclusion: CC-486 and Ven is an all-oral regimen currently being investigated for the treatment of R/R AML. Our Ph I dose escalation demonstrated a favorable safety profile for this regimen with a MTD of 300mg CC-486. Responses were seen in both dose cohorts including 2 CRs and 1 PR, and patients have been successfully bridged to hematopoietic stem cell transplant. Analyses performed in patient samples from this study suggested a similar effect in LSCs in CC-486/Ven compared to conventional IV Aza/Ven.

Polyamines Are Required for AML LSC Function through Their Role in Regulating eIF5A Dependent Protein Synthesis

Outcomes for patients with acute myeloid leukemia (AML) remain poor due to the inability of current therapies to fully eradicate disease initiating leukemia stem cells (LSCs) (Shlush et al., 2017). Many studies have demonstrated that LSCs have unique metabolic properties compared to AML blasts and normal hematopoietic stem and progenitor cells (HSPCs) (Jones et al., 2021). In this study we sought to quantify metabolite levels in LSCs compared to HSPCs using an unbiased metabolites screen. To examine metabolite levels in enriched LSCs and HSPCs we used mass spectrometry-based metabolomics analysis on enriched LSCs from 18 AML patients and HSPCs from 5 normal bone marrow (BM) specimens. Pathway analysis showed that arginine metabolism and biosynthesis were the most significantly enriched pathways in LSCs compared to HSPCs. Clinical studies have shown limited efficacy of targeting arginine levels using arginine degrading enzymes; therefore, we sought to target pathways downstream of arginine. To identify the pathways that arginine metabolism supports in LSCs, we used stable isotope labeled tracing analysis which showed arginine was metabolized through the urea cycle into polyamines in LSCs. Interestingly, the polyamine spermidine was the most significantly enriched metabolite in LSCs compared to HSPCs in our metabolomics analysis. Moreover, expression of SAT1, the enzyme catalyzing the export of polyamines from the cells, was decreased in AML compared to normal BM. Based on these observations, we sought to determine if the polyamine pathway represents a metabolic vulnerability that can be exploited to target LSCs. Polyamines are cationic compounds which have been previously shown to be important for the growth of various cancers but their role in AML LSCs has yet to be determined. To investigate if polyamines are essential for LSC survival and function, we treated LSCs and HSPCs with N 1, N 11-diethylnorspermine (DENSpm), a polyamine analog causing polyamine depletion through increased SAT1 expression and subsequent cellular export. DENSpm treatment decreased the viability of LSCs in 10 out of 12 of patients tested but had no impact on HSPCs viability. Further, treatment with DENSpm resulted in decreased engraftment potential of 5 AML specimens but did not alter the engraftment of HSPCs from 3 normal BM specimens, suggesting that targeting polyamines represents a promising approach to kill LSCs while sparing HSPCs. We then investigated the mechanisms by which polyamines are essential in LSCs. Using RNA-sequencing analysis on enriched LSCs from 5 AML patients and HSPCs from 3 normal BM specimens we observed an enrichment in myeloid differentiation signatures in DENSpm-treated LSCs but not in DENSpm-treated HSPCs. In line with this, expression of myeloid markers CD11b and CD15 were increased in patient-derived xenograft models engrafted with DENSpm-treated LSCs. As we did not observe such dysregulation in mice engrafted with DENSpm-treated HSPCs, these data suggest polyamine depletion promotes differentiation of LSCs but not HSPCs. Our transcriptomic analysis also unveiled decreased expression of genes involved in protein synthesis in DENSpm-treated LSCs but not in normal HSPCs. Protein synthesis and its regulation are critical for AML survival (Chen et al., 2019; Messling et al., 2022) but the role of polyamines in protein synthesis in LSCs has not been explored. Polyamines stimulate translation notably by serving as precursors for the hypusination of eukaryotic translation initiation factor 5A (eIF5A) (Park et al., 2010). Accordingly, DENSpm led to decreased hypusination of eIF5A in AML cells. This was associated with reduced protein synthesis level in AML cell lines and LSCs but not in normal HSPCs. Strikingly, eIF5A hypusination, protein synthesis and viability were rescued upon co-treatment with spermidine. Moreover, knockdown of eIF5A using siRNA resulted in impaired colony forming potential of AML and altered engraftment in patient-derived xenograft models. Altogether, these results suggest that DENSpm alters AML cell and LSC viability and function at least in part through decreased eIF5A-mediated protein translation. Altogether, our data demonstrates that depletion of polyamines decreased LSC function while sparing normal HSPCs. Mechanistically, our data suggest that LSC targeting is accomplished through decreased eIF5A-mediated synthesis of proteins crucial for LSCs.

Liquid Chromatography-Tandem Mass Spectrometry-Based Metabolomics Analysis of Indigo Naturalis Treatment of Ulcerative Colitis in Mice.

Ulcerative colitis (UC), often known as UC, is an inflammatory disease of the intestines that has frequent and long-lasting flare-ups. It is unknown precisely how the traditional Chinese drug Indigo Naturalis (IN) heals inflammatory bowel disease, despite its long-standing use in China and Japan. Finding new metabolite biomarkers linked to UC could improve our understanding of the disease, speed up the diagnostic process, and provide insight into how certain drugs work to treat the condition. Our work is designed to use a metabolomic method to analyze potential alterations in endogenous substances and their impact on metabolic pathways in a mouse model of UC. To determine which biomarkers and metabolisms are more frequently connected with IN's effects on UC, liquid chromatography-tandem mass spectrometry analysis of the serum metabolomics of UC mice and normal mice was performed. The outcomes demonstrated that IN boosted the health of UC mice and reduced the severity of their metabolic dysfunction. In the UC model, it was also found that IN changed the way 17 biomarkers and 3 metabolisms functioned.

Polygoni Cuspidati Rhizoma et Radix extract attenuates high-fat diet-induced NAFLD in rats: Impact on untargeted serum metabolomics and liver lipidomics

BackgroundPolygoni Cuspidati Rhizoma et Radix (PCRR; the root and rhizome of Polygonum cuspidatum Sieb. et Zucc) has long been used to treat atherosclerosis, gastrointestinal disorders, and liver disease. However, the underlying mechanism of PCRR against liver steatosis remains unclear. PurposeThe aim of this study was to determine the potential therapeutic targets and molecular mechanisms of PCRR in improving liver steatosis. MethodsA high-fat diet (HFD)-induced simple steatosis model in rats was used to evaluate the therapeutic effect of polyphenol-rich water extract from PCRR. Its underlying mechanisms were revealed using untargeted mass spectrometry-based serum metabolomics, hepatic lipidomic profiling approaches, qPCR, and Western blotting assays. ResultsOur study showed that PCRR-treated rats displayed significant reduction of serum TC and LDL-C, hepatic TG, TC levels, and total liver lipid content under a HFD feeding condition. Untargeted metabolomics showed that PCRR significantly restored the overall levels of nine lipid classes in liver tissues and elevated the bile acid levels in the serum samples. We demonstrated that PCRR prevented HFD-induced hepatic steatosis by regulating the expressions of TG metabolism proteins, including p-AMPK, p-ACC, PPARα, and FAS, as well as the expressions of TC metabolism proteins, including p-AMPK, LDLR, and CYP7A1. Moreover, resveratrol and/or polydatin­-derived metabolites were solely detected in the serum samples of the PCRR-treated group, indicating these microbial transformed metabolites might partly contribute to the beneficial effects of PCRR. ConclusionPCRR can be employed as a therapeutic agent to improve non-alcoholic fatty liver disease via regulating lipid metabolism.

Altered Gut Microbiota and Short-chain Fatty Acids in Chinese Children with Constipated Autism Spectrum Disorder

Gastrointestinal symptoms are more prevalent in children with autism spectrum disorder (ASD) than in typically developing (TD) children. Constipation is a significant gastrointestinal comorbidity of ASD, but the associations among constipated autism spectrum disorder (C-ASD), microbiota and short-chain fatty acids (SCFAs) are still debated. We enrolled 80 children, divided into the C-ASD group (n = 40) and the TD group (n = 40). In this study, an integrated 16S rRNA gene sequencing and gas chromatography–mass spectrometry-based metabolomics approach was applied to explore the association of the gut microbiota and SCFAs in C-ASD children in China. The community diversity estimated by the Observe, Chao1, and ACE indices was significantly lower in the C-ASD group than in the TD group. We observed that Ruminococcaceae_UCG_002, Erysipelotrichaceae_UCG_003, Phascolarctobacterium, Megamonas, Ruminiclostridium_5, Parabacteroides, Prevotella_2, Fusobacterium, and Prevotella_9 were enriched in the C-ASD group, and Anaerostipes, Lactobacillus, Ruminococcus_gnavus_group, Lachnospiraceae_NK4A136_group, Ralstonia, Eubacterium_eligens_group, and Ruminococcus_1 were enriched in the TD group. The propionate levels, which were higher in the C-ASD group, were negatively correlated with the abundance of Lactobacillus taxa, but were positively correlated with the severity of ASD symptoms. The random forest model, based on the 16 representative discriminant genera, achieved a high accuracy (AUC = 0.924). In conclusion, we found that C-ASD is related to altered gut microbiota and SCFAs, especially decreased abundance of Lactobacillus and excessive propionate in faeces, which provide new clues to understand C-ASD and biomarkers for the diagnosis and potential strategies for treatment of the disorder. This study was registered in the Chinese Clinical Trial Registry (www.chictr.org.cn; trial registration number ChiCTR2100052106; date of registration: October 17, 2021).

Genetic Polymorphisms in the Ferrireductase STEAP3 Regulate a Ferroptosis-like Process of Lipid Peroxidation-Induced Hemolysis in Murine and Human Red Blood Cells

Red blood cell (RBC) storage in the blood bank induces a series of biochemical and morphological alterations, collectively denoted as the storage lesion(s). Membrane damage by lipid peroxidation is a hallmark of the storage lesion, a process thought to be triggered by oxidant stress. To identify the genetics underlying this phenomenon, we leveraged a novel murine system, the Jackson lab Diversity Outbred (JDO) mouse colony, which was obtained by extensively cross-breeding 8 founder mouse strains with extreme genetically heterogeneity ( Figure 1.A). A total of 350 fresh and stored (up to 7 days) murine RBC samples were tested by mass spectrometry-based metabolomics and lipidomics. At the end of storage, post-transfusion recovery (PTR), which measures intra- and extravascular hemolysis and is a gold standard for determining RBC storage quality, was determined by quantifying the percentage of stored RBCs that were still circulating 24h after their transfusion into Ubi-GFP+ recipient mice ( Figure 1.A). Genome wide-association studies identified a strong association between PTR and a polymorphic region on chromosome 1 ( Figure 1.A), which encodes STEAP3, a ferrireductase. This region was associated with altered metabolism of stored RBCs ( Figure 1.A), especially an elevation of lipid peroxidation products (hive plot in Figure 1.A). Mechanistically, these data support a role for STEAP3 in promoting Fenton and Haber-Weiss chemistry in iron-loaded RBCs. Specifically, ferrous iron participates in this chemistry, becoming oxidized to its ferric state with concomitant generation of hydroxyl or hydroperoxyl radicals; these in turn attack fatty acids (preferentially, poly- and highly-unsaturated fatty acids, such as octadecadienoic and eicosatetraenoic acid), thereby promoting lipid peroxidation (to hydroxyoctadecadienoic (HODE) and hydroxyeicosatetraenoic (HETE) acids, respectively). By reducing Fe 3+ to Fe 2+, STEAP3 can shift the balance of this reaction by increasing the availability of the reactant, thereby favoring the generation of product radicals; this process is analogous to ferroptosis, as described in other biological systems. To extend the relevance of these findings to humans, we performed metabolomics on end-of-storage (i.e., Day 42) packed RBCs from 13,091 human donors in the Recipient Epidemiology and Donor Evaluation Study (REDS RBC Omics; Figure 1.B), enrolled in four blood centers across the United States. We stratified donors based on oxylipin levels (e.g., acids - HETEs - Figure 1.B) and common STEAP3 polymorphisms (e.g., a representative non-synonymous coding single nucleotide polymorphism (SNP), rs17013371, was observed with ~10% prevalence in these donors), along with 37 other common SNPs observed in this study ( Figure 1.B). When correlating metabolic and hematological parameters to common STEAP3 non-synonymous coding SNPs, we found strong associations of such polymorphisms with RBC susceptibility to hemolysis (either osmotic or oxidative), lipid peroxidation, RBC numbers, and hemoglobin levels ( Figure 1.B). These associations held true for a subset of the original donors with extreme hemolytic propensity (n=643) who donated a second RBC unit that was again stored for 42 (i.e., the “recalled donor population”). In the initial (n=13,091) and recalled donor (n=643) populations, lipid peroxidation products, HETEs, and HODEs ranked as the top predictors of hemolysis and vesiculation. In summary, we identified a role for the STEAP3 ferrireductase in contributing to a ferroptosis-like phenotype of lipid peroxidation that is associated with increased susceptibility to hemolysis in vitro and in vivo in murine and human RBCs following storage under blood bank conditions. Figure 1 - A. Jackson Lab diversity outbred (JDO) mice were bred from 8 founder mouse strains with extreme genetic heterogeneity. A total of 350 fresh and stored murine red blood cells (RBCs) were tested for metabolomics, lipidomics, and post-transfusion recovery (PTR). A polymorphic region on chromosome 1, coding for the ferrireductase STEAP3 was associated with heterogeneous PTR and elevation in lipid peroxidation products. B. Metabolomics analyses of 13,091 donors from the REDS RBC Omics identified an association between the end of storage levels of oxylipins and common polymorphisms for STEAP3, both linked to an increased RBC susceptibility to hemolysis (either osmotic or oxidative.

Discovering Nature's shield: Metabolomic insights into green zinc oxide nanoparticles Safeguarding Brassica parachinensis L. from cadmium stress

Heavy metal cadmium (Cd) hinders plants' growth and productivity by causing different morphological and physiological changes. Nanoparticles (NPs) are promising for raising plant yield and reducing Cd toxicity. Nonetheless, the fundamental mechanism of nanoparticle-interfered Cd toxicity in Brassica parachineses L. remains unknown. A novel ZnO nanoparticle (ZnO-NPs) was synthesized using a microalgae strain (Chlorella pyrenoidosa) through a green process and characterized by different standard parameters through TEM, EDX, and XRD. This study examines the effect of different concentrations of ZnO-NPs (50 and 100 mgL−1) in B. parachineses L. under Cd stress through ultra-high-performance liquid chromatography/high-resolution mass spectrometry-based untargeted metabolomics profiling. In the presence of Cd toxicity, foliar spraying with ZnO-NPs raised Cu, Fe, Zn, and Mg levels in the roots and/or leaves, improved seedling development, as demonstrated by increased plant height, root length, and shoot and root fresh weight. Furthermore, the ZnO-NPs significantly enhanced the photosynthetic pigments and changed the antioxidant activities of the Cd-treated plants. Based on a metabolomics analysis, 481 untargeted metabolites were accumulated in leaves under normal and Cd-stressed conditions. These metabolites were highly enriched in producing organic acids, amino acids, glycosides, flavonoids, nucleic acids, and vitamin biosynthesis. Surprisingly, ZnO-NPs restored approximately 60% of Cd stress metabolites to normal leaf levels. Our findings suggest that green synthesized ZnO-NPs can balance ions’ absorption, modulate the antioxidant activities, and restore more metabolites associated with plant growth to their normal levels under Cd stress. It can be applied as a plant growth regulator to alleviate heavy metal toxicity and improve crop yield in heavy metal-contaminated regions.

Metabolic Reprogramming By PRDM16 Drives Cytarabine Resistance in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) patients with high PRDM16 expression frequently experience induction failure and have a poor prognosis. However, the underlying molecular mechanisms are poorly understood. Here, we show that AML cells with high PRDM16 expression acquire resistance to cytarabine (AraC) through the activation of oxidative phosphorylation (OxPHOS) via regulation of c-MYC. Initially, we established a murine model of AML with high Prdm16 expression. We transduced c-Kit + bone marrow cells from wild-type mice with a retrovirus vector encoding MLL-AF9 (MF9) and the oncogenic short form of Prdm16 (sPrdm16). Using MF9/sPrdm16 cells, we next investigated whether AML cells with high Prdm16 expression exhibited resistance to AraC and/or daunorubicin (DNR), chemotherapeutic agents commonly used for induction chemotherapy. In the cell viability assay, MF9/sPrdm16 cells showed significantly higher IC 50 against AraC, but not against DNR, compared to MF9/control (control) cells, suggesting that high sPrdm16 expression confers relative resistance to AraC on AML cells. Colony-forming assay also confirmed resistant to AraC in MF9/sPrdm16 cells compared to control. Moreover, MF9/sPrdm16 cells were also resistant to AraC in vivo as demonstrated by the shortened survival of mice receiving MF9/sPrdm16 cells. To elucidate the mechanism of AraC resistance, we first examined cell cycle status of MF9/sPrdm16 cells since AraC exerts cytotoxicity in cell cycle dependent manner. To our surprise, MF9/sPrdm16 cells were cycling more rapidly than control cells as demonstrated by decreased G 0 phase and increased S/G 2/M phase. Intriguingly, RNA-sequencing analysis revealed that MF9/sPrdm16 cells displayed a signature of high OxPHOS by gene set enrichment analysis (GSEA). Indeed, oxygen consumption rate, superoxide production from mitochondria, and mitochondrial membrane potential were significantly elevated in MF9/sPrdm16 cells compared to control cells. The inhibition of mitochondrial respiration with metformin, the electron transport chain complex I inhibitor, or tigecycline, the mitochondrial protein synthesis inhibitor, abrogated AraC resistance in MF9/sPrdm16 cells by inducing an energetic shift towards a lower OxPHOS status. These results clearly indicated that sPrdm16 overexpression conferred MF9 cells with AraC resistance byincreasing OxPHOS in mitochondria. Next, we explored the mechanism how sPrdm16 regulates OxPHOS. In addition to elevated OxPHOS signature, RNA-sequencing data also showed strong enrichment of Myc target-signature in MF9/sPrdm16 cells. Western blot analysis showed that sPrdm16 overexpression induced up-regulation of c-Myc and its transcriptional target, Slc1a5, a glutamine transporter. We went on to analyze metabolic changes induced by sPrdm16 overexpression by capillary electrophoresis and mass spectrometry-based metabolome analysis. We found that sPrdm16 induced the accumulation of glutamine, glutamate, α-ketoglutaric acid, succinate, fumarate, and malate in MF9 cells, possibly by activating glutaminolysis via the regulation of c-Myc and Slc1a5 expression, leading to the activation of tricarboxylic acid (TCA) cycle and OxPHOS. We also confirmed the contribution of c-Myc to AraC resistance by overexpressing c-Myc in MF9 cells. As expected, MF9/c-Myc cells mimicked the phenotype of MF9/sPrdm16 cells such as resistance to AraC and high OxPHOS status. Furthermore, 10058-F4, a c-Myc inhibitor, abrogated AraC resistance in MF9/sPrdm16 cells. Next, we asked if the observation in MF9/sPrdm16 cells could be translated into human AML cells. Human AML cell lines, MOLM-13 and THP-1, with sPRDM16 overexpression also showed significantly higher IC 50 against AraC compared to Mock expressed cells. Moreover, RNA-seq data from the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML-05 clinical trial showed that AML blasts with high PRDM16 expression demonstrated a gene expression signature associated with “OxPHOS” and “Myc Targets”. In conclusion, our findings demonstrate that PRDM16 overexpression activates mitochondrial respiration through metabolic reprogramming via c-MYC, thereby conferres AraC resistance on AML cells. These results suggest that targeting mitochondrial respiration might be a novel treatment strategy to overcome chemoresistance in AML patients with high PRDM16 expression.

Molecular and Metabolic Phenotyping of Hepatocellular Carcinoma for Biomarker Discovery: A Meta-Analysis.

Identifying and translating hepatocellular carcinoma (HCC) biomarkers from bench to bedside using mass spectrometry-based metabolomics and lipidomics is hampered by inconsistent findings. Here, we investigated HCC at systemic and metabolism-centric multiomics levels by conducting a meta-analysis of quantitative evidence from 68 cohorts. Blood transcript biomarkers linked to the HCC metabolic phenotype were externally validated and prioritized. In the studies under investigation, about 600 metabolites were reported as putative HCC-associated biomarkers; 39, 20, and 10 metabolites and 52, 12, and 12 lipids were reported in three or more studies in HCC vs. Control, HCC vs. liver cirrhosis (LC), and LC vs. Control groups, respectively. Amino acids, fatty acids (increased 18:1), bile acids, and lysophosphatidylcholine were the most frequently reported biomarkers in HCC. BAX and RAC1 showed a good correlation and were associated with poor prognosis. Our study proposes robust HCC biomarkers across diverse cohorts using a data-driven knowledge-based approach that is versatile and affordable for studying other diseases.

Mass spectrometry-based untargeted metabolomics approaches for comprehensive structural annotation of bioactive metabolites from bushy cashew (Anacardium humile) fruits

Anacardium humile (bushy cashew) is a native Brazilian plant with substantial pharmacological potential and noteworthy commercial significance in the food industry. This study introduces an untargeted metabolomics approach based on mass spectrometry for the comprehensive structural annotation of bioactive metabolites. The fruits were collected from three distinct sites and subjected to LC-HRMS/MS analysis. A total of eighty-eight compounds were putatively annotated across various metabolite classes. This unveiled a metabolic profile characterized by notable concentrations of polyphenols, including flavonoids, tannins, phenolic acids, and quinones, while aliphatic acids and terpenes were found in limited quantities. Noteworthy, no significant disparities in the metabolic content were observed among the collection sites. The three principal metabolites (peonidin 3-O-glucopyranoside, methylcyanidin and methyldelphinidin) underwent assessment for antioxidant activity via molecular docking analysis, subsequently generating structure-based feature pharmacophores. The process of annotation propagation yielded a comprehensive qualitative appraisal of the A. humile metabolome. The outcomes obtained offer potential candidates for further exploration of their nutraceutical attributes.

Dynamic Changes in the Microbial Community and Metabolite Profile during the Pile Fermentation Process of Fuzhuan Brick Tea.

The pile fermentation process of Fuzhuan brick tea is unique in that it involves preheating without the use of starter cultures. The detailed metabolite changes and their drivers during this procedure are not known. Characterizing these unknown changes that occur in the metabolites and microbes during pile fermentation of Fuzhuan brick tea is important for industrial modernization of this traditional fermented food. Using microbial DNA amplicon sequencing, mass spectrometry-based untargeted metabolomics, and feature-based molecular networking, we herein reveal that significant changes in the microbial community occur before changes in the metabolite profile. These changes were characterized by a decrease in Klebsiella and Aspergillus, alongside an increase in Bacillus and Eurotium. The decrease in lysophosphatidylcholines, unsaturated fatty acids, and some astringent flavan-3-ols and bitter amino acids, as well as the increase in some less astringent flavan-3-ols and sweet or umami amino acids, contributed importantly to the overall changes observed in the metabolite profile. The majority of these changes was caused by bacterial metabolism and the corresponding heat generated by it.

Study on the effect of calibration standards prepared with different matrix on the accuracy of bile acid quantification using LC-MS/MS

The transition from relative to absolute quantification of metabolites is the future development trend of mass spectrometry-based metabolomics research, which could fundamentally solve the problem of comparability of data between different laboratories. However, absolute quantification of endogenous molecules is largely hampered by the lack of analyte-free matrix, leading to uncertainty and inconsistency in the preparation of calibration standards. Bile acids (BAs) are an important class of biomarkers that play a key role in disease progression. In this paper, the quantitative accuracy of calibration curves prepared in neat solvent (NSCCs), charcoal stripped matrix (SMCCs) and authentic matrix (AMCCs) were validated using quality control samples (QCs) prepared in authentic matrix. Results suggested that AMCCs could largely minimize the confidence interval (C.I.) and the deviation in accuracy compared with NSCCs and SMCCs when measured concentration is higher than 20% of the background level. In addition, experimental data demonstrated that two-step calibration strategy proposed here is a promising and reliable alternative strategy to quantify endogenous BAs in biological sample.

Metabolomic Diversity in Microbial Mats Under Different Environmental Conditions: A Tool to Test Microbial Ecosystem Chemical Change.

Microbial mats are microbial communities capable of recycling the essential elements of life and considered to be the oldest evidence of microbial communities on Earth. Due to their uniqueness and limited sampling material, analyzing their metabolomic profile in different seasons or conditions is challenging. In this study, microbial mats from a small pond in the Cuatro Cienegas Basin in Coahuila, Mexico, were collected in wet and dry seasons. In addition to these samples, mesocosm experiments from the wet samples were set. These mats are elastic and rise after heavy rainfall by forming gas domes structures known as "Archean domes", by the outgassing of methanogenic bacteria, archaea, and sulfur bacteria. Extracts from all mats and mesocosms were subjected to untargeted mass spectrometry-based metabolomics and molecular networking analysis. Interestingly, each mat showed high chemical diversity that may be explained by the temporal dynamic processes in which they were sampled.

Discovery of a new highly pathogenic toxin involved in insect sepsis.

Insect sepsis is a severe consequence that arises from the invasion of the hemocoel by symbionts of entomopathogenic nematodes and bacteria. In the present study, we unveiled the heightened virulence of the entomopathogenic nematode Steinernema feltiae and the entomopathogenic bacteria Xenorhabdus bovienii, which operate symbiotically, against the wax moth Galleria mellonella. Maximum mortality was observed at 25°C while the optimal infestation efficiency was 20 nematodes per host. After infestation, G. mellonella displayed rapid darkening and softening, accompanied by an escalated esterase activity at 9 h. The X. bovienii, released by S. feltiae, underwent substantial proliferation and discharged toxins that attacked hemocytes, thus triggering extensive hemolysis and sepsis. The host G. mellonella was usually killed within 24 h due to disseminated septicemia. Additionally, X. bovienii infestation led to the upregulation of metabolites like 3-hydroxyanthranilic acid. Strikingly, we identified the perilous actinomycin D, generated through kynurenine metabolites, representing a novel biomarker of insect sepsis. Furthermore, a comprehensive transcriptomic analysis unveiled a noteworthy upregulation of gene expression associated with actinomycin D. Overall, X. bovienii induced apoptosis and sepsis through actinomycin D production, indicating its pivotal role in infestation activity. These findings open up new avenues for studying the mechanism of sepsis and developing innovative biotic pesticides. IMPORTANCE As a current biocontrol resource, entomopathogenic nematodes and their symbiotic bacterium can produce many toxin factors to trigger insect sepsis, having the potential to promote sustainable pest management. In this study, we found Steinernema feltiae and Xenorhabdus bovienii were highly virulent against the insects. After infective juvenile injection, Galleria mellonella quickly turned black and softened with increasing esterase activity. Simultaneously, X. bovienii attacked hemocytes and released toxic components, resulting in extensive hemolysis and sepsis. Then, we applied high-resolution mass spectrometry-based metabolomics and found multiple substances were upregulated in the host hemolymph. We found extremely hazardous actinomycin D produced via 3-hydroxyanthranilic acid metabolites. Moreover, a combined transcriptomic analysis revealed that gene expression of proteins associated with actinomycin D was upregulated. Our research revealed actinomycin D might be responsible for the infestation activity of X. bovienii, indicating a new direction for exploring the sepsis mechanism and developing novel biotic pesticides.

Kynurenine pathway metabolism evolves with development of preclinical and scleroderma-associated pulmonary arterial hypertension.

Understanding metabolic evolution underlying pulmonary arterial hypertension (PAH) development may clarify pathobiology and reveal disease-specific biomarkers. Patients with systemic sclerosis (SSc) are regularly surveilled for PAH, presenting an opportunity to examine metabolic change as disease develops in an at-risk cohort. We performed mass spectrometry-based metabolomics on longitudinal serum samples collected before and near SSc-PAH diagnosis, compared with time-matched SSc subjects without PAH, in a SSc surveillance cohort. We validated metabolic differences in a second cohort and determined metabolite-phenotype relationships. In parallel, we performed serial metabolomic and hemodynamic assessments as the disease developed in a preclinical model. For differentially expressed metabolites, we investigated corresponding gene expression in human and rodent PAH lungs. Kynurenine and its ratio to tryptophan (kyn/trp) increased over the surveillance period in patients with SSc who developed PAH. Higher kyn/trp measured two years before diagnostic right heart catheterization increased the odds of SSc-PAH diagnosis (OR 1.57, 95% CI 1.05-2.36, P = 0.028). The slope of kyn/trp rise during SSc surveillance predicted PAH development and mortality. In both clinical and experimental PAH, higher kynurenine pathway metabolites correlated with adverse pulmonary vascular and RV measurements. In human and rodent PAH lungs, expression of TDO2, which encodes tryptophan 2,3 dioxygenase (TDO), a protein that catalyzes tryptophan conversion to kynurenine, was significantly upregulated and tightly correlated with pulmonary hypertensive features. Upregulated kynurenine pathway metabolism occurs early in PAH, localizes to the lung, and may be modulated by TDO2. Kynurenine pathway metabolites may be candidate PAH biomarkers and TDO warrants exploration as a potential novel therapeutic target.NEW & NOTEWORTHY Our study shows an early increase in kynurenine pathway metabolism in at-risk subjects with systemic sclerosis who develop pulmonary arterial hypertension (PAH). We show that kynurenine pathway upregulation precedes clinical diagnosis and that this metabolic shift is associated with increased disease severity and shorter survival times. We also show that gene expression of TDO2, an enzyme that generates kynurenine from tryptophan, rises with PAH development.

Unlocking Potentially Therapeutic Phytochemicals in Capadulla (Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics.

Doliocarpus dentatus is thought to have a wide variety of therapeutic phytochemicals that allegedly improve libido and cure impotence. Although a few biomarkers have been identified with potential antinociceptive and cytotoxic properties, an untargeted mass spectrometry-based metabolomics approach has never been undertaken to identify therapeutic biofingerprints for conditions, such as erectile dysfunction, in men. This study executes a preliminary phytochemical screening of the woody vine of two ecotypes of D. dentatus with renowned differences in therapeutic potential for erectile dysfunction. Liquid chromatography-mass spectrometry-based metabolomics was used to screen for flavonoids, terpenoids, and other chemical classes found to contrast between red and white ecotypes. Among the metabolite chemodiversity found in the ecotype screens, using a combination of GNPS, MS-DIAL, and SIRIUS, approximately 847 compounds were annotated at levels 2 to 4, with the majority of compounds falling under lipid and lipid-like molecules, benzenoids and phenylpropanoids, and polyketides, indicative of the contributions of the flavonoid, shikimic acid, and terpenoid biosynthesis pathways. Despite the extensive annotation, we report on 138 tentative compound identifications of potentially therapeutic compounds, with 55 selected compounds at a level-2 annotation, and 22 statistically significant therapeutic biomarkers, the majority of which were polyphenols. Epicatechin methyl gallate, catechin gallate, and proanthocyanidin A2 had the greatest significant differences and were also relatively abundant among the red and white ecotypes. These putatively identified compounds reportedly act as antioxidants, neutralizing damaging free radicals, and lowering cell oxidative stress, thus aiding in potentially preventing cellular damage and promoting overall well-being, especially for treating erectile dysfunction (ED).

Identification of Xenobiotic Biotransformation Products Using Mass Spectrometry-Based Metabolomics Integrated with a Structural Elucidation Strategy by Assembling Fragment Signatures.

The identification of xenobiotic biotransformation products is crucial for delineating toxicity and carcinogenicity that might be caused by xenobiotic exposures and for establishing monitoring systems for public health. However, the lack of available reference standards and spectral data leads to the generation of multiple candidate structures during identification and reduces the confidence in identification. Here, a UHPLC-HRMS-based metabolomics strategy integrated with a metabolite structure elucidation approach, namely, FragAssembler, was proposed to reduce the number of false-positive structure candidates. biotransformation product candidates were filtered by mass defect filtering (MDF) and multiple-group comparison. FragAssembler assembled fragment signatures from the MS/MS spectra and generated the modified moieties corresponding to the identified biotransformation products. The feasibility of this approach was demonstrated by the three biotransformation products of di(2-ethylhexyl)phthalate (DEHP). Comprehensive identification was carried out, and 24 and 13 biotransformation products of two xenobiotics, DEHP and 4'-Methoxy-α-pyrrolidinopentiophenone (4-MeO-α-PVP), were annotated, respectively. The number of 4-MeO-α-PVP biotransformation product candidates in the FragAssembler calculation results was approximately 2.1 times lower than that generated by BioTransformer 3.0. Our study indicates that the proposed approach has great potential for efficiently and reliably identifying xenobiotic biotransformation products, which is attributed to the fact that FragAssembler eliminates false-positive reactions and chemical structures and distinguishes modified moieties on isomeric biotransformation products. The FragAssembler software and associated tutorial are freely available at https://cosbi.ee.ncku.edu.tw/FragAssembler/ and the source code can be found at https://github.com/YuanChihChen/FragAssembler.

Human blood vessel organoids reveal a critical role for CTGF in maintaining microvascular integrity

The microvasculature plays a key role in tissue perfusion and exchange of gases and metabolites. In this study we use human blood vessel organoids (BVOs) as a model of the microvasculature. BVOs fully recapitulate key features of the human microvasculature, including the reliance of mature endothelial cells on glycolytic metabolism, as concluded from metabolic flux assays and mass spectrometry-based metabolomics using stable tracing of 13C-glucose. Pharmacological targeting of PFKFB3, an activator of glycolysis, using two chemical inhibitors results in rapid BVO restructuring, vessel regression with reduced pericyte coverage. PFKFB3 mutant BVOs also display similar structural remodelling. Proteomic analysis of the BVO secretome reveal remodelling of the extracellular matrix and differential expression of paracrine mediators such as CTGF. Treatment with recombinant CTGF recovers microvessel structure. In this work we demonstrate that BVOs rapidly undergo restructuring in response to metabolic changes and identify CTGF as a critical paracrine regulator of microvascular integrity.

Recent advances in mass spectrometry-based proteomics and metabolomics in chronic rhinosinusitis with nasal polyps.

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a complex and heterogeneous disease, typically diagnosed through endoscopy and computed tomography and treated with glucocorticoid or surgery. There is an urgent need to develop molecular-level diagnostic or prognostic tools to better understand the pathophysiology of CRSwNP. Proteomics and metabolomics, emerging fields, offer significant potential in elucidating the mechanisms underlying CRSwNP. Mass spectrometry, a powerful and sensitive tool for trace substance detection, is broadly applied for proteomics and metabolomics analysis in CRSwNP research. While previous literature has summarized the advancement of mass spectrometry-based CRSwNP proteomics from 2004 to 2018, recent years have seen new advances in this field, particularly about non-invasive samples and exosomes. Furthermore, mass spectrometry-based CRSwNP metabolomics research has opened new avenues for inquiry. Therefore, we present a comprehensive review of mass spectrometry-based proteomics and metabolomics studies on CRSwNP conducted between 2019 and 2022. Specifically, we highlight protein and metabolic biomarkers that have been utilized as diagnostic or prognostic markers for CRSwNP. Lastly, we conclude with potential directions for future mass spectrometry-based omics studies of CRSwNP.