Selected Ion Monitoring for Orbitrap-Based Metabolomics.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.

Prevalence and natural course of incidental gastric subepithelial tumors.

Background/Aims: Gastric subepithelial tumors (SETs) are often encountered during the upper gastrointestinal endoscopic screening. We assessed the prevalence of gastric SETs and the risk factors for their progression. Methods: We reviewed the electronic medical records of 30,754 patients who underwent upper gastrointestinal endoscopic screening at our medical center between January 2013 and December 2016. Results: Among the 30,754 patients examined, 599 (1.94%) had gastric SETs. The prevalence increased with age and was 9.56% in patients aged ≥70 years. In total, 262 patients underwent serial endoscopy for more than 6 months. The median age was 68 years (interquartile range [IQR], 61-74), and the number of females was 167 (63.7%). During a median follow-up of 58 months (IQR, 38-75), 22 patients (8.4%) showed significant changes in tumor size. An irregular border (odds ratio, 4.623; 95% confidence interval, 1.093-19.558; p=0.037) was a significant risk factor for progression. Seven patients underwent surgical or endoscopic resections. The pathologies of gastric SETs included leiomyomas (n=3), gastrointestinal stromal tumors (n=2), and lipomas (n=2). Conclusions: The prevalence of gastric SETs increases with age. Most gastric SETs do not progress during long-term endoscopic examinations, and the risk of an increase in size is low in asymptomatic small SETs without irregular borders.

Successful Endoscopic Submucosal Dissection Using Open Peroral Endoscopic Myotomy for Duodenal Neuroendocrine Tumor.

Duodenal neuroendocrine tumors (NETs) are subepithelial tumors that are difficult to remove endoscopically, particularly when located just beyond the pylorus. This paper reports a case of a successful endoscopic submucosal dissection (ESD) using open gastric peroral endoscopic myotomy (POEM) for a remnant duodenal NET detected after endoscopic mucosal resection (EMR). A 67-year-old male presented with a 5 mm remnant duodenal NET close to the pylorus after EMR for a duodenal polypoid lesion performed four months earlier. Duodenal ESD was performed under conscious sedation using I-type and IT II knives. The tumor adhered to the fibrotic tissue, and the submucosal cushion was insufficient. Open gastric POEM was performed concurrently during ESD, resulting in the complete resection of the NET. This case suggests that while challenging, open gastric POEM can serve as a valuable technique for endoscopic resection in cases of early gastric cancer or duodenal masses located around the pylorus.

mTORC1 controls murine postprandial hepatic glycogen synthesis via Ppp1r3b.

In response to a meal, insulin drives hepatic glycogen synthesis to help regulate systemic glucose homeostasis. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-established insulin target and contributes to the postprandial control of liver lipid metabolism, autophagy, and protein synthesis. However, its role in hepatic glucose metabolism is less understood. Here, we used metabolomics, isotope tracing, and mouse genetics to define a role for liver mTORC1 signaling in the control of postprandial glycolytic intermediates and glycogen deposition. We show that mTORC1 is required for glycogen synthase activity and glycogenesis. Mechanistically, hepatic mTORC1 activity promotes the feeding-dependent induction of Ppp1r3b, a gene encoding a phosphatase important for glycogen synthase activity whose polymorphisms are linked to human diabetes. Reexpression of Ppp1r3b in livers lacking mTORC1 signaling enhances glycogen synthase activity and restores postprandial glycogen content. mTORC1-dependent transcriptional control of Ppp1r3b is facilitated by FOXO1, a well characterized transcriptional regulator involved in the hepatic response to nutrient intake. Collectively, we identify a role for mTORC1 signaling in the transcriptional regulation of Ppp1r3b and the subsequent induction of postprandial hepatic glycogen synthesis.

Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution.

The inability to inspect metabolic activities within distinct subcellular compartments has been a major barrier to our understanding of eukaryotic cell metabolism. Previous work addressed this challenge by analyzing metabolism in isolated organelles, which grossly bias metabolic activity. Here, we describe a method for inferring physiological metabolic fluxes and metabolite concentrations in mitochondria and cytosol based on isotope tracing experiments performed with intact cells. This is made possible by computational deconvolution of metabolite isotopic labeling patterns and concentrations into cytosolic and mitochondrial counterparts, coupled with metabolic and thermodynamic modelling. Our approach lowers the uncertainty regarding compartmentalized fluxes and concentrations by one and three orders of magnitude compared to existing modelling approaches, respectively. We derive a quantitative view of mitochondrial and cytosolic metabolic activities in central carbon metabolism across cultured cell lines without performing cell fractionation, finding major variability in compartmentalized malate-aspartate shuttle fluxes. We expect our approach for inferring metabolism at a subcellular resolution to be instrumental for a variety of studies of metabolic dysfunction in human disease and for bioengineering.

Impact of acute stress on murine metabolomics and metabolic flux.

Plasma metabolite concentrations and labeling enrichments are common measures of organismal metabolism. In mice, blood is often collected by tail snip sampling. Here, we systematically examined the effect of such sampling, relative to gold-standard sampling from an in-dwelling arterial catheter, on plasma metabolomics and stable isotope tracing. We find marked differences between the arterial and tail circulating metabolome, which arise from two major factors: handling stress and sampling site, whose effects were deconvoluted by taking a second arterial sample immediately after tail snip. Pyruvate and lactate were the most stress-sensitive plasma metabolites, rising ~14 and ~5-fold. Both acute handling stress and adrenergic agonists induce extensive, immediate production of lactate, and modest production of many other circulating metabolites, and we provide a reference set of mouse circulatory turnover fluxes with noninvasive arterial sampling to avoid such artifacts. Even in the absence of stress, lactate remains the highest flux circulating metabolite on a molar basis, and most glucose flux into the TCA cycle in fasted mice flows through circulating lactate. Thus, lactate is both a central player in unstressed mammalian metabolism and strongly produced in response to acute stress.

Osteoblast-intrinsic defect in glucose metabolism impairs bone formation in type II diabetic male mice.

Skeletal fragility is associated with type 2 diabetes mellitus (T2D), but the underlying mechanism is not well understood. Here, in a mouse model for youth-onset T2D, we show that both trabecular and cortical bone mass is reduced due to diminished osteoblast activity. Stable isotope tracing in vivo with 13C-glucose demonstrates that both glycolysis and glucose fueling of the TCA cycle are impaired in diabetic bones. Similarly, Seahorse assays show suppression of both glycolysis and oxidative phosphorylation by diabetes in bone marrow mesenchymal cells as a whole, whereas single-cell RNA sequencing reveals distinct modes of metabolic dysregulation among the subpopulations. Metformin not only promotes glycolysis and osteoblast differentiation in vitro, but also improves bone mass in diabetic mice. Finally, osteoblast-specific overexpression of either Hif1a, a general inducer of glycolysis, or Pfkfb3 which stimulates a specific step in glycolysis, averts bone loss in T2D mice. The study identifies osteoblast-intrinsic defects in glucose metabolism as an underlying cause of diabetic osteopenia, which may be targeted therapeutically.

Slow TCA flux and ATP production in primary solid tumours but not metastases.

Tissues derive ATP from two pathways-glycolysis and the tricarboxylic acid (TCA) cycle coupled to the electron transport chain. Most energy in mammals is produced via TCA metabolism1. In tumours, however, the absolute rates of these pathways remain unclear. Here we optimize tracer infusion approaches to measure the rates of glycolysis and the TCA cycle in healthy mouse tissues, Kras-mutant solid tumours, metastases and leukaemia. Then, given the rates of these two pathways, we calculate total ATP synthesis rates. We find that TCA cycle flux is suppressed in all five primary solid tumour models examined and is increased in lung metastases of breast cancer relative to primary orthotopic tumours. As expected, glycolysis flux is increased in tumours compared with healthy tissues (the Warburg effect2,3), but this increase is insufficient to compensate for low TCA flux in terms of ATP production. Thus, instead of being hypermetabolic, as commonly assumed, solid tumours generally produce ATP at a slower than normal rate. In mouse pancreatic cancer, this is accommodated by the downregulation of protein synthesis, one of this tissue's major energy costs. We propose that, as solid tumours develop, cancer cells shed energetically expensive tissue-specific functions, enabling uncontrolled growth despite a limited ability to produce ATP.

Osteoblast-intrinsic defect in glucose metabolism impairs bone formation in type II diabetic mice.

Skeletal fragility is associated with type 2 diabetes mellitus (T2D), but the underlying mechanism is not well understood. Here, in a mouse model for youth-onset T2D, we show that both trabecular and cortical bone mass are reduced due to diminished osteoblast activity. Stable isotope tracing in vivo with 13 C-glucose demonstrates that both glycolysis and glucose fueling of the TCA cycle are impaired in diabetic bones. Similarly, Seahorse assays show suppression of both glycolysis and oxidative phosphorylation by diabetes in bone marrow mesenchymal cells as a whole, whereas single-cell RNA sequencing reveals distinct modes of metabolic dysregulation among the subpopulations. Metformin not only promotes glycolysis and osteoblast differentiation in vitro, but also improves bone mass in diabetic mice. Finally, targeted overexpression of Hif1a or Pfkfb3 in osteoblasts of T2D mice averts bone loss. The study identifies osteoblast-intrinsic defects in glucose metabolism as an underlying cause of diabetic osteopenia, which may be targeted therapeutically.

The efficacy of newly proposed gastric open peroral endoscopic myotomy (GO-POEM) in preventing post-endoscopic submucosal dissection stenosis: A comparison with non-GO-POEM group.

Extensive endoscopic submucosal dissection (ESD) for gastric adenoma or early cancer can lead to post-ESD stenosis. This may cause a decrease in quality of life and an increase in medical issues. Therefore, this study examined the safety and effectiveness of gastric open peroral endoscopic myotomy (GO-POEM) in preventing stenosis following ESD. A retrospective investigation was carried out on 31 patients who underwent gastric ESD for > 75% of the lumen in the antrum or pylorus at the Presbyterian Medical Center in Korea between December 2004 and October 2022. The patients were divided into GO-POEM (n = 11) and non-GO-POEM groups (n = 20). The average age of the 31 patients was 73.23 years, and 18 were male. There were no differences in age, sex, location, gross findings, or procedure time between the 2 groups. In the GO-POEM group, only 1 patient (9 %) developed stenosis, compared to 11 patients (55 %) in the control group (P = .02). Multivariate analysis showed that the GO-POEM group had a significantly lower risk of post-ESD stenosis (P < .05). Stenosis symptoms resolved with a single endoscopic balloon dilatation (EBD) in 1 patient in the GO-POEM group. In contrast, 5 of 11 patients with stenosis in the non-GO-POEM group required a median of 2 EBD sessions (range, 1-8). GO-POEM may be an effective and reliable method for preventing stenosis post extensive gastric ESD. Further investigations are necessary to establish its efficacy and safety.

Endoscopic Ultrasonography-guided Gastrojejunostomy for Patients with Gastric Outlet Obstruction and Pyloric Metal Stent Dysfunction.

A 52-year-old woman with a gastric outlet obstruction (GOO) caused by pyloric cancer underwent pyloric endoscopic self-expandable metal stent (SEMS) insertion. She presented with abdominal distension 40 days later. The SEMS was dysfunctional, and endoscopic ultrasound-guided gastrojejunostomy (EUS-GJ) was performed using an endoscopic nasobiliary drainage tube. A 16 mm×31 mm Niti-S ™ HOT SPAXUS™ (TaeWoong Medical, Gimpo, Korea) was inserted successfully between the stomach and the adjacent jejunum. After the procedure, the patient had a good oral intake for more than seven months. GOO is a mechanical obstructive condition caused by various benign and malignant conditions. Traditionally, surgical GJ and SEMS insertion have been used to treat GOOs. EUS-GJ is a feasible treatment option for patients with GOO and a pyloric metal stent dysfunction.

Safety and efficacy of prophylactic gastric open peroral endoscopic myotomy for prevention of post-ESD stenosis: A case series (with video).

OBJECTIVE: Endoscopic resection of over 3/4 of the lumen of the antrum or pylorus is a known risk factor for post-endoscopic submucosal dissection (ESD) stenosis. Local or systemic steroids may reduce the risk of stenosis, but their overall role in stenosis prevention remains controversial. We aimed to evaluate the efficacy and safety of prophylactic gastric open peroral endoscopic myotomy (GO-POEM) in preventing post-ESD stenosis. METHODS: Ten patients who underwent GO-POEM during or immediately after ESD in the Presbyterian Medical Center between June 2017 and November 2020 were included. All patients underwent excision of over 3/4 of the lumen of the antrum or pylorus. GO-POEM was performed without submucosal tunneling. RESULTS: Well-differentiated tubular adenocarcinoma, tubulovillous adenoma with high-grade dysplasia, and tubular adenoma with low-grade dysplasia were diagnosed in three, one, and six patients, respectively. GO-POEM was performed successfully in all the 10 patients. Stenosis could not be evaluated in one patient, whereas one of the remaining nine patients developed post-ESD stenosis. GO-POEM decreased the risk of post-ESD stenosis in the other eight patients. Two patients presented with intraprocedural bleeding, both of whom were managed endoscopically successfully. CONCLUSIONS: Prophylactic GO-POEM may be a novel, effective and safe treatment modality for preventing post-ESD stenosis in the stomach. Well-designed, multicenter studies with large sample sizes are needed to confirm our results.

Circulating metabolite homeostasis achieved through mass action.

Homeostasis maintains serum metabolites within physiological ranges. For glucose, this requires insulin, which suppresses glucose production while accelerating its consumption. For other circulating metabolites, a comparable master regulator has yet to be discovered. Here we show that, in mice, many circulating metabolites are cleared via the tricarboxylic acid cycle (TCA) cycle in linear proportionality to their circulating concentration. Abundant circulating metabolites (essential amino acids, serine, alanine, citrate, 3-hydroxybutyrate) were administered intravenously in perturbative amounts and their fluxes were measured using isotope labelling. The increased circulating concentrations induced by the perturbative infusions hardly altered production fluxes while linearly enhancing consumption fluxes and TCA contributions. The same mass action relationship between concentration and consumption flux largely held across feeding, fasting and high- and low-protein diets, with amino acid homeostasis during fasting further supported by enhanced endogenous protein catabolism. Thus, despite the copious regulatory machinery in mammals, circulating metabolite homeostasis is achieved substantially through mass action-driven oxidation.

[Cannulation of the Portal Vein during Endoscopic Retrograde Cholangiopancreatography in a Patient with Choledocholithiasis].

Cannulation of the portal vein is a rare complication of ERCP. This paper reports a case of portal vein catheterization during ERCP in a patient with choledocholithiasis. A 62-year-old man was admitted to the Presbyterian Medical Center with right upper quadrant pain and jaundice. ERCP was performed under the suspicion of obstructive jaundice caused by a radiolucent stone. Bile duct cannulation using a pull-type papillotome was attempted, but it failed. After needle-knife fistulotomy, wire-guided cannulation was performed successfully, and 10 mL contrast was injected. On the other hand, the fluoroscopy image showed that the contrast medium disappeared very quickly. Pure blood was collected when the catheter was aspirated to identify the bile reflux, indicating possible cannulation of the portal vein. The procedure was terminated immediately and abdominal computed tomography showed air in the portal vein. One day after, a follow-up CT scan showed no air in the portal vein. The patient underwent repeated ERCP, and the common bile duct was cannulated. In most cases, isolated portal vein cannulation does not result in severe morbidity. However, it is important to aware of this rare complication so that no further invasive procedure is performed on the patient.

Tumor Reliance on Cytosolic versus Mitochondrial One-Carbon Flux Depends on Folate Availability.

Folate metabolism supplies one-carbon (1C) units for biosynthesis and methylation and has long been a target for cancer chemotherapy. Mitochondrial serine catabolism is considered the sole contributor of folate-mediated 1C units in proliferating cancer cells. Here, we show that under physiological folate levels in the cell environment, cytosolic serine-hydroxymethyltransferase (SHMT1) is the predominant source of 1C units in a variety of cancers, while mitochondrial 1C flux is overly repressed. Tumor-specific reliance on cytosolic 1C flux is associated with poor capacity to retain intracellular folates, which is determined by the expression of SLC19A1, which encodes the reduced folate carrier (RFC). We show that silencing SHMT1 in cells with low RFC expression impairs pyrimidine biosynthesis and tumor growth in vivo. Overall, our findings reveal major diversity in cancer cell utilization of the cytosolic versus mitochondrial folate cycle across tumors and SLC19A1 expression as a marker for increased reliance on SHMT1.

Combined use of rosuvastatin and ezetimibe improves hepatic steatosis in patients with dyslipidemia.

BACKGROUND AND AIMS: Rosuvastatin plus ezetimibe are beneficial for the management of dyslipidemia. We investigated whether rosuvastatin plus ezetimibe improves hepatic steatosis in patients with dyslipidemia. METHODS: Between January and August 2018, 114 patients with dyslipidemia treated for 6 months with rosuvastatin plus ezetimibe were analyzed in this retrospective cohort study. The degree of hepatic steatosis was assessed using the hepatic steatosis index (HSI). Hepatic steatosis improvement and presence of fatty liver were defined as a ≥5% reduction in HSI score and HSI ≥36, respectively. RESULTS: The mean age of the study population (50 males and 64 females) was 57.4 years. At baseline, the mean BMI total cholesterol level, low-density lipoprotein cholesterol level, high-density lipoprotein cholesterol level, triglyceride level, and HSI were 25.1 kg/m, 207.4 mg/dL, 126.1 mg/dL, 52.9 mg/dL, 146.4 mg/dL, and 36.1, respectively. During the 6-month treatment, hepatic steatosis burden was constant (mean HSI = 36.3 and 36.4 at 3 and 6 months, respectively). On multivariate analyses, ultrasonographic fatty liver and HSI ≥36 were selected as independent predictors of hepatic steatosis improvement. However, when 53 (46.5%) patients with fatty liver (HSI ≥ 36) were selected, hepatic steatosis burden was significantly improved (mean HSI = 40.8, 39.3, and 39.7 at baseline, 3 months, and 6 months, respectively). CONCLUSIONS: The use of rosuvastatin plus ezetimibe for the management of dyslipidemia did not improve hepatic steatosis burden in all patients with dyslipidemia, but it improved hepatic steatosis burden in the subgroup with fatty liver.

Inferring cancer dependencies on metabolic genes from large-scale genetic screens.

BACKGROUND: Cancer cells reprogram their metabolism to survive and propagate. Thus, targeting metabolic rewiring in tumors is a promising therapeutic strategy. Genome-wide RNAi and CRISPR screens are powerful tools for identifying genes essential for cancer cell proliferation and survival. Integrating loss-of-function genetic screens with genomics and transcriptomics datasets reveals molecular mechanisms that underlie cancer cell dependence on specific genes; though explaining cell line-specific essentiality of metabolic genes was recently shown to be especially challenging. RESULTS: We find that variability in tissue culture medium between cell lines in a genetic screen is a major confounding factor affecting cell line-specific essentiality of metabolic genes-while, quite surprisingly, not being previously accounted for. Additionally, we find that altered expression level of a metabolic gene in a certain cell line is less indicative of its essentiality than for other genes. However, cell line-specific essentiality of metabolic genes is significantly correlated with changes in the expression of neighboring enzymes in the metabolic network. Utilizing a machine learning method that accounts for tissue culture media and functional association between neighboring enzymes, we generated predictive models for cancer cell line-specific dependence on 162 metabolic genes (representing a ~ 2.2-fold increase compared to previous studies). The generated predictive models reveal numerous novel associations between molecular features and cell line-specific dependency on metabolic genes. Specifically, we demonstrate how cancer cell dependence on one-carbon metabolic enzymes is explained based on cancer lineage, oncogenic mutations, and RNA expression of neighboring enzymes. CONCLUSIONS: Considering culture media as well as accounting for molecular features of functionally related metabolic enzymes in a metabolic network significantly improves our understanding of cancer cell line-specific dependence on metabolic genes. We expect our approach and predictive models of metabolic gene essentiality to be a useful tool for investigating metabolic abnormalities in cancer.

Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells.

The inability to inspect metabolic activities within subcellular compartments has been a major barrier to our understanding of eukaryotic cell metabolism. Here, we describe a spatial-fluxomics approach for inferring metabolic fluxes in mitochondria and cytosol under physiological conditions, combining isotope tracing, rapid subcellular fractionation, LC-MS-based metabolomics, computational deconvolution, and metabolic network modeling. Applied to study reductive glutamine metabolism in cancer cells, shown to mediate fatty acid biosynthesis under hypoxia and defective mitochondria, we find a previously unappreciated role of reductive IDH1 as the sole net contributor of carbons to fatty acid biosynthesis under standard normoxic conditions in HeLa cells. In murine cells with defective SDH, we find that reductive biosynthesis of citrate in mitochondria is followed by a reversed CS activity, suggesting a new route for supporting pyrimidine biosynthesis. We expect this spatial-fluxomics approach to be a highly useful tool for elucidating the role of metabolic dysfunction in human disease.

Diversity and abundance of human-pathogenic fungi associated with pigeon faeces in urban environments.

Pathogenic fungi are a growing health concern worldwide, particularly in large, densely populated cities. The dramatic upsurge of pigeon populations in cities has been implicated in the increased incidence of invasive fungal infections. In this study, we used a culture-independent, high-throughput sequencing approach to describe the diversity of clinically relevant fungi (CRF) associated with pigeon faeces and map the relative abundance of CRF across Seoul, Korea. In addition, we tested whether certain geographical, sociological and meteorological factors were significantly associated with the diversity and relative abundance of CRF. Finally, we compared the CRF diversity of fresh and old pigeon faeces to identify the source of the fungi and the role of pigeons in dispersal. Our results demonstrated that both the composition and relative abundance of CRF are unevenly distributed across Seoul. The green area ratio and the number of multiplex houses were positively correlated with species diversity, whereas wind speed and number of households were negatively correlated. The number of workers and green area ratio were positively correlated with the relative abundance of CRF, whereas wind speed was negatively correlated. Because many CRF were absent in fresh faeces, we inferred that most species cannot survive the gastrointestinal tract of pigeons and instead are likely transmitted through soil or air and use pigeon faeces as a substrate for proliferation.