Mammalian Cell Metabolism Research Articles

Phosphoglycolate phosphatase homologs act as glycerol-3-phosphate phosphatase to control stress and healthspan in C. elegans

Metabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model organism, we study the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol-3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol. We identify three Pgp homologues in C. elegans (pgph) and demonstrate in vivo that their protein products have G3PP activity, essential for glycerol synthesis. We demonstrate that PGPH/G3PP regulates the adaptation to various stresses, in particular hyperosmolarity and glucotoxicity. Enhanced G3PP activity reduces fat accumulation, promotes healthy aging and acts as a calorie restriction mimetic at normal food intake without altering fertility. Thus, PGP/G3PP can be considered as a target for age-related metabolic disorders.

CelloSelect – A synthetic cellobiose metabolic pathway for selection of stable transgenic CHO cell lines

Current protocols for generating stable transgenic cell lines mostly rely on antibiotic selection or the use of specialized cell lines lacking an essential part of their metabolic machinery, but these approaches require working with either toxic chemicals or knockout cell lines, which can reduce productivity. Since most mammalian cells cannot utilize cellobiose, a disaccharide consisting of two β-1,4-linked glucose molecules, we designed an antibiotic-free selection system, CelloSelect, which consists of a selection cassette encoding Neurospora crassa cellodextrin transporter CDT1 and β-glucosidase GH1-1. When cultivated in glucose-free culture medium containing cellobiose, CelloSelect-transfected cells proliferate by metabolizing cellobiose as a primary energy source, and are protected from glucose starvation. We show that the combination of CelloSelect with a PiggyBac transposase-based integration strategy provides a platform for the swift and efficient generation of stable transgenic cell lines. Growth rate analysis of metabolically engineered cells in cellobiose medium confirmed the expansion of cells stably expressing high levels of a cargo fluorescent marker protein. We further validated this strategy by applying the CelloSelect system for stable integration of sequences encoding two biopharmaceutical proteins, erythropoietin and the monoclonal antibody rituximab, and confirmed that the proteins are efficiently produced in either cellobiose- or glucose-containing medium in suspension-adapted CHO cells cultured in chemically defined media. We believe coupling heterologous metabolic pathways additively to the endogenous metabolism of mammalian cells has the potential to complement or to replace current cell-line selection systems.

Down-regulation of AMPD3 Is Associated With Poor Survival in Head and Neck Squamous Cell Carcinoma.

Adenosine monophosphate deaminase 3 (AMPD3) is an isoenzyme involved in the regulation of the energetic metabolism of mammalian cells. Cancer cells have a high demand for their energy supply. This experimental study aimed to illustrate the role of AMPD3 in human head and neck squamous cell carcinoma (HNSCC). Real-time quantitative reverse transcription-polymerase chain reaction was used to investigate the expression of the AMPD3 gene in human HNSCC tissues to assess the changes in cancerous and noncancerous parts and the correlation with different tumor behavior. The functions of AMPD3 were investigated using wound-healing and migration assays. AMPD3 was significantly down-regulated in cancerous tissues of HNSCC (p=0.001) and this was correlated with more advanced tumor and clinical stages. Patients with high expression had better 5-year survival. AMPD3 knock-down in SCC-4 and SCC-25 cells demonstrated reduction of proliferation but increased migration and invasion. To our knowledge, this is the first report evidencing the expression pattern of AMPD3 in HNSCC and demonstrated that high AMPD3 expression might represent a good prognostic biomarker. AMPD3 may have an antiproliferative potential but its down-regulation may not contribute to reducing the migration and invasion of HNSCC cells.

G3PP/PGP: A Novel Calorie Restriction Enzyme in C. Elegans

Metabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model, we studied the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol 3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol. Gro3P is a key metabolite that regulates flux of various metabolic pathways and particularly the glycerolipid/fatty acid (GL/FA) cycle associated with obesity, type 2 diabetes, and cardiometabolic disorders.

Evaluation of the effect of enzymatic hydrolyzate of the bursa of broiler chickens on cytotoxic activity and nonspecific immunity

The use of biologically active substances of tissue origin for the creation of biologically active additives and immunomodulatory drugs is an important area of scientific research in the field of nutrition and pharmacology. The aim of the work is to evaluate the effect of enzymatic hydrolysate from the fabricium bag of broiler chickens on the cytotoxicity and nonspecific immunity of mice against the background of experimental salmonella infection using biotechnological methods. For the experiment, three equal experimental groups of white mongrel mice were formed. All laboratory animals were fed daily for seven days with enzymatic hydrolysate at a dose of 750 mg/kg (therapeutic dose), 150 mg/kg (0.2 therapeutic dose) and 3,750 mg/kg (five therapeutic doses). At the same time, the control group of animals received intragastric water in the same volume. 24 hours after the last intake of the enzymatic hydrolysate, the animals were intraperitoneally infected with a culture of Salmonella enteritidis 92. The study reveals the absence of cytotoxic properties and impaired cell viability in cultures L929, J774.1A, HeLa S3, K562, and HST116 against the background of exposure to various concentrations of enzymatic hydrolysate from 0.02 to 10 mg/ml. It should be noted that there is a pronounced cytotoxic effect on MCF-7 tumor cells of the concentration of enzymatic hydrolysate in culture of 5 and 10 mg/ml, which suggests the possibility of using enzymatic hydrolysate for the prevention of tumor diseases. As a result of the experiment, it has been proved that the administration of enzymatic hydrolysate to mice increased the LD50 index and the survival rate of mice infected with the culture of the causative agent of salmonellosis by 1.5 times. Based on the conducted studies, it has been shown that the enzymatic hydrolysate of the lymphoid tissue of broiler chickens does not violate the viability of mammalian cells and does not exhibit cytotoxic properties on the metabolism of healthy mammalian cells, which indicates its safety. In an experiment on mice, the effect of enzymatic hydrolysate of the fabricium bag of broiler chickens on the activation of nonspecific immunity against salmonella infection has been revealed.

The disassembly of lipid droplets in Chlamydomonas.

Lipid droplets (LDs) are ubiquitous and specialized organelles in eukaryotic cells. Consisting of a triacylglycerol core surrounded by a monolayer of membrane lipids, LDs are decorated with proteins and have myriad functions, from carbon/energy storage to membrane lipid remodeling and signal transduction. The biogenesis and turnover of LDs are therefore tightly coordinated with cellular metabolic needs in a fluctuating environment. Lipid droplet turnover requires remodeling of the protein coat, lipolysis, autophagy and fatty acid β-oxidation. Several key components of these processes have been identified in Chlamydomonas (Chlamydomonas reinhardtii), including the major lipid droplet protein, a CXC-domain containing regulatory protein, the phosphatidylethanolamine-binding DTH1 (DELAYED IN TAG HYDROLYSIS1), two lipases and two enzymes involved in fatty acid β-oxidation. Here, we review LD turnover and discuss its physiological significance in Chlamydomonas, a major model green microalga in research on algal oil.

Complex II subunit SDHD is critical for cell growth and metabolism, which can be partially restored with a synthetic ubiquinone analog

BackgroundSuccinate dehydrogenase (Complex II) plays a dual role in respiration by catalyzing the oxidation of succinate to fumarate in the mitochondrial Krebs cycle and transferring electrons from succinate to ubiquinone in the mitochondrial electron transport chain (ETC). Mutations in Complex II are associated with a number of pathologies. SDHD, one of the four subunits of Complex II, serves by anchoring the complex to the inner-membrane and transferring electrons from the complex to ubiquinone. Thus, modeling SDHD dysfunction could be a valuable tool for understanding its importance in metabolism and developing novel therapeutics, however no suitable models exist.ResultsVia CRISPR/Cas9, we mutated SDHD in HEK293 cells and investigated the in vitro role of SDHD in metabolism. Compared to the parent HEK293, the knockout mutant HEK293ΔSDHD produced significantly less number of cells in culture. The mutant cells predictably had suppressed Complex II-mediated mitochondrial respiration, but also Complex I-mediated respiration. SDHD mutation also adversely affected glycolytic capacity and ATP synthesis. Mutant cells were more apoptotic and susceptible to necrosis. Treatment with the mitochondrial therapeutic idebenone partially improved oxygen consumption and growth of mutant cells.ConclusionsOverall, our results suggest that SDHD is vital for growth and metabolism of mammalian cells, and that respiratory and growth defects can be partially restored with treatment of a ubiquinone analog. This is the first report to use CRISPR/Cas9 approach to construct a knockout SDHD cell line and evaluate the efficacy of an established mitochondrial therapeutic candidate to improve bioenergetic capacity.

Glycerol‐3‐Phosphate Phosphatase/ PGP: A Novel Dietary Restriction Mimetic Enzyme that Protects from Glucotoxicity and Prolongs Healthspan in C. elegans

Metabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model organism, we studied the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol 3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate (Gro3P) to glycerol. Gro3P is a key metabolite that regulates flux of various metabolic pathways and particularly, the glycerolipid/fatty acid (GL/FA) cycle associated with obesity, type-2-diabetes, and cardiometabolic disorders. We identify three Pgp homologues in C. elegans (pgph1, pgph-2, and pgph-3) and demonstrate in vivo that their protein products have G3PP activity, essential for glycerol synthesis and contributes to stress responses and healthy aging. Hyperosmotic and high glucose stresses induce pgph transcripts, glycerol production, and salt stress adaptation in a PGPH-dependent manner. Using targeted metabolomics, we find that Gro3P accumulates in pgph mutant animals in basal conditions and more prominently following salt and glucose stresses, while most intermediary metabolites are rarely altered by PGPH loss. Using an unbiased transcription factors RNAi screen, we further identify transcriptional regulators of pgph-2 and pgph-3 salt-mediated expression. Loss of PGPH increases fat deposition, exacerbates glucotoxicity, decreases resistance to various stresses, shortens median lifespan and decreases healthspan parameters. Importantly, pgph-2 overexpression reduces fat deposition with age at basal and glucose excess conditions without restricting animal feeding or decreasing reproduction. Overexpression of pgph-2 improves healthspan and protects from glucotoxicity retarding age-related locomotor decline in normal and high glucose conditions. Strikingly, our data suggest that the overexpression of pgph-2 partly mimics the beneficial effects of dietary restriction. Overall, the results demonstrate that G3PP/PGP is a novel evolutionary conserved regulator of glucose and fat metabolism that protects against nutrient and environmental stresses and is involved in glucose detoxification and healthy aging.

Theoretical justification of selecting a method for cultivation of mammal cells as a basis for designing membrane bioreactors in accordance with the requirements of good manufacturing practice

The object of research is technological cultivation systems, the central element of which are bioreactors, which ensure efficient metabolism of mammalian cells (Metazoa). Fundamental differences in the phenotypic characteristics of mammalian cells from microorganisms and the special phase-hydrodynamic state of the cultivation system form special requirements for the design and operation of bioreactors. One of the most problematic areas in the process of using cell cultures to obtain medicinal products of biological origin is to ensure the correct cultivation conditions in order to obtain the maximum amount of the target product. The quality assurance system for drug production is based on good manufacturing practice, which puts forward a number of general requirements for the organization of production of drugs of specified quality, efficacy and safety. The study analyzed the phenotypic characteristics of mammalian cells. The analysis of industrial cultivation systems is carried out and a new classification is proposed, which takes into account the phase-hydrodynamic state of the culture and the specifics of the hydrodynamics of the bioreactor. The analysis made it possible to determine membrane cultivation systems as the most promising. The choice of this cultivation system has a number of features, in particular, the provision of favorable conditions during a long process of cultivation of support-dependent cells. This system guarantees a constant and efficient supply of nutrients, including dissolved oxygen, and the removal of waste products. A wide range of materials for the manufacture of membranes allows to use an individual approach to different types of cell lines. Due to this, it is ensured that high cultivation rates are obtained - the density of cells on the growth surface, the provision of the necessary substances during the entire cultivation process without negative mechanical effects on the cells. The modular design of the membrane elements allows for scalability of the cultivation process from laboratory development to industrial cultivation. The results obtained in this work can be the initial data in the study of hydrodynamic and mass transfer characteristics and in the development or construction of new bioreactors, which will reduce the stage of laboratory development and accelerate the introduction of innovative drugs.

Targeting Mitochondrial Metabolism in Clear Cell Carcinoma of the Ovaries.

Ovarian clear cell carcinoma (OCCC) is a rare but chemorefractory tumor. About 50% of all OCCC patients have inactivating mutations of ARID1A, a member of the SWI/SNF chromatin-remodeling complex. Members of the SWI/SNF remodeling have emerged as regulators of the energetic metabolism of mammalian cells; however, the role of ARID1A as a modulator of the mitochondrial metabolism in OCCCs is yet to be defined. Here, we show that ARID1A loss results in increased mitochondrial metabolism and renders ARID1A-mutated cells increasingly and selectively dependent on it. The increase in mitochondrial activity following ARID1A loss is associated with increase in c-Myc expression and increased mitochondrial number and reduction of their size consistent with a higher mitochondrial cristae/outer membrane ratio. Significantly, preclinical testing of the complex I mitochondrial inhibitor IACS-010759 showed it extends overall survival in a preclinical model of ARID1A-mutated OCCC. These findings provide for the targeting mitochondrial activity in ARID1A-mutated OCCCs.

Complex I protein NDUFS2 is vital for growth, ROS generation, membrane integrity, apoptosis, and mitochondrial energetics

Complex I is the largest and most intricate of the protein complexes of mitochondrial electron transport chain (ETC). This L-shaped enzyme consists of a peripheral hydrophilic matrix domain and a membrane-bound orthogonal hydrophobic domain. The interfacial region between these two arms is known to be critical for binding of ubiquinone moieties and has also been shown to be the binding site of Complex I inhibitors. Knowledge on specific roles of the ETC interfacial region proteins is scarce due to lack of knockout cell lines and animal models. Here we mutated nuclear encoded NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (NDUFS2), one of three protein subunits of the interfacial region, in a human embryonic kidney cell line 293 using a CRISPR/Cas9 procedure. Disruption of NDUFS2 significantly decreased cell growth in medium, Complex I specific respiration, glycolytic capacity, ATP pool and cell-membrane integrity, but significantly increased Complex II respiration, ROS generation, apoptosis, and necrosis. Treatment with idebenone, a clinical benzoquinone currently being investigated in other indications, partially restored growth, ATP pool, and oxygen consumption of the mutant. Overall, our results suggest that NDUFS2 is vital for growth and metabolism of mammalian cells, and respiratory defects of NDUFS2 dysfunction can be partially corrected with treatment of an established mitochondrial therapeutic candidate. This is the first report to use CRISPR/Cas9 approach to construct a knockout NDUFS2 cell line and use the constructed mutant to evaluate the efficacy of a known mitochondrial therapeutic to enhance bioenergetic capacity.

In-silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO-K1.

The cell culture is the central piece of a biotechnological industrial process. It includes upstream (e.g. media preparation, fixed costs, etc.) and downstream steps (e.g. product purification, waste disposal, etc.). In the continuous mode of cell culture, a constant flow of fresh media replaces culture fluid until the system reaches a steady state. This steady state is the standard operation mode which, under very general conditions, is a function of the ratio between the cell density and the dilution rate and depends on the media supplied to the culture. To optimize the production process it is widely accepted that the concentration of the metabolites in this media should be carefully tuned. A poor media may not provide enough nutrients to the culture, while a media too rich in nutrients may be a waste of resources because, either the cells do not use all of the available nutrients, or worse, they over-consume them producing toxic byproducts. In this study, we show how an in-silico study of a genome scale metabolic network coupled to the dynamics of a chemostat could guide the strategy to optimize the media to be used in a continuous process. Given a known media we model the concentrations of the cells in a chemostat as a function of the dilution rate. Then, we cast the problem of optimizing the production process within a linear programming framework in which the goal is to minimize the cost of the media keeping fixed the cell concentration for a given dilution rate in the chemostat. We evaluate our results in two metabolic models: first a simplified model of mammalian cell metabolism, and then in a realistic genome-scale metabolic network of mammalian cells, the Chinese hamster ovary cell line. We explore the latter in more detail given specific meaning to the predictions of the concentrations of several metabolites.

Synergistic Combination of Calcium and Citrate in Mesoporous Nanoparticles Targets Pleural Tumors

Summary Conventional chemotherapy leads to severe adverse effects since it involves systemic administration of toxic drugs at high dosage. Unlike traditional chemotherapeutics, calcium phosphate and citrate have both been discussed as very promising anticancer agents and are not inherently toxic. Yet, their breakthrough has been hampered by the lack of an administration approach that overcomes the strict regulatory mechanisms of the cell. Here, we present a combinatorial administration of calcium, phosphate, and citrate as colloidal, amorphous nanoparticles (CPCs) that selectively kill cancer cells without involvement of inherently toxic drugs. The particles are toxic neither before endosomal release nor after their degradation. This highly selective toxicity allowed us to successfully treat two different aggressive pleural tumors in mice, reducing their size by about 40% and 70% after only two local applications. Safety assessment studies over 2 months show no signs of adverse effects except for slightly enhanced pleural thickening after eight applications.

Role of Inositols and Inositol Phosphates in Energy Metabolism.

Recently, inositols, especially myo-inositol and inositol hexakisphosphate, also known as phytic acid or IP6, with their biological activities received much attention for their role in multiple health beneficial effects. Although their roles in cancer treatment and prevention have been extensively reported, interestingly, they may also have distinctive properties in energy metabolism and metabolic disorders. We review inositols and inositol phosphate metabolism in mammalian cells to establish their biological activities and highlight their potential roles in energy metabolism. These molecules are known to decrease insulin resistance, increase insulin sensitivity, and have diverse properties with importance from cell signaling to metabolism. Evidence showed that inositol phosphates might enhance the browning of white adipocytes and directly improve insulin sensitivity through adipocytes. In addition, inositol pyrophosphates containing high-energy phosphate bonds are considered in increasing cellular energetics. Despite all recent advances, many aspects of the bioactivity of inositol phosphates are still not clear, especially their effects on insulin resistance and alteration of metabolism, so more research is needed.

A simple colorimetric experiment using mammalian cell culture to study metabolism.

The goal of this laboratory exercise is to give upper-level undergraduate students an introduction to sterile technique in mammalian cell culture and metabolism. The experiment can be completed within a 3-h lab period and can be performed either in conjunction with other biochemistry/metabolism experiments or used as a stand-alone experiment. In this experiment, students are tasked with relating the acidification of cell culture medium to metabolism in order to elucidate the mechanism of action for a compound. Students can relate their experimental results to topics covered on glycolysis and oxidative phosphorylation in upper-level biochemistry classes as well as gain valuable experience relating metabolism to drug discovery.

Abstract 226: Pathways of nucleotide synthesis in NSCLC

Abstract Tracer-based mapping of metabolic networks is a powerful approach for revealing metabolic reprogramming in human cancer. Nucleotide synthesis and turnover is critical for cell proliferation and is tightly regulated [1,2]. We have developed NMR and tandem MS methods for determining the active pathways of the synthesis of free nucleotides and nucleotide sugars including UDP-Glucose and UDPGlcNAc using multiplexed stable isotope resolved metabolomics (mSIRM)[3] in a variety of models including freshly resected lung tumor tissue, mouse PDX and organoids. Using multiple isotopic labels (13C, 2H and 15N) we determined the relative contributions to purine and pyrimidine nucleotide synthesis of both exogenous glucose, glutamine, serine and glycine and metabolically-derived intracellular precursors. We have used these approaches to compare the relative importance of different metabolic pathways in NSCLC under various conditions to assess the role of the tumor microenvironment, and how these pathways are impacted by arsenite and selenite. Our findings indicate that the substrates for de novo nucleotide synthesis may differ profoundly between cancer cell lines and fresh human lung cancer tissues; for purines, the latter preferred glucose to exogenous serine or glycine but not the former. Pyrimidine nucleotides also utilize glucose for ribose synthesis via the pentose phosphate pathway, but both glucose and glutamine for the pyrimidine rings depending on the conditions and cell type. This distinction in substrate utilization in nucleotide synthesis in human cancer tissues should be considered when targeting one-carbon metabolism for cancer therapy. Acknowledgements: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL).

Novel Noncompetitive Type Three Secretion System ATPase Inhibitors Shut Down Shigella Effector Secretion.

Shigella is the causative agent of bacillary dysentery and is responsible for an estimated 165 million infections and 600,000 deaths annually. Like many Gram-negative pathogens, Shigella relies on a type three secretion system (T3SS) to initiate and sustain infection by directly injecting effector proteins into host cells. Protein secretion through the needle-like injectisome and overall Shigella virulence rely on the T3SS ATPase Spa47, making it a likely means for T3SS regulation and an attractive target for therapeutic small molecule inhibitors. Here, we utilize a recently solved 2.15 Å crystal structure of Spa47 to computationally screen 7.6 million drug-like compounds for candidates which avoid the highly conserved active site by targeting a distal, but critical, interface between adjacent protomers of the Spa47 homohexamer. Ten of the top inhibitor candidates were characterized, identifying novel Spa47 inhibitors that reduce in vitro ATPase activity by as much as 87.9 ± 10.5% with IC50's as low as 25 ± 20 μM and reduce in vivo Shigella T3SS protein secretion by as much as 94.7 ± 3.0%. Kinetic analyses show that the inhibitors operate through a noncompetitive mechanism that likely supports the inhibitors' low cytotoxicity, as they avoid off-target ATPases involved in either Shigella or mammalian cell metabolism. Interestingly, the inhibitors display nearly identical inhibition profiles for Spa47 and the T3SS ATPases EscN from E. coli and FliI from Salmonella. Together, the results of this study provide much-needed insight into T3SS ATPase inhibition mechanisms and a strong platform for developing broadly effective cross-pathogen T3SS ATPase inhibitors.

Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism.

Co-essentiality mapping has been useful to systematically cluster genes into biological pathways and identify gene functions1–3. Here, using the debiased sparse partial correlation (DSPC) method3, we construct a functional co-essentiality map for cellular metabolic processes across human cancer cell lines. This analysis reveals 35 modules associated with known metabolic pathways and further assigns metabolic functions to unknown genes. In particular, we discover C12orf49 as an essential regulator of cholesterol and fatty acid metabolism in mammalian cells. Mechanistically, C12orf49 localizes to the Golgi, binds site 1 protease (MBTPS1) and is necessary for the cleavage of its substrates, including SREBP transcription factors. This function depends on the evolutionarily conserved uncharacterized domain (DUF2054) and promotes cell proliferation under cholesterol depletion. Notably, c12orf49 depletion in zebrafish blocks dietary lipid clearance in vivo, phenocopying mbtps1 mutants. Finally, in an EHR-linked DNA biobank, C12orf49 is associated with hyperlipidemia through phenome analysis. Altogether, our findings reveal a conserved role for C12orf49 in cholesterol and lipid homeostasis and provide a platform to identify unknown components of other metabolic pathways.

OXIDATIVE STRESS AND MITOCHONDRIAL DYSFUNCTION

The process of cell damage resulting from the action of free radicals – reactive oxygen species (ROS) – is called oxidative stress. Most ROS are constantly formed in the cell – about 5 % of the oxygen consumed by tissues is converted into free radicals, but their level is normally so small that the cell inactivates them with the help of an antioxidant system. Different organs and tissues are exposed to different degrees of ROS and demonstrate different stability during the implementation of oxidative stress. The mechanisms of ROS formation by mitochondria under oxidative stress are still unclear. At the same time, it was found that mitochondrial dysfunction and the accumulation of mitochondrial mutations in tissues make a significant contribution to the aging process, as well as to the pathogenesis of a number of diseases characterized by neurodegeneration. Mutations lead to increased generation of free radicals, reduced ATP levels, and energy failure of cells. Coenzyme Q10 is a component of the mitochondrial respiratory chain. Violation of the biosynthesis of coenzyme Q10 can lead to a number of mitochondrial diseases. When coenzyme Q10 is deficient, sulfide metabolism plays a critical role. Sulfide metabolism in mammalian cells includes trans-sulfuration (biosynthetic) and hydrogen sulfide oxidation (H2S) (catabolic). Violation of H2S oxidation may contribute to oxidative stress in coenzyme Q deficiency or may play a synergistic role with oxidative stress in the pathogenesis of tissue specificity in coenzyme Q deficiency.

Simultaneous Measurement of Metabolite Concentration and Isotope Incorporation by Mass Spectrometry.

Studies of the topology, functioning, and regulation of metabolic systems are based on two main types of information that can be measured by mass spectrometry: the (absolute or relative) concentration of metabolites and their isotope incorporation in 13C-labeling experiments. These data are currently obtained from two independent experiments because the 13C-labeled internal standard (IS) used to determine the concentration of a given metabolite overlaps the 13C-mass fractions from which its 13C-isotopologue distribution (CID) is quantified. Here, we developed a generic method with a dedicated processing workflow to obtain these two sets of information simultaneously in a unique sample collected from a single cultivation, thereby reducing by a factor of 2 both the number of cultivations to perform and the number of samples to collect, prepare, and analyze. The proposed approach is based on an IS labeled with other isotope(s) that can be resolved from the 13C-mass fractions of interest. As proof-of-principle, we analyzed amino acids using a doubly labeled 15N13C-cell extract as IS. Extensive evaluation of the proposed approach shows a similar accuracy and precision compared to state-of-the-art approaches. We demonstrate the value of this approach by investigating the dynamic response of amino acids metabolism in mammalian cells upon activation of the protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK), a key component of the unfolded protein response. Integration of metabolite concentrations and isotopic profiles reveals a reduced de novo biosynthesis of amino acids upon PERK activation. The proposed approach is generic and can be applied to other (micro)organisms, analytical platforms, isotopic tracers, or classes of metabolites.