Determination of amino acids in colon cancer cells by using UHPLC-MS/MS and [U-13C5]-glutamine as the isotope tracer

Targeting of SLC25A22 boosts the immunotherapeutic response in KRAS-mutant colorectal cancer

KRAS is an important tumor intrinsic factor driving immune suppression in colorectal cancer (CRC). In this study, we demonstrate that SLC25A22 underlies mutant KRAS-induced immune suppression in CRC. In immunocompetent male mice and humanized male mice models, SLC25A22 knockout inhibits KRAS-mutant CRC tumor growth with reduced myeloid derived suppressor cells (MDSC) but increased CD8+ T-cells, implying the reversion of mutant KRAS-driven immunosuppression. Mechanistically, we find that SLC25A22 plays a central role in promoting asparagine, which binds and activates SRC phosphorylation. Asparagine-mediated SRC promotes ERK/ETS2 signaling, which drives CXCL1 transcription. Secreted CXCL1 functions as a chemoattractant for MDSC via CXCR2, leading to an immunosuppressive microenvironment. Targeting SLC25A22 or asparagine impairs KRAS-induced MDSC infiltration in CRC. Finally, we demonstrate that the targeting of SLC25A22 in combination with anti-PD1 therapy synergizes to inhibit MDSC and activate CD8+ T cells to suppress KRAS-mutant CRC growth in vivo. We thus identify a metabolic pathway that drives immunosuppression in KRAS-mutant CRC.

New quantification method for monitoring eighteen L-amino acids levels in schizophrenic patients by high-performance liquid chromatography coupled to tandem quadrupole mass spectrometer

A fast, uncomplicated, sensitive, and fully validated high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method has been developed for estimating L-amino acids in the plasma of schizophrenic patients. The gradient-elution chromatographic method was implemented with the Luna® PFP column (50 × 2.0 mm, 5-μm), and a mobile phase of 0.1% formic acid in water and methanol was used. The intraday and interday variability of the L-amino acids were less than 13.11%, and their accuracy ranged from 85.14 - 116.75% at the quality control levels and the lower limit of quantification (LLOQ) ranged from 2.5 - 15 nM. The extraction efficiency (apparent recovery) of amino acids from healthy plasma was employed by spiking the plasma with standard amino acids at the quality control levels. Their percentage recoveries ranged from 80.4% to 119.94%. Our method has a short run time and fast sample preparation compared with existing methods, which are suffered from long preparative steps and/or time-consuming analysis, restricted reagents, and suboptimal performance characteristics presently available technologies. Therefore, the proposed HPLC-MS/MS method was effectively applied for monitoring the L-amino acids in the plasma of schizophrenic patients and healthy volunteers.

Characterization and Determination of 13C-Labeled Nonessential Amino Acids in a 13C5-Glutamine Isotope Tracer Experiment with a Mass Spectrometry Strategy Combining Parallel Reaction Monitoring and Multiple Reaction Monitoring

Isotopic tracer, a powerful technique for metabolic pathway analysis, is currently widely applied in metabolic flux analysis. However, the qualitative and quantitative analyses of ¹³C-labeled metabolites pose great challenges, especially in complex biological sample matrices. Here, we present an integrated method for the qualitative and quantitative analyses of various isotopologues and isotopomers of ¹³C-labeled nonessential amino acids (NEAAs) in HepG2 cells incubated with ¹³C₅-glutamine (Gln) based on ultra-high-performance liquid chromatography (UHPLC) coupled with tandem mass spectrometry (MS). First, accurate mass-to-charge (m/z) values of protonated isotopologues and elution time of standards were simultaneously analyzed to characterize ¹³C-labeled NEAAs by high-resolution Orbitrap MS in the parallel reaction monitoring (PRM) mode. Second, isotopologues and isotopomers of ¹³C-labeled NEAAs were investigated in HepG2 cells incubated with ¹³C₅-Gln at different time points. Ultimately, a total of 66 multiple reaction monitoring (MRM) transitions were performed by UHPLC coupled with triple quadrupole MS. Among them, 29 MRM transitions were monitored for pure metabolites (unambiguously identified). The other 37 MRM transitions were monitored for mixtures with exactly identical MRM transitions and retention time. The application of targeted profiling of ¹³C-labeled NEAAs in the dynamic ¹³C-labeling experiment indicated that the concentration-time profiles of NEAAs were different from each other. The concentrations of most ¹³C-labeled Gln, Glu, Pro, and Asp altered after ¹³C₅-Gln incubation, indicating that Gln plays a fundamental role in the biosynthesis of Glu, Pro, and Asp. The proposed PRM-MRM combination mode LC-MS approach is expected to provide valuable insights into analyses of isotope-labeled metabolites in isotope tracer experiments.

Cross platform solutions to improve the zebrafish polar metabolome coverage using LC-QTOF MS: Optimization of separation mechanisms, solvent additives, and resuspension solvents

Untargeted metabolomics has been widely used for studies with zebrafish embryos. Until now, the number of analytical approaches to determine metabolites in zebrafish is limited, and there is a lack of consensus on the best platforms for comprehensive metabolomics analysis of zebrafish embryos. In addition, the capacity of these methods to detect metabolites is unsatisfactory and the confidence level for identifying compounds is relatively low. To improve the metabolome coverage, we mainly focused on the optimization of separation mechanisms, mobile phase additives, and resuspension solvents based on liquid chromatography (LC) coupling to high-resolution mass spectrometry (HRMS) techniques. Moreover, the procedures for optimizing methods were assessed when taking metabolite profiles in both positive and negative ionization modes into account. Four LC columns were studied: C18, T3, PFP, and HILIC. In positive ionization mode, it was strongly recommended to employ the HILIC approach operated at the neutral condition, which led to the presence of more than 4700 features and the annotation of 151 metabolites, mainly zwitterionic and basic compounds, in comparison to reverse phase (RP)-based methods with less than 1000 features. In negative ionization mode, the PFP column operated at 0.02% acetic acid showed the best performance in terms of metabolite coverage: 3100 metabolic features were detected and 218 metabolites were annotated in zebrafish embryos. Metabolite profiles mainly contained acidic and zwitterionic compounds. HILIC-based platforms were complementary to RP columns when analyzing highly polar metabolites. Additionally, it was preferable to reconstitute zebrafish extracts in 100% water for analysis of metabolites on RP columns, with a 20-30% increase in the number of identified metabolites compared to a 50% water in methanol solution. However, water/methanol (1:9, v/v), as resuspension solution, was advantageous over water/methanol (1:1, v/v) for HILIC analysis showing an 8-15% increase in detected metabolites. In total 336 polar metabolites were annotated by the combination of the optimized HILIC (positive) and PFP (negative) approaches. The largest metabolome coverage of polar metabolites in zebrafish embryos was obtained when three approaches were combined (negative PFP and HILIC, and HILIC positive) resulting in more than 420 annotated compounds.

Direct quantitative profiling of amino acids in tissues for the assessment of lung cancer

Direct molecular analysis of tissue samples is a promising approach to increase the accuracy, speed and molecular specificity of cancer diagnosis. Herein, alterations of amino acids between human lung cancer tissues and matched adjacent normal tissues were profiled by internal extraction electrospray ionization mass spectrometry (iEESI-MS). The results indicated that the levels of 11 detected amino acids (including serine, proline, valine, threonine, asparagine, aspartic acid, methionine, histidine, phenylalanine, arginine and tyrosine) in the cancerous tissues were lower than that in the adjacent normal tissues. Based on the orthogonal partial least squares discriminant analysis (OPLS-DA) model, cancerous and adjacent normal tissues were clearly discriminated, and the amino acids that played the major role in the differentiation between cancerous and adjacent normal tissues were identified. Moreover, metabolic pathway analysis revealed alterations of differential amino acids in several metabolic pathways upon lung cancer. The current study extends the power of iEESI-MS as a promising tool for quantitative characterization of amino acids in tissues, and allows the study of alterations in amino acids metabolism associated with the development of lung cancer.

Simultaneous determination of methionine cycle metabolites, urea cycle intermediates and polyamines in serum, urine and intestinal tissue by using UHPLC-MS/MS

Metabolites of methionine cycle, urea cycle and polyamine metabolism play important roles in regulating the metabolic processes and the development of diseases. It is rewarding and interesting to monitor the levels of the above metabolites in biological matrices to investigate pathological mechanisms. However, their quantitation is still unsatisfactory due to the poor retention behavior of the analytes on the traditional reversed-phase column. And never a single analytical method simultaneously quantify these three classes of metabolites. Besides, the concentrations of some metabolites are too low to be detected in the biological samples. In this study, we developed a UHPLC-ESI-MS/MS method to simultaneously determine the levels of 14 metabolites, including 4 methionine metabolism metabolites (methionine, homocysteine, S-adenosylmethionine and S-adenosylhomocysteine), 3 urea cycle intermediates (arginine, citrulline and ornithine) and 7 polyamines (putrescine, spermidine, spermine, N¹-acetylputrescine, N¹-acetylspermidine, N¹-acetylspermine and N¹,N¹²-diacetylspermine). The chromatographic separation was performed on the BEH amide column within 14 min using water and acetonitrile (both with 0.1% formic acid) as the mobile phases. The results of method validation showed good selectivity, linearity (r² > 0.99), recovery (93.1%-112.1%), inter-day and intra-day precision (RSD < 13.6% and RSD < 11.0%, respectively), stability (RSD < 15.1%) and matrix effect (76.0%-113.2%). The method is simple, quick and sensitive without derivatization processes and the use of ion-pairing reagents. This approach was successfully applied in urine, serum and tissue matrices, as well as in identifying potential biomarkers for hyperthyroidism and hypothyroidism. The method is promising to provide more information on pathophysiological mechanisms in metabolomics study.

Development of an LC-MS Targeted Metabolomics Methodology to Study Proline Metabolism in Mammalian Cell Cultures

A growing interest in metabolomics studies of cultured cells requires development not only untargeted methods capable of fingerprinting the complete metabolite profile but also targeted methods enabling the precise and accurate determination of a selected group of metabolites. Proline metabolism affects many crucial processes at the cellular level, including collagen biosynthesis, redox balance, energetic processes as well as intracellular signaling. The study aimed to develop a robust and easy-to-use targeted metabolomics method for the determination of the intracellular level of proline and the other two amino acids closely related to proline metabolism: glutamic acid and arginine. The method employs hydrophilic interaction liquid chromatography followed by high-resolution, accurate-mass mass spectrometry for reliable detection and quantification of the target metabolites in cell lysates. The sample preparation consisted of quenching by the addition of ice-cold methanol and subsequent cell scraping into a quenching solution. The method validation showed acceptable linearity (r > 0.995), precision (%RSD < 15%), and accuracy (88.5–108.5%). Pilot research using HaCaT spontaneously immortalized human keratinocytes in a model for wound healing was performed, indicating the usefulness of the method in studies of disturbances in proline metabolism. The developed method addresses the need to determine the intracellular concentration of three key amino acids and can be used routinely in targeted mammalian cell culture metabolomics research.

A reliable LC-MS/MS method for the quantification of natural amino acids in mouse plasma: Method validation and application to a study on amino acid dynamics during hepatocellular carcinoma progression

A simple and fast LC-MS/MS method was developed and validated for simultaneous quantification of 20 proteinogenic l-amino acids (AAs) in a small volume (5 μL) of mouse plasma. Chromatographic separation was achieved on an Intrada Amino Acid column within 13 min via gradient elution with an aqueous solution containing 100 mM ammonium formate and an organic mobile phase containing acetonitrile, water and formic acid (v:v:v = 95:5:0.3), at the flow rate of 0.6 mL/min. Individual AAs and corresponding stable-isotope-labeled AAs internal standards were analyzed by multiple reaction monitoring (MRM) in positive ion mode under optimized conditions. Method validation consisted of linearity, sensitivity, accuracy and precision, recovery, matrix effect, and stability, and the results demonstrated this LC-MS/MS method as a specific, accurate, and reliable assay. This LC-MS/MS method was thus utilized to compare the dynamics of individual plasma AAs between healthy and orthotopic hepatocellular carcinoma (HCC) xenograft mice housed under identical conditions. Our results revealed that, 5 weeks after HCC tumor progression, plasma l-arginine concentrations were significantly decreased in HCC mice while l-alanine and l-threonine levels were sharply increased. These findings support the utilities of this LC-MS/MS method and the promise of specific AAs as possible biomarkers for HCC.

Simultaneous determination of amino acids, purines and derivatives in serum by ultrahigh-performance liquid chromatography/tandem mass spectrometry

RATIONALE

Amino acids, purines and derivatives play a key role in physiological and pathological processes, such as the development of gestational diabetes mellitus. However, little literature has reported the simultaneous quantification of amino acids and purines. Therefore, a reliable and robust method for the determination of amino acids and purines is necessary.

METHODS

A rapid and simple method based on ultrahigh-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) was developed to determine the concentrations of twenty amino acids or derivatives and three purines or derivatives in serum.

RESULTS

The method was validated for linearity of calibration curve, limit of detection, limit of quantification, inter-day and intra-day precision, recovery, stability and matrix effect. The correlation coefficients of calibration curves were higher than 0.993 except for isoleucine. The recoveries ranged from 78.4% to 128.0% for three different concentrations of the spiked analytes. The matrix effect value ranged from -7.3% to 9.2%.

CONCLUSIONS

A rapid and simple UHPLC/MS/MS method for the simultaneous measurement of amino acids, purines and derivatives in serum samples was developed. The method was successfully applied to determine and compare the concentrations of analytes between gestational diabetes mellitus samples and controls.

Serum exosomes mediate delivery of arginase 1 as a novel mechanism for endothelial dysfunction in diabetes

Exosomes, abundant in blood, deliver various molecules to recipient cells. Endothelial cells are directly exposed to circulating substances. However, how endothelial cells respond to serum exosomes (SExos) and the implications in diabetes-associated vasculopathy have never been explored. In the present study, we showed that SExos from diabetic db/db mice (db/db SExos) were taken up by aortic endothelial cells, which severely impaired endothelial function in nondiabetic db/m⁺ mice. The exosomal proteins, rather than RNAs, mostly account for db/db SExos-induced endothelial dysfunction. Comparative proteomics analysis showed significant increase of arginase 1 in db/db SExos. Silence or overexpression of arginase 1 confirmed its essential role in db/db SExos-induced endothelial dysfunction. This study is a demonstration that SExos deliver arginase 1 protein to endothelial cells, representing a cellular mechanism during development of diabetic endothelial dysfunction. The results expand the scope of blood-borne substances that monitor vascular homeostasis.

Investigation of the reverse effect of Danhong injection on doxorubicin-induced cardiotoxicity in H9c2 cells: Insight by LC-MS based non-targeted metabolomic analysis

Although Danhong injection (DHI) has been clearly shown to attenuate ischemic myocardial injury and improve heart function, there is no research regarding its role in doxorubicin (DOX)-induced cardiomyopathy. In this study, we aimed to investigate the reverse effect of DHI on DOX-induced cardiotoxicity in H9c2 cells. The results of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay demonstrated that DHI had no cytotoxicity towards the relevant cell line unless the concentration was as high as 50 μL/mL. The satisfactory cardioprotective effect of DHI exerted at the concentration of 10 μL/mL, which agreed well with the result of real-time cell viability assay. Then non-targeted metabolomics based on LC-MS was employed to characterize metabolic alterations in DOX-induced cells with DHI treatment. Multivariate analysis, including PCA and PLS-DA, revealed 31 altered metabolites after DOX treatment that were primarily related to the disturbance of amino acids and nucleotides metabolism. While DHI could intervene in some disturbed metabolic pathways, such as the metabolism of arginine, glutathione (GSH), pantothenic acid, cytidine, inosine and 5'-methylthioadenosine. These results suggested that DHI exerted the therapeutic effect by improving energy metabolism and attenuating oxidative stress. The present study can lay a foundation for further research on the promising therapeutic effect of DHI in managing DOX-induced cardiotoxicity.

Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review

With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.

LC-MS-based metabolomics revealed SLC25A22 as an essential regulator of aspartate-derived amino acids and polyamines in KRAS-mutant colorectal cancer

SLC25A22, which encodes the mitochondrial glutamate transporter, is overexpressed in colorectal cancer (CRC) and is essential for the proliferation of CRC cells harboring KRAS mutations. However, the role of SLC25A22 on metabolic regulation in KRAS-mutant CRC cells has not been comprehensively characterized. We performed non-targeted metabolomics, targeted metabolomics and isotope kinetic analysis of KRAS-mutant DLD1 cells with or without SLC25A22 knockdown using ultra-high-performance liquid chromatography (UHPLC) coupled to Orbitrap mass spectrometry (MS) or tandem MS (MS/MS). Global metabolomics analysis identified 35 altered metabolites, which were attributed to alanine, aspartate and glutamate metabolism, urea cycle and polyamine metabolism. Targeted metabolomics including 24 metabolites revealed that most tricarboxylic acid (TCA) cycle intermediates, aspartate-derived asparagine, alanine and ornithine-derived polyamines were strongly down-regulated in SLC25A22 knockdown cells. Moreover, targeted kinetic isotope analysis showed that most of the ¹³C-labeled ornithine-derived polyamines were significantly decreased in SLC25A22 knockdown cells and culture medium. Exogenous addition of polyamines could significantly promote cell proliferation in DLD1 cells, highlighting their potential role as oncogenic metabolites that function downstream of SLC25A22-mediated glutamine metabolism. Collectively, SLC25A22 acts as an essential metabolic regulator during CRC progression as it promotes the synthesis of aspartate-derived amino acids and polyamines in KRAS mutant CRC cells.