bims-mascan 2019-12-29 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2019–12–29
twenty papers selected by
Giovanny Rodríguez Blanco, The Beatson Institute for Cancer Research

A Variant of SLC1A5 Is a Mitochondrial Glutamine Transporter for Metabolic Reprogramming in Cancer Cells.
Tissue pretreatment for LC-MS/MS analysis of PUFA and eicosanoid distribution in mouse brain and liver.
The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles.
Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection.
Crebl2 regulates cell metabolism in muscle and liver cells.
TCA Cycle Rewiring as Emerging Metabolic Signature of Hepatocellular Carcinoma.
Evaluation of lipid coverage and high spatial resolution MALDI-imaging capabilities of oversampling combined with laser post-ionisation.
Comparative Membrane N-Glycomics of Different Breast Cancer Cell Lines to Understand Breast Cancer Brain Metastasis.
n-3 PUFA and caloric restriction diet alters lipidomic profiles in obese men with metabolic syndrome: a preliminary open study.
Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State.
High-resolution metabolomics study revealing L-homocysteine Sulfinic acid, Cysteic acid, and Carnitine as novel biomarkers for high acute myocardial infarction risk.
Lipidomic profiling identifies signatures of metabolic risk.
Endoplasmic Reticulum Stress Pathway, the Unfolded Protein Response, Modulates Immune Function in the Tumor Microenvironment to Impact Tumor Progression and Therapeutic Response.
Mass Activated Droplet Sorting (MADS) Enables High Throughput Screening of Enzymatic Reactions at Nanoliter Scale.
Glucose restriction reverses the Warburg effect and modulates PKM2 and mTOR expression in breast cancer cell lines.
Implementation of a High-Resolution Liquid Chromatography-Mass Spectrometry Method in Quality Control Laboratories for Release and Stability Testing of a Commercial Antibody Product.
Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance.
Increased Glutaminolysis Marks Active Scarring in Nonalcoholic Steatohepatitis Progression.
Untargeted LC-HRMS-based metabolomics to identify novel biomarkers of metastatic colorectal cancer.
Development and validation of a new gas chromatography-tandem mass spectrometry method for the measurement of enrichment of glyoxylate metabolism analytes in hyperoxaluria patients using a stable isotope procedure.

Cell Metab. 2019 Dec 13. pii: S1550-4131(19)30664-3. [Epub ahead of print]

A Variant of SLC1A5 Is a Mitochondrial Glutamine Transporter for Metabolic Reprogramming in Cancer Cells.

Hee Chan Yoo, Seung Joon Park, Miso Nam, Juwon Kang, Kibum Kim, Joo Hye Yeo, Joon-Ki Kim, Yunkyung Heo, Hee Seung Lee, Myeong Youl Lee, Chang Woo Lee, Jong Soon Kang, Yun-Hee Kim, Jinu Lee, Junjeong Choi, Geum-Sook Hwang, Seungmin Bang, Jung Min Han.

  Glutamine is an essential nutrient that regulates energy production, redox homeostasis, and signaling in cancer cells. Despite the importance of glutamine in mitochondrial metabolism, the mitochondrial glutamine transporter has long been unknown. Here, we show that the SLC1A5 variant plays a critical role in cancer metabolic reprogramming by transporting glutamine into mitochondria. The SLC1A5 variant has an N-terminal targeting signal for mitochondrial localization. Hypoxia-induced gene expression of the SLC1A5 variant is mediated by HIF-2α. Overexpression of the SLC1A5 variant mediates glutamine-induced ATP production and glutathione synthesis and confers gemcitabine resistance to pancreatic cancer cells. SLC1A5 variant knockdown and overexpression alter cancer cell and tumor growth, supporting an oncogenic role. This work demonstrates that the SLC1A5 variant is a mitochondrial glutamine transporter for cancer metabolic reprogramming.

Keywords:  ASCT2; HIF-2α; SLC1A5; SLC1A5 variant; cancer metabolism; gemcitabine resistance; glutamine; hypoxia; metabolic reprogramming; mitochondrial glutamine transporter

DOI:  https://doi.org/10.1016/j.cmet.2019.11.020
Anal Bioanal Chem. 2019 Dec 21.

Tissue pretreatment for LC-MS/MS analysis of PUFA and eicosanoid distribution in mouse brain and liver.

Madlen Reinicke, Juliane Dorow, Karoline Bischof, Judith Leyh, Ingo Bechmann, Uta Ceglarek.

  Polyunsaturated fatty acids (PUFAs) and eicosanoids are important mediators of inflammation. The functional role of eicosanoids in metabolic-syndrome-related diseases has been extensively studied. However, their role in neuroinflammation and the development of neurodegenerative diseases is still unclear. The aim of this study was the development of a sample pretreatment protocol for the simultaneous analysis of PUFAs and eicosanoids in mouse liver and brain. Liver and brain samples of male wild-type C57BL/6J mice (11-122 mg) were used to investigate conditions for tissue rinsing, homogenization, extraction, and storage. A targeted liquid chromatography-negative electrospray ionization tandem mass spectrometry method was applied to quantify 7 PUFAs and 94 eicosanoids. The final pretreatment protocol consisted of a 5-min homogenization step by sonication in 650 μL n-hexane/2-propanol (60:40 v/v) containing 2,6-di-tert-butyl-4-methylphenol at 50 μg/mL. Homogenates representing 1 mg tissue were extracted in a single step with n-hexane/2-propanol (60:40 v/v) containing 0.1% formic acid. Autoxidation was prevented by addition of 2,6-di-tert-butyl-4-methylphenol at 50 μg/mL and keeping the samples at 4 °C during sample preparation. Extracts were dried under nitrogen and reconstituted in liquid chromatography eluent before analysis. Recovery was determined to range from 45% to 149% for both liver and brain tissue. Within-run and between-run variability ranged between 7% and 18% for PUFAs and between 1% and 24% for eicosanoids. In liver, 7 PUFAs and 15 eicosanoids were quantified; in brain, 6 PUFAs and 21 eicosanoids had significant differences within the brain substructures. In conclusion, a robust and reproducible sample preparation protocol for the multiplexed analysis of PUFAs and eicosanoids by liquid chromatography-tandem mass spectrometry in liver and discrete brain substructures was developed.

Keywords:  Brain lipids; Eicosanoids; Extraction; Mass spectrometry; Polyunsaturated fatty acids; Tissue sample preparation

DOI:  https://doi.org/10.1007/s00216-019-02170-w
J Assist Reprod Genet. 2019 Dec 21.

The lipidome of endometrial fluid differs between implantative and non-implantative IVF cycles.

Roberto Matorras, Ibon Martinez-Arranz, Enara Arretxe, Marta Iruarrizaga-Lejarreta, Blanca Corral, Jone Ibañez-Perez, Antonia Exposito, Begoña Prieto, Felix Elortza, Cristina Alonso.

   OBJECTIVE: To characterize the most relevant changes in the lipidome of endometrial fluid aspirate (EFA) in non-implantative cycles.
DESIGN: Lipidomics in a prospective cohort study.
SETTINGS: Reproductive unit of a university hospital.
PATIENTS: Twenty-nine women undergoing an IVF cycle. Fifteen achieved pregnancy and 14 did not.
INTERVENTION: Endometrial fluid aspiration immediately before performing embryo transfer.
MAIN OUTCOME MEASURES: Clinical pregnancy rate and lipidomic profiles obtained on an ultra-high performance liquid chromatography coupled to time-of-flight mass spectrometry (UHPLC-ToF-MS)-based analytical platform.
RESULTS: The comparative analysis of the lipidomic patterns of endometrial fluid in implantative and non-implantative IVF cycles revealed eight altered metabolites: seven glycerophospholipids and an omega-6 polyunsaturated fatty acid. Then, women with a non-implantative cycle were accurately classified with a support vector machine algorithm including these eight lipid metabolites. The diagnostic performances of the algorithm showed an area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of 0.893 ± 0.07, 85.7%, 80.0%, and 82.8%, respectively.
CONCLUSION: A predictive lipidomic signature linked to the implantative status of the endometrial fluid has been found.

Keywords:  Assisted reproduction; Endometrial fluid; Implantation; In vitro fertilization; Lipidomics; Machine learning algorithms; Pregnancy

DOI:  https://doi.org/10.1007/s10815-019-01670-z
Methods Mol Biol. 2020 ;2099 173-194

Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection.

Carrie D Nicora, Amy C Sims, Kent J Bloodsworth, Young-Mo Kim, Ronald J Moore, Jennifer E Kyle, Ernesto S Nakayasu, Thomas O Metz.

  Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snapshot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of biosafety level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins, and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes, and their subsequent informatics pipelines.

Keywords:  Lipidomics; MERS-CoV; MPLEx; Mass spectrometry (MS); Metabolomics; Proteomics; Virus inactivation; Virus-host interactions

DOI:  https://doi.org/10.1007/978-1-0716-0211-9_14
Sci Rep. 2019 Dec 27. 9(1): 19869

Crebl2 regulates cell metabolism in muscle and liver cells.

Marcel Tiebe, Marilena Lutz, Deniz Senyilmaz Tiebe, Aurelio A Teleman.

We previously identified Drosophila REPTOR and REPTOR-BP as transcription factors downstream of mTORC1 that play an important role in regulating organismal metabolism. We study here the mammalian ortholog of REPTOR-BP, Crebl2. We find that Crebl2 mediates part of the transcriptional induction caused by mTORC1 inhibition. In C2C12 myoblasts, Crebl2 knockdown leads to elevated glucose uptake, elevated glycolysis as observed by lactate secretion, and elevated triglyceride biosynthesis. In Hepa1-6 hepatoma cells, Crebl2 knockdown also leads to elevated triglyceride levels. In sum, this works identifies Crebl2 as a regulator of cellular metabolism that can link nutrient sensing via mTORC1 to the metabolic response of cells.

DOI: https://doi.org/10.1038/s41598-019-56407-w
Cancers (Basel). 2019 Dec 25. pii: E68. [Epub ahead of print]12(1):

TCA Cycle Rewiring as Emerging Metabolic Signature of Hepatocellular Carcinoma.

Simona Todisco, Paolo Convertini, Vito Iacobazzi, Vittoria Infantino.

  Hepatocellular carcinoma (HCC) is a common malignancy. Despite progress in treatment, HCC is still one of the most lethal cancers. Therefore, deepening molecular mechanisms underlying HCC pathogenesis and development is required to uncover new therapeutic strategies. Metabolic reprogramming is emerging as a critical player in promoting tumor survival and proliferation to sustain increased metabolic needs of cancer cells. Among the metabolic pathways, the tricarboxylic acid (TCA) cycle is a primary route for bioenergetic, biosynthetic, and redox balance requirements of cells. In recent years, a large amount of evidence has highlighted the relevance of the TCA cycle rewiring in a variety of cancers. Indeed, aberrant gene expression of several key enzymes and changes in levels of critical metabolites have been observed in many solid human tumors. In this review, we summarize the role of the TCA cycle rewiring in HCC by reporting gene expression and activity dysregulation of enzymes relating not only to the TCA cycle but also to glutamine metabolism, malate/aspartate, and citrate/pyruvate shuttles. Regarding the transcriptional regulation, we focus on the link between NF-κB-HIF1 transcriptional factors and TCA cycle reprogramming. Finally, the potential of metabolic targets for new HCC treatments has been explored.

Keywords:  HIF1; NF-κB; citrate/pyruvate shuttle; glutamine; hepatocellular carcinoma (HCC); malate/aspartate shuttle (MAS); metabolic reprogramming; tricarboxylic acid (TCA) cycle rewiring

DOI:  https://doi.org/10.3390/cancers12010068
Anal Bioanal Chem. 2019 Dec 26.

Evaluation of lipid coverage and high spatial resolution MALDI-imaging capabilities of oversampling combined with laser post-ionisation.

Andrew P Bowman, Jeroen F J Bogie, Jerome J A Hendriks, Mansour Haidar, Mikhail Belov, Ron M A Heeren, Shane R Ellis.

  Matrix-assisted laser desorption/ionisation-mass spectrometry imaging (MALDI-MSI) is a powerful technique for visualising the spatial locations of lipids in biological tissues. However, a major challenge in interpreting the biological significance of local lipid compositions and distributions detected using MALDI-MSI is the difficulty in associating spectra with cellular lipid metabolism within the tissue. By-and-large this is due to the typically limited spatial resolution of MALDI-MSI (30-100 μm) meaning individual spectra represent the average spectrum acquired from multiple adjacent cells, each potentially possessing a unique lipid composition and biological function. The use of oversampling is one promising approach to decrease the sampling area and improve the spatial resolution in MALDI-MSI, but it can suffer from a dramatically decreased sensitivity. In this work we overcome these challenges through the coupling of oversampling MALDI-MSI with laser post-ionisation (MALDI-2). We demonstrate the ability to acquire rich lipid spectra from pixels as small as 6 μm, equivalent to or smaller than the size of typical mammalian cells. Coupled with an approach for automated lipid identification, it is shown that MALDI-2 combined with oversampling at 6 μm pixel size can detect up to three times more lipids and many more lipid classes than even conventional MALDI at 20 μm resolution in the positive-ion mode. Applying this to mouse kidney and human brain tissue containing active multiple sclerosis lesions, where 74 and 147 unique lipids are identified, respectively, the localisation of lipid signals to individual tubuli within the kidney and lipid droplets with lesion-specific macrophages is demonstrated. Graphical abstract.

Keywords:  Brain; Kidney; Lipids; MALDI; Mass spectrometry imaging; Multiple sclerosis

DOI:  https://doi.org/10.1007/s00216-019-02290-3
J Proteome Res. 2019 Dec 26.

Comparative Membrane N-Glycomics of Different Breast Cancer Cell Lines to Understand Breast Cancer Brain Metastasis.

Wenjing Peng, Parvin Mirzaei, Rui Zhu, Shiyue Zhou, Yehia Mechref.

The mechanism of brain metastatic breast cancer has gained attention due to its increased incidence rate and its low survival rate. Aberrant protein glycosylation is thought to be a contributing factor in this metastatic mechanism, in which metastatic cancer cells can pass through the blood-brain barrier. The cell membrane is the outermost layer of a cell and in direct contact with the environment and with other cells, making membrane glycans especially important in many biological processes that include mediating cell-cell adhesion, cell signaling, and interactions. Thus, membrane glycomics has attracted more interest for a variety of disease studies in recent years. To reveal the role that membrane N-glycans play in breast cancer brain metastasis, in this study, membrane enrichment was achieved by ultracentrifugation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed to analyze enriched membrane N-glycomes from five breast cancer cell lines and one brain cancer cell line. Relative quantitative glycomic data from each cell line was compared to MDA-MB-231BR, which is the brain-seeking cell line. The higher sialylation level observed in MDA-MB-231BR suggested the importance of sialylation as it might assist with cell invasion and the penetration of the blood-brain barrier. Some highly sialylated N-glycans, such as HexNAc5Hex6DeoxyHex1NeuAc3 and HexNAc6Hex7DeoxyHex1NeuAc3, exhibited higher abundances in 231BR, indicating their possible contributions to breast cancer brain metastasis as well as their potential to be indicators for the breast cancer brain metastasis.

DOI: https://doi.org/10.1021/acs.jproteome.9b00664
Eur J Nutr. 2019 Dec 21.

n-3 PUFA and caloric restriction diet alters lipidomic profiles in obese men with metabolic syndrome: a preliminary open study.

A Shabrina, T-H Tung, N T K Nguyen, H-C Lee, H-T Wu, W Wang, S-Y Huang.

   PURPOSE: For people with metabolic syndrome (MetS), altering the macronutrient composition of their diets might ameliorate metabolic abnormalities. The common method of clinical assessment only measures total lipid concentrations but ignores the individual species that contribute to these total concentrations. Thus, to predict the amelioration of MetS following caloric restriction (CR) and the intake of fish oil, we used lipidomics to investigate changes in plasma lipids and identify potential lipid metabolites.
METHODS: Lipidomics was performed using ultra-high-performance liquid chromatography-tandem mass spectrometry on plasma samples from a clinical trial conducted over 12 weeks. Subjects were randomized into two groups: CR (n = 12) and CR with fish oil (CRF, n = 9). Anthropometric and clinical parameters were measured and correlated with plasma lipidomics data.
RESULTS: Compared with baseline, significant differences were observed in body weight, waist circumference, blood pressure and interleukin-6 in both groups, but triglyceride (TG) levels significantly decreased in only the CRF group (all p < 0.05). A total of 138 lipid species were identified. Levels of species containing long-chain polyunsaturated fatty acids were significantly elevated-greater than twofold-following fish oil intake, these included TG (60:9) and phosphatidylcholine (p40:6) (all q < 0.05). TG (60:9) tended to correlate negatively with body weight, body mass index, blood pressure, and HbA1c following fish oil intake.
CONCLUSION: CR and fish oil can ameliorate MetS features, including anthropometric parameters, blood pressure, and blood lipid concentrations. The levels of particular lipid species such as TG-containing docosapentaenoic acid were elevated post-intervention and negatively associated with MetS features. TG (60:9) may be proposed as a lipid metabolite to predict amelioration in MetS following the intake of CR and fish oil.

Keywords:  Caloric restriction; Clinical trial; Fish oil; Lipidomics; Metabolic syndrome; n-3 PUFA

DOI:  https://doi.org/10.1007/s00394-019-02149-4
Mol Cell Proteomics. 2019 Dec 26. pii: mcp.RA119.001779. [Epub ahead of print]

Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State.

Anna M Nguyen, Jianhong Zhou, Brihget Sicairos, Sangeetha Sonney, Yuchun Du.

  The molecular mechanisms underlying exceptional radioresistance in pancreatic cancer remain elusive. In the present study, we established a stable radioresistant pancreatic cancer cell line MIA PaCa-2-R by exposing the parental MIA PaCa-2 cells to fractionated ionizing radiation (IR). Systematic proteomics and bioinformatics analysis of protein expression in MIA PaCa-2 and MIA PaCa-2-R cells revealed that several growth factor-/cytokine-mediated pathways, including the OSM/STAT3, PI3K/AKT and MAPK/ERK pathways, were activated in the radioresistant cells, leading to inhibition of apoptosis and increased epithelial-mesenchymal plasticity. In addition, the radioresistant cells exhibited enhanced capabilities of DNA repair and antioxidant defense compared to the parental cells. We focused functional analysis on one of the most upregulated proteins in the radioresistant cells, ecto-5'-nucleotidase (CD73), which is a cell surface protein that is overexpressed in a variety types of cancer. Ectopic overexpression of CD73 in the parental cells resulted in radioresistance and conferred resistance to IR-induced apoptosis. Knockdown of CD73 re-sensitized the radioresistant cells to IR and IR-induced apoptosis. The effect of CD73 on radioresistance and apoptosis is independent of the enzymatic activity of CD73. Further studies demonstrate that CD73 upregulation promotes Ser-136 phosphorylation of the proapoptotic protein BAD and is required for maintaining the radioresistant cells in a mesenchymal state. Our findings suggest that expression alterations in the IR-selected pancreatic cancer cells result in hyperactivation of the growth factor/cytokine signaling that promotes epithelial-mesenchymal plasticity and enhancement of DNA repair. Our results also suggest that CD73, potentially a novel downstream factor of the enhanced growth factor/cytokine signaling, confers acquired radioresistance by inactivating proapoptotic protein BAD via phosphorylation of BAD at Ser-136 and by maintaining the radioresistant pancreatic cancer cells in a mesenchymal state.

Keywords:  Apoptosis*; CD73; Cancer Biology*; Pancreatic cancer; Radioresistance; SILAC; Tandem Mass Spectrometry

DOI:  https://doi.org/10.1074/mcp.RA119.001779
Metabolism. 2019 Dec 21. pii: S0026-0495(19)30266-5. [Epub ahead of print] 154051

High-resolution metabolomics study revealing L-homocysteine Sulfinic acid, Cysteic acid, and Carnitine as novel biomarkers for high acute myocardial infarction risk.

Adnan Khan, Yoonjeong Choi, Joung Hwan Back, Sunmi Lee, Sun Ha Jee, Youngja H Park.

   BACKGROUND: Identifying changes in serum metabolites before the occurrence of acute myocardial infarction (AMI) is an important approach for finding novel biomarkers of AMI.
METHODS: In this prospective cohort study, serum samples obtained from patients at risk of AMI (n = 112) and non-risk controls (n = 89) were tested using high-resolution metabolomics (HRM). Partial least-squares discriminant analysis (PLS-DA), along with univariate analysis using a false discovery rate (FDR) of q = 0.05 were performed to discriminate metabolic profiles and to determine significantly different metabolites between healthy control and AMI risk groups.
RESULTS: PLS-DA significantly separated the AMI risk sera from control sera. The metabolites associated with amino acid biosynthesis, 2-oxocarboxylic acid, tryptophan, and amino sugar and nucleotide sugar metabolism pathways were mainly elevated in patients at risk of AMI. Further validation and quantification by MS/MS showed that tryptophan, carnitine, L-homocysteine sulfinic acid (L-HCSA), and cysteic acid (CA) were upregulated, while L-cysteine and L-cysteine sulfinic acid (L-CSA) were downregulated, specifically among AMI risk sera. Additionally, these discriminant metabolic profiles were not related to hypertension, smoking or alcoholism.
CONCLUSION: In conclusion, detecting upregulated L-HCSA and CA along with carnitine among patients at risk for AMI could serve as promising non-invasive biomarkers for early AMI detection.

Keywords:  Biomarker; Homocysteine; Mass spectrometry; Metabolomics; Myocardial infarction

DOI:  https://doi.org/10.1016/j.metabol.2019.154051
EBioMedicine. 2019 Dec 23. pii: S2352-3964(19)30716-9. [Epub ahead of print]51 102520

Lipidomic profiling identifies signatures of metabolic risk.

Xiaoyan Yin, Christine M Willinger, Joshua Keefe, Jun Liu, Antonio Fernández-Ortiz, Borja Ibáñez, José Peñalvo, Aram Adourian, George Chen, Dolores Corella, Reinald Pamplona, Manuel Portero-Otin, Mariona Jove, Paul Courchesne, Cornelia M van Duijn, Valentín Fuster, José M Ordovás, Ayşe Demirkan, Martin G Larson, Daniel Levy.

   BACKGROUND: Metabolic syndrome (MetS), the clustering of metabolic risk factors, is associated with cardiovascular disease risk. We sought to determine if dysregulation of the lipidome may contribute to metabolic risk factors.
METHODS: We measured 154 circulating lipid species in 658 participants from the Framingham Heart Study (FHS) using liquid chromatography-tandem mass spectrometry and tested for associations with obesity, dysglycemia, and dyslipidemia. Independent external validation was sought in three independent cohorts. Follow-up data from the FHS were used to test for lipid metabolites associated with longitudinal changes in metabolic risk factors.
RESULTS: Thirty-nine lipids were associated with obesity and eight with dysglycemia in the FHS. Of 32 lipids that were available for replication for obesity and six for dyslipidemia, 28 (88%) replicated for obesity and five (83%) for dysglycemia. Four lipids were associated with longitudinal changes in body mass index and four were associated with changes in fasting blood glucose in the FHS.
CONCLUSIONS: We identified and replicated several novel lipid biomarkers of key metabolic traits. The lipid moieties identified in this study are involved in biological pathways of metabolic risk and can be explored for prognostic and therapeutic utility.

Keywords:  Biomarker; Cardiovascular disease; Dysglycemia; Dyslipidemia; Metabolic risk; Metabolic syndrome

DOI:  https://doi.org/10.1016/j.ebiom.2019.10.046
Int J Mol Sci. 2019 Dec 25. pii: E169. [Epub ahead of print]21(1):

Endoplasmic Reticulum Stress Pathway, the Unfolded Protein Response, Modulates Immune Function in the Tumor Microenvironment to Impact Tumor Progression and Therapeutic Response.

Manuel U Ramirez, Salvador R Hernandez, David R Soto-Pantoja, Katherine L Cook.

  Despite advances in cancer therapy, several persistent issues remain. These include cancer recurrence, effective targeting of aggressive or therapy-resistant cancers, and selective treatments for transformed cells. This review evaluates the current findings and highlights the potential of targeting the unfolded protein response to treat cancer. The unfolded protein response, an evolutionarily conserved pathway in all eukaryotes, is initiated in response to misfolded proteins accumulating within the lumen of the endoplasmic reticulum. This pathway is initially cytoprotective, allowing cells to survive stressful events; however, prolonged activation of the unfolded protein response also activates apoptotic responses. This balance is key in successful mammalian immune response and inducing cell death in malignant cells. We discuss how the unfolded protein response affects cancer progression, survival, and immune response to cancer cells. The literature shows that targeting the unfolded protein response as a monotherapy or in combination with chemotherapy or immunotherapies increases the efficacy of these drugs; however, systemic unfolded protein response targeting may yield deleterious effects on immune cell function and should be taken into consideration. The material in this review shows the promise of both approaches, each of which merits further research.

Keywords:  Activating transcription factor 6 (ATF6); Glucose-regulated protein 78 (GRP78); Inositol-requiring enzyme 1 (IRE1); PKR-like endoplasmic reticulum kinase (PERK); T cell; immune cells; macrophage; tumor microenvironment; unfolded protein response

DOI:  https://doi.org/10.3390/ijms21010169
Angew Chem Int Ed Engl. 2019 Dec 23.

Mass Activated Droplet Sorting (MADS) Enables High Throughput Screening of Enzymatic Reactions at Nanoliter Scale.

Daniel Aaron Holland-Moritz, Michael Wismer, Benjamin Mann, Iman Farasat, Erik Guetschow, Shuwen Sun, Jeffrey Moore, Robert Kennedy, Ian Mangion, Christopher J Welch, Paul Devine.

  Microfluidic droplet sorting enables the high throughput screening and selection of water-in-oil microreactors at speeds and volumes unparalleled by traditional well-plate approaches. Most such systems sort using fluorescent reporters on modified substrates or reactions that are rarely industrially relevant. We describe a microfluidic system for high throughput sorting of nanoliter droplets based on direct detection using electrospray ionization mass spectrometry (ESI-MS). Droplets are split, one portion is analyzed by ESI-MS, and the second portion is sorted based on the MS result. Throughput of 0.7 samples/s is achieved with 98% accuracy using a self-correcting and adaptive sorting algorithm. We use the system to screen ~15,000 samples in 6 h and demonstrate its utility by sorting 25 nL droplets containing transaminase expressed in vitro . Label-free ESI-MS droplet screening expands the toolbox for droplet detection and recovery, improving the applicability of droplet sorting to protein engineering, drug discovery, and diagnostic workflows.

Keywords:  High throughput screening; biocatalysis; droplet microfluidics; mass spectrometry; microreactors

DOI:  https://doi.org/10.1002/anie.201913203
Cell Mol Biol (Noisy-le-grand). 2019 Sep 30. 65(7): 26-33

Glucose restriction reverses the Warburg effect and modulates PKM2 and mTOR expression in breast cancer cell lines.

Roula Tahtouh, Layal Wardi, Riad Sarkis, Ray Hachem, Issam Raad, Nabil El Zein, George Hilal.

Aerobic glycolysis, known as the "Warburg effect", is one of several hallmarks of cancer cells. The conversion of phosphoenolpyruvate (PEP) to pyruvate can be down regulated by the re-expression of the embryonic isoform 2 of pyruvate kinase (PKM2). This mechanism allows the accumulation of glycolytic intermediates for the biosynthesis of macromolecules, such as proteins, lipids and nucleic acids. PKM2 is favored by the well-known PI3K/Akt/mTOR proliferative pathway. This pathway is induced by high glucose levels, and the mTOR kinase is the central activator of the Warburg effect. In this study, we investigated the role of glucose restriction (GR) and mTOR inhibition in reversing the Warburg effect in MDA-MB 231 and MCF-7 breast cancer cell lines. PKM2 expression was measured by western blot. Lactate production by cells was determined by a colorimetric assay. The concentration of glucose in the supernatant of cells was measured using the Trinder method. ATP level was evaluated by using a Colorimetric/Fluorometric ATP Assay Kit. Our results showed that MDA-MB 231 cells increased glucose consumption when the glucose concentration was 0 g/L (P <0.01). In MCF-7 cells, glucose deprivation reduced lactate secretion by 80% (P =0.0001) but tripled glucose consumption (P = 0.0041). ATP concentration increased approximately when MCF-7 cells were deprived of glucose (P = 0.02). GSK1059615 does not significantly modulate lactate secretion and glucose uptake in both cell lines. Glucose restriction contribute to the reduction of the Warburg effect through mTOR inhibition and regulation of PKM2 kinases.

Keywords: GSK1059615.; Glucose restriction; MCF-7; MDA-MB 231; PKM2; mTOR
Anal Chem. 2019 Dec 27.

Implementation of a High-Resolution Liquid Chromatography-Mass Spectrometry Method in Quality Control Laboratories for Release and Stability Testing of a Commercial Antibody Product.

Izabela Sokolowska, Jingjie Mo, Fatie Rahimi Pirkolachahi, Carol McVean, Lars A T Meijer, Linda Switzar, Crina Balog, Michael J Lewis, Ping Hu.

Liquid chromatography-mass spectrometry (LC-MS) has been widely used throughout biotherapeutic development. However, its implementation in GMP-compliant commercial quality control (QC) laboratories remains a challenge. In this publication, we describe the covalidation and implementation of an automated, high-throughput, and GMP compliant subunit LC-MS method for monitoring antibody oxidation for commercial product release and stability testing. To our knowledge, this is the first report describing the implementation of a high-resolution LC-MS method in commercial QC laboratories for product release and stability testing in the biopharmaceutical industry. This work paves the road for implementing additional LC-MS methods to modernize testing in commercial QC with more targeted control of product quality.

DOI: https://doi.org/10.1021/acs.analchem.9b05036
ACS Omega. 2019 Dec 17. 4(25): 21596-21603

Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance.

Martin Jakubec, Espen Bariås, Fedor Kryuchkov, Linda Veka Hjørnevik, Øyvind Halskau.

Global lipid analysis still lags behind proteomics with respect to the availability of databases, experimental protocols, and specialized software. Determining the lipidome of cellular model systems in common use is of particular importance, especially when research questions involve lipids directly. In Parkinson's disease research, there is a growing awareness for the role of the biological membrane, where individual lipids may contribute to provoking α-synuclein oligomerisation and fibrillation. We present an analysis of the whole cell and plasma membrane lipid isolates of a neuroblastoma cell line, SH-SY5Y, a commonly used model system for research on this and other neurodegenerative diseases. We have used two complementary lipidomics methods. The relative quantities of PC, PE, SMs, CL, PI, PG, and PS were determined by 31P NMR. Fatty acid chain composition and their relative abundances within each phospholipid group were evaluated by liquid chromatography-tandem mass spectrometry. For this part of the analysis, we have developed and made available a set of Matlab scripts, LipMat. Our approach allowed us to observe several deviations of lipid abundances when compared to published reports regarding phospholipid analysis of cell cultures or brain matter. The most striking was the high abundance of PC (54.7 ± 1.9%) and low abundance of PE (17.8 ± 4.8%) and SMs (2.7 ± 1.2%). In addition, the observed abundance of PS was smaller than expected (4.7 ± 2.7%), similar to the observed abundance of PG (4.5 ± 1.8%). The observed fatty acid chain distribution was similar to the whole brain content with some notable differences: a higher abundance of 16:1 PC FA (17.4 ± 3.4% in PC whole cell content), lower abundance of 22:6 PE FA (15.9 ± 2.2% in plasma membrane fraction), and a complete lack of 22:6 PS FA.

DOI: https://doi.org/10.1021/acsomega.9b03463
Cell Mol Gastroenterol Hepatol. 2019 Dec 24. pii: S2352-345X(19)30182-1. [Epub ahead of print]

Increased Glutaminolysis Marks Active Scarring in Nonalcoholic Steatohepatitis Progression.

Kuo Du, Satish K Chitneni, Ayako Suzuki, Ying Wang, Ricardo Henao, Jeongeun Hyun, Richard T Premont, Susanna Naggie, Cynthia A Moylan, Mustafa R Bashir, Manal F Abdelmalek, Anna Mae Diehl.

   BACKGROUND AND AIMS: Nonalcoholic steatohepatitis (NASH) occurs in the context of aberrant metabolism. Glutaminolysis is required for metabolic reprograming of hepatic stellate cells (HSC) and liver fibrogenesis in mice. However, it is unclear how changes in HSC glutamine metabolism contribute to net changes in hepatic glutaminolytic activity during fibrosis progression, or whether this could be used to track fibrogenic activity in NASH. We postulated that increased HSC glutaminolysis marks active scarring in NASH.
METHODS: Glutaminolysis was assessed in mouse NASH-fibrosis models and NASH patients. Serum and liver levels of glutamine and glutamate and hepatic expression of glutamine transporter/metabolic enzymes were correlated with each other and with fibrosis severity. Glutaminolysis was disrupted in HSCs to examine if this directly influenced fibrogenesis. 18F-fluoroglutamine-positron emission tomography (PET) was used to determine how liver glutamine assimilation tracked with hepatic fibrogenic activity in situ.
RESULTS: The serum glutamate/glutamine ratio increased and correlated with its hepatic ratio, myofibroblast content, and fibrosis severity. Healthy livers almost exclusively expressed liver-type glutaminase (Gls2); Gls2 protein localized in zone 1 hepatocytes, while glutamine synthase (GS) was restricted to zone 3 hepatocytes. In fibrotic livers, Gls2 nearly disappeared and GS zonality was lost, but both Slc1a5 (glutamine transporter) and kidney-type Gls1 were up-regulated; Gls1 protein was restricted to stromal cells and accumulated in fibrotic septa. Hepatocytes did not compensate for decreased Gls2 by inducing Gls1. Limiting glutamine or directly inhibiting GLS1 inhibited growth and fibrogenic activity in cultured human HSCs. Compared to healthy livers, fibrotic livers were 18F-fluoroglutamine-avid by PET, suggesting that glutamine-addicted myofibroblasts drive increased hepatic utilization of glutamine as fibrosis progresses.
CONCLUSIONS: Glutaminolysis is a potential diagnostic marker and therapeutic target during NASH-fibrosis progression.

Keywords:  Amino Acid; Biomarker; Liver Diseases; Metabolomics

DOI:  https://doi.org/10.1016/j.jcmgh.2019.12.006
Sci Rep. 2019 Dec 27. 9(1): 20198

Untargeted LC-HRMS-based metabolomics to identify novel biomarkers of metastatic colorectal cancer.

Ariadna Martín-Blázquez, Caridad Díaz, Encarnación González-Flores, Daniel Franco-Rivas, Cristina Jiménez-Luna, Consolación Melguizo, José Prados, Olga Genilloud, Francisca Vicente, Octavio Caba, José Pérez Del Palacio.

Colorectal cancer is one of the main causes of cancer death worldwide, and novel biomarkers are urgently needed for its early diagnosis and treatment. The utilization of metabolomics to identify and quantify metabolites in body fluids may allow the detection of changes in their concentrations that could serve as diagnostic markers for colorectal cancer and may also represent new therapeutic targets. Metabolomics generates a pathophysiological 'fingerprint' that is unique to each individual. The purpose of our study was to identify a differential metabolomic signature for metastatic colorectal cancer. Serum samples from 60 healthy controls and 65 patients with metastatic colorectal cancer were studied by liquid chromatography coupled to high-resolution mass spectrometry in an untargeted metabolomic approach. Multivariate analysis revealed a separation between patients with metastatic colorectal cancer and healthy controls, who significantly differed in serum concentrations of one endocannabinoid, two glycerophospholipids, and two sphingolipids. These findings demonstrate that metabolomics using liquid-chromatography coupled to high-resolution mass spectrometry offers a potent diagnostic tool for metastatic colorectal cancer.

DOI: https://doi.org/10.1038/s41598-019-55952-8
Anal Chem. 2019 Dec 23.

Development and validation of a new gas chromatography-tandem mass spectrometry method for the measurement of enrichment of glyoxylate metabolism analytes in hyperoxaluria patients using a stable isotope procedure.

Dewi van Harskamp, Sander F Garrelfs, Michiel J S Oosterveld, Jaap W Groothoff, Johannes B van Goudoever, Henk Schierbeek.

Primary hyperoxalurias (PH) are inborn errors of glyoxylate metabolism characterized by an increase in endogenous oxalate production. Oxalate overproduction may cause calcium-oxalate crystal formation leading to kidney stones, nephrocalcinosis, and ultimately kidney failure. Twenty-four hour urine oxalate excretion is an inaccurate measure for endogenous oxalate production in PH patients and not applicable in those with kidney failure. Treatment efficacy cannot be assessed with this measure during clinical trials. We describe the development and validation of a gas chromatography-tandem mass spectrometry method to analyze the samples obtained following a stable isotope infusion protocol of 13C2-oxalate and 1-13C-glycolate in both healthy individuals and PH patients. Isotopic enrichments of plasma oxalate, glycolate, and glyoxylate were measured on a gas chromatography-triple quadrupole mass spectrometry system using ethylhydroxylamine and N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) for analyte derivatization. Method precision was good for oxalate and glycolate (coefficients of variation [CV] were <6.3% and <4.2% for inter- and intra-day precision, respectively) and acceptable for glyoxylate (CV <18.3% and <6.7% for inter- and intra-day precision, respectively). The enrichment curves were linear over the specified range. Sensitivity was sufficient to accurately analyze enrichments. This new method allowed calculation of kinetic features of these metabolites, thus enabling a detailed analysis of the various pathways involved in glyoxylate metabolism. The method will further enhance the investigation of the metabolic PH derangements, provides a tool to accurately assess the therapeutic efficacy of new promising therapeutic interventions for PH, and could serve as a clinical tool to improve personalized therapeutic strategies.

DOI: https://doi.org/10.1021/acs.analchem.9b03670