bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019–11–24
twenty papers selected by
Giovanny Rodriguez Blanco, The Beatson Institute for Cancer Research
  1. Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis.
  2. Generation and quality control of lipidomics data for the alzheimer's disease neuroimaging initiative cohort.
  3. Label-Based Mass Spectrometry Approaches for Robust Quantification of the Phosphoproteome and Total Proteome in Toxoplasma gondii.
  4. Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction.
  5. Lipid Metabolism at the Nexus of Diet and Tumor Microenvironment.
  6. Targeting citrate as a novel therapeutic strategy in cancer treatment.
  7. Nanoextraction coupled to liquid chromatography mass spectrometry delivers improved spatially resolved analysis.
  8. A New Classification Method of Metastatic Cancers Using a 1H-NMR-Based Approach: A Study Case of Melanoma, Breast, and Prostate Cancer Cell Lines.
  9. Mitochondrial Arginase-2 is a cell autonomous regulator of CD8+ T cell function and anti-tumor efficacy.
  10. Lineage-Restricted Regulation of SCD and Fatty Acid Saturation by MITF Controls Melanoma Phenotypic Plasticity.
  11. Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography.
  12. Lactate in the Regulation of Tumor Microenvironment and Therapeutic Approaches.
  13. Serum metabolomics reveals personalized metabolic patterns for macular neovascular patient stratification.
  14. Proline-dependent regulation of collagen metabolism.
  15. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion.
  16. Microarray and mass spectrometry-based Methodology for lipid profiling of tissues and cell cultures.
  17. Statistically-driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network.
  18. Effects of Aging and Methionine Restriction on Rat Kidney Metabolome.
  19. Lipid mechanisms in hallmarks of cancer.
  20. Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity.
  1. J Biol Chem. 2019 Nov 20. pii: jbc.RA119.010903. [Epub ahead of print]
    Evolved resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different state of glycolysis.
    Maria V Liberti, Annamarie E Allen, Vijyendra Ramesh, Ziwei Dai, Katherine R Singleton, Zufeng Guo, Jun O Liu, Kris C Wood, Jason W Locasale.
      Aerobic glycolysis or the Warburg effect (WE) is characterized by increased glucose uptake and incomplete oxidation to lactate. Although the WE is ubiquitous, its biological role remains controversial and whether glucose metabolism is functionally different during fully oxidative glycolysis or during the WE is unknown. To investigate this question, here we evolved resistance to koningic acid (KA), a natural product that specifically inhibits glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-controlling glycolytic enzyme during the WE. We found that KA-resistant cells lose the WE but continue to conduct glycolysis and surprisingly remain dependent on glucose as a carbon source and also on central carbon metabolism. Consequently, this altered state of glycolysis led to differential metabolic activity and requirements, including emergent activities in and dependencies on fatty acid metabolism. These findings reveal that aerobic glycolysis is a process functionally distinct from conventional glucose metabolism and leads to distinct metabolic requirements and biological functions.
    Keywords:  Warburg effect; cancer; glucose metabolism; glyceraldehyde-3-phosphate dehydrogenase GAPDH; glycolysis; mass spectrometry (MS); metabolic regulation; metabolic reprogramming; metabolomics; oxidative metabolism
    DOI:  https://doi.org/10.1074/jbc.RA119.010903
  2. Sci Data. 2018 Nov 20. 5(1): 180263
    Generation and quality control of lipidomics data for the alzheimer's disease neuroimaging initiative cohort.
    Alzheimer’s Disease Neuroimaging Initiative
      Alzheimer's disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/.
    DOI:  https://doi.org/10.1038/sdata.2018.263
  3. Methods Mol Biol. 2020 ;2071 453-468
    Label-Based Mass Spectrometry Approaches for Robust Quantification of the Phosphoproteome and Total Proteome in Toxoplasma gondii.
    Malgorzata Broncel, Moritz Treeck.
      Protein phosphorylation plays a key role in regulating biological processes. Over 30% of the proteome is phosphorylated in most organisms and unraveling the function of the kinases that mediate these phosphorylation events requires the technology to reliably measure phosphorylation on proteins under various conditions. Advances in mass-spectrometry instrumentation, sample preparation, and labeling technologies now offer a range of quantification methods, each with their advantages and disadvantages. Here we describe in detail two different quantification methods, that is, stable isotope labeling by amino acids in cell culture and tandem mass tagging, combined with phosphopeptide enrichment strategies to measure the phosphoproteome of Toxoplasma parasites.
    Keywords:  High pH reverse phase fractionation; IMAC; LC-MS/MS; Phosphoproteome; Proteome; SILAC; TMT; TiO2; Toxoplasma gondii
    DOI:  https://doi.org/10.1007/978-1-4939-9857-9_23
  4. Mol Cell Proteomics. 2019 Nov 21. pii: mcp.TIR119.001616. [Epub ahead of print]
    Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction.
    Joerg Doellinger, Andy Schneider, Marcell Hoeller, Peter Lasch.
      The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.
    Keywords:  Automation; Bacteria; Detergent-free; Label-free quantification; Lysis; Mass Spectrometry; Microbiome; Pathogens; Protein Denaturation*; Sample Preparation; TFA
    DOI:  https://doi.org/10.1074/mcp.TIR119.001616
  5. Trends Cancer. 2019 Nov;pii: S2405-8033(19)30190-6. [Epub ahead of print]5(11): 693-703
    Lipid Metabolism at the Nexus of Diet and Tumor Microenvironment.
    Barrie Peck, Almut Schulze.
      Obesity is a leading contributing factor to cancer development worldwide. Epidemiological evidence suggests that diet affects cancer risk and also substantially alters therapeutic outcome. Therefore, studying the impact of diet in the development and treatment of cancer should be a clinical priority. In this Review, we set out the evidence supporting the role of lipid metabolism in shaping the tumor microenvironment (TME) and cancer cell phenotype. We will discuss how dietary lipids can impact phenotype thereby affecting disease trajectory and treatment response. Finally, we will posit potential strategies on how this knowledge can be exploited to increase treatment efficacy and patient survival.
    Keywords:  cancer; cancer metabolism; diet; environmental heterogeneity; lipids; nutrient stress; obesity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2019.09.007
  6. Biochim Biophys Acta Rev Cancer. 2019 Nov 18. pii: S0304-419X(19)30159-3. [Epub ahead of print] 188332
    Targeting citrate as a novel therapeutic strategy in cancer treatment.
    Lan Huang, Cindy Wang, Huaxi Xu, Guangyong Peng.
      An important feature shared by many cancer cells is drastically altered metabolism that is critical for rapid growth and proliferation. The distinctly reprogrammed metabolism in cancer cells makes it possible to manipulate the levels of metabolites for cancer treatment. Citrate is a key metabolite that bridges many important metabolic pathways. Recent studies indicate that manipulating the level of citrate can impact the behaviors of both cancer and immune cells, resulting in induction of cancer cell apoptosis, boosting immune responses, and enhanced cancer immunotherapy. In this review, we discuss the recent developments in this emerging area of targeting citrate in cancer treatment. Specifically, we summarize the molecular basis of altered citrate metabolism in both tumors and immune cells, explore the seemingly conflicted growth promoting and growth inhibiting roles of citrate in various tumors, discuss the use of citrate in the clinic as a novel biomarker for cancer progression and outcomes, and highlight the new development of combining citrate with other therapeutic strategies in cancer therapy. An improved understanding of complex roles of citrate in the suppressive tumor microenvironment should open new avenues for cancer therapy.
    Keywords:  Citrate; Glucose metabolism; Glycolysis; Immune checkpoint; Immunotherapy; Tricarboxylic acid cycle; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.bbcan.2019.188332
  7. Anal Chem. 2019 Nov 20.
    Nanoextraction coupled to liquid chromatography mass spectrometry delivers improved spatially resolved analysis.
    Holly-May Lewis, Roger Webb, Guido F Verbeck, Josephine Bunch, Janella de Jesus, Catia Costa, Vladimir Palitsin, John G Swales, Richard J A Goodwin, Patrick Sears, Melanie Jane Bailey.
      Direct analyte probed nanoextraction (DAPNe) is a technique that allows extraction of drug and endogenous compounds from a discrete location on a tissue sample using a nano capillary filled with solvent. Samples can be extracted from a spot diameters as low as 6 µm. Studies previously undertaken by our group have shown that the technique can provide good precision (5%) for analysing drug molecules in 150 µm diameter areas of homogenised tissue, provided an internal standard is sprayed on to the tissue prior to analysis. However, without an isotopically labelled standard, the repeatability is poor, even after normalisation to and the spot area or matrix compounds. By application to tissue homogenates spiked with drug compounds, we can demonstrate that it is possible to significantly improve the repeatability of the technique by incorporating a liquid chromatography separation step. Liquid chromatography is a technique for separating compounds prior to mass spectrometry (LC-MS) which enables separation of isomeric compounds that cannot be discriminated using mass spectrometry alone, as well as reducing matrix interferences. Conventionally, LC-MS is carried out on bulk or homogenised samples, which means analysis is essentially an average of the sample and does not take into account discrete areas. This work opens a new opportunity for spatially resolved liquid chromatography mass spectrometry with precision better than 20%.
    DOI:  https://doi.org/10.1021/acs.analchem.9b02821
  8. Metabolites. 2019 Nov 17. pii: E281. [Epub ahead of print]9(11):
    A New Classification Method of Metastatic Cancers Using a 1H-NMR-Based Approach: A Study Case of Melanoma, Breast, and Prostate Cancer Cell Lines.
    Corentin Schepkens, Matthieu Dallons, Jonas Dehairs, Ali Talebi, Jérôme Jeandriens, Lise-Marie Drossart, Guillaume Auquier, Vanessa Tagliatti, Johannes V Swinnen, Jean-Marie Colet.
      In this study, metastatic melanoma, breast, and prostate cancer cell lines were analyzed using a 1H-NMR-based approach in order to investigate common features and differences of aggressive cancers metabolomes. For that purpose, 1H-NMR spectra of both cellular extracts and culture media were combined with multivariate data analysis, bringing to light no less than 20 discriminant metabolites able to separate the metastatic metabolomes. The supervised approach succeeded in classifying the metastatic cell lines depending on their glucose metabolism, more glycolysis-oriented in the BRAF proto-oncogene mutated cell lines compared to the others. Other adaptive metabolic features also contributed to the classification, such as the increased total choline content (tCho), UDP-GlcNAc detection, and various changes in the glucose-related metabolites tree, giving additional information about the metastatic metabolome status and direction. Finally, common metabolic features detected via 1H-NMR in the studied cancer cell lines are discussed, identifying the glycolytic pathway, Kennedy's pathway, and the glutaminolysis as potential and common targets in metastasis, opening up new avenues to cure cancer.
    Keywords:  NMR; breast cancer; melanoma; metabonomics; metastasis; prostate cancer
    DOI:  https://doi.org/10.3390/metabo9110281
  9. JCI Insight. 2019 Nov 21. pii: 132975. [Epub ahead of print]
    Mitochondrial Arginase-2 is a cell autonomous regulator of CD8+ T cell function and anti-tumor efficacy.
    Adrià-Arnau Martí I Líndez, Isabelle Dunand-Sauthier, Mark Conti, Florian Gobet, Nicolás Núñez, J Thomas Hannich, Howard Riezman, Geiger Roger, Alessandra Piersigilli, Kerstin Hahn, Sylvain Lemeille, Burkhard Becher, Thibaut De Smedt, Stéphanie Hugues, Walter Reith.
      As sufficient extracellular arginine is crucial for T cell function, depletion of extracellular arginine by elevated Arginase 1 (Arg1) activity has emerged as a hallmark immunosuppressive mechanism. However, the potential cell-autonomous roles of arginases in T cells have remained unexplored. Here we show that the arginase isoform expressed by T cells, the mitochondrial Arginase 2 (Arg2), is a cell-intrinsic regulator of CD8+ T cell activity. Both germ-line Arg2 deletion and adoptive transfer of Arg2-/- CD8+ T cells significantly reduced tumor growth in preclinical cancer models by enhancing CD8+ T cell activation, effector function and persistence. Transcriptomic, proteomic and high-dimensional flow cytometry characterization revealed a CD8+ T cell-intrinsic role of Arg2 in modulating T cell activation, anti-tumor cytoxicity and memory formation, independently of extracellular arginine availability. Furthermore, specific deletion of Arg2 in CD8+ T cells strongly synergized with PD-1 blockade for the control of tumor growth and animal survival. These observations coupled with the finding that pharmacologic arginase inhibition accelerates activation of ex vivo human T cells unveil Arg2 as a new therapeutic target for T cell-based cancer therapies.
    Keywords:  Amino acid metabolism; Cancer immunotherapy; Immunology; Mitochondria; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.132975
  10. Mol Cell. 2019 Oct 30. pii: S1097-2765(19)30792-0. [Epub ahead of print]
    Lineage-Restricted Regulation of SCD and Fatty Acid Saturation by MITF Controls Melanoma Phenotypic Plasticity.
    Yurena Vivas-García, Paola Falletta, Jana Liebing, Pakavarin Louphrasitthiphol, Yongmei Feng, Jagat Chauhan, David A Scott, Nicole Glodde, Ana Chocarro-Calvo, Sarah Bonham, Andrei L Osterman, Roman Fischer, Ze'ev Ronai, Custodia García-Jiménez, Michael Hölzel, Colin R Goding.
      Phenotypic and metabolic heterogeneity within tumors is a major barrier to effective cancer therapy. How metabolism is implicated in specific phenotypes and whether lineage-restricted mechanisms control key metabolic vulnerabilities remain poorly understood. In melanoma, downregulation of the lineage addiction oncogene microphthalmia-associated transcription factor (MITF) is a hallmark of the proliferative-to-invasive phenotype switch, although how MITF promotes proliferation and suppresses invasion is poorly defined. Here, we show that MITF is a lineage-restricted activator of the key lipogenic enzyme stearoyl-CoA desaturase (SCD) and that SCD is required for MITFHigh melanoma cell proliferation. By contrast MITFLow cells are insensitive to SCD inhibition. Significantly, the MITF-SCD axis suppresses metastasis, inflammatory signaling, and an ATF4-mediated feedback loop that maintains de-differentiation. Our results reveal that MITF is a lineage-specific regulator of metabolic reprogramming, whereby fatty acid composition is a driver of melanoma phenotype switching, and highlight that cell phenotype dictates the response to drugs targeting lipid metabolism.
    Keywords:  ATF4; MITF; fatty acid saturation; melanoma; metastatic dissemination; phenotype switching; stearoyl CoA desaturase
    DOI:  https://doi.org/10.1016/j.molcel.2019.10.014
  11. J Am Soc Mass Spectrom. 2019 Nov 21.
    Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography.
    Dahang Yu, Zhe Wang, Kellye A Cupp-Sutton, Xiaowen Liu, Si Wu.
      Post-translational modifications (PTMs) play critical roles in biological processes and have significant effects on the structures and dynamics of proteins. Top-down proteomics methods were developed for and applied to the study of intact proteins and their PTMs in human samples. However, the large dynamic range and complexity of human samples makes the study of human proteins challenging. To address these challenges, we developed a 2D pH RP/RPLC-MS/MS technique that fuses high-resolution separation and intact protein characterization to study the human proteins in HeLa cell lysate. Our results provide a deep coverage of soluble proteins in human cancer cells. Compared to 225 proteoforms from 124 proteins identified when 1D separation was used, 2778 proteoforms from 628 proteins were detected and characterized using our 2D separation method. Many proteoforms with critically functional PTMs including phosphorylation were characterized. Additionally, we present the first detection of intact human GcvH proteoforms with rare modifications such as octanoylation and lipoylation. Overall, the increase in the number of proteoforms identified using 2DLC separation is largely due to the reduction in sample complexity through improved separation resolution, which enables the detection of low-abundance PTM-modified proteoforms. We demonstrate here that 2D pH RP/RPLC is an effective technique to analyze complex protein samples using top-down proteomics.
    Keywords:  Intact proteoforms; Liquid chromatography; Mass spectrometry; RPLC; Top-down proteomics
    DOI:  https://doi.org/10.1007/s13361-019-02315-2
  12. Front Oncol. 2019 ;9 1143
    Lactate in the Regulation of Tumor Microenvironment and Therapeutic Approaches.
    Karen G de la Cruz-López, Leonardo Josué Castro-Muñoz, Diego O Reyes-Hernández, Alejandro García-Carrancá, Joaquín Manzo-Merino.
      Tumor cells must generate sufficient ATP and biosynthetic precursors in order to maintain cell proliferation requirements. Otto Warburg showed that tumor cells uptake high amounts of glucose producing large volumes of lactate even in the presence of oxygen, this process is known as "Warburg effect or aerobic glycolysis." As a consequence of such amounts of lactate there is an acidification of the extracellular pH in tumor microenvironment, ranging between 6.0 and 6.5. This acidosis favors processes such as metastasis, angiogenesis and more importantly, immunosuppression, which has been associated to a worse clinical prognosis. Thus, lactate should be thought as an important oncometabolite in the metabolic reprogramming of cancer. In this review, we summarized the role of lactate in regulating metabolic microenvironment of cancer and discuss its relevance in the up-regulation of the enzymes lactate dehydrogenase (LDH) and monocarboxilate transporters (MCTs) in tumors. The goal of this review is to expose that lactate is not only a secondary product of cellular metabolic waste of tumor cells, but also a key molecule involved in carcinogenesis as well as in tumor immune evasion. Finally, the possible targeting of lactate production in cancer treatment is discussed.
    Keywords:  acidification; immune response; lactate; therapy; tumor microenvironment (TME)
    DOI:  https://doi.org/10.3389/fonc.2019.01143
  13. J Proteome Res. 2019 Nov 22.
    Serum metabolomics reveals personalized metabolic patterns for macular neovascular patient stratification.
    Kun Liu, Junwei Fang, Jing Jin, Shaopin Zhu, Xiaoyin Xu, Yupeng Xu, Bin Ye, Shu-Hai Lin, Xun Xu.
      Macular neovascular disease is a group disorder with complex pathogenesis of neovascularization for vision impairment and irreversible blindness, posing great challenges to precise diagnosis and management. We prospectively recruited participants with age-related macular degeneration (AMD), polypoidal choroidal vasculopathy (PCV) and pathological myopia (PM), compared with cataract patients without fundus diseases as control group. The serum metabolome was profiled by gas chromatography coupled with time-of-flight mass spectrometry (GC-TOFMS) analysis. Multivariate statistical methods as well as data mining were performed for interpretation of macular neovascularization. A total of 446 participants with macular neovascularization and 138 cataract subjects as control group were enrolled in this study. By employing GC-TOFMS, 131 metabolites were identified and 33 differentiating metabolites were highlighted in patients with macular neovascularization. For differential diagnosis, 3 panels of specific metabolomics-based biomarkers provided areas under the curve of 0.967, 0.938 and 0.877 in the discovery phase (n= 328), predictive values of 87.3%, 79% and 85.7% in the test phase (n= 256). Personalized pathway dysregulation scores measurement using lilikoi package in R language revealed pentose phosphate pathway and mitochondrial electron transport chain as the most important pathways in AMD; purine metabolism and glycolysis were identified as the major disturbed pathways in PCV while the altered thiamine metabolism and purine metabolism may contribute to PM phenotypes. Serum metabolomics are powerful for characterizing metabolic disturbances of macular neovascular. Differences in metabolic pathways may reflect underlying macular neovascularand serve as therapeutic targets for macular neovascular treatment.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00574
  14. Cell Mol Life Sci. 2019 Nov 18.
    Proline-dependent regulation of collagen metabolism.
    Ewa Karna, Lukasz Szoka, Thi Yen Ly Huynh, Jerzy A Palka.
      This review is focused on recent data on the role of proline (Pro) in collagen biosynthesis and cellular metabolism. It seems obvious that one of the main substrates for collagen biosynthesis Pro is required to form collagen molecule. The question raised in this review is whether the Pro for collagen biosynthesis is synthesized "de novo", comes directly from degraded proteins or it is converted from other amino acids. Recent data provided evidence that extracellular Pro (added to culture medium) had significant, but relatively little impact on collagen biosynthesis in fibroblasts (the main collagen synthesized cells) cultured in the presence of glutamine (Gln). However, extracellular Pro drastically increased collagen biosynthesis in the cells cultured in Gln-free medium. It suggests that Pro availability determines the rate of collagen biosynthesis and demand for Pro in fibroblasts is predominantly met by conversion from Gln. The potential mechanism of this process as well as possible implication of this knowledge in pharmacotherapy of connective tissue diseases is discussed in this review.
    Keywords:  Amino acids; Cell metabolism; Collagen; Prolidase; Signaling
    DOI:  https://doi.org/10.1007/s00018-019-03363-3
  15. J Proteome Res. 2019 Nov 22.
    ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion.
    Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol.
      The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we present ThermoRawFileParser, an open-source, cross-platform tool that converts Thermo RAW files into open file formats such as MGF and the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda package and BioContainers container around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00328
  16. Anal Chem. 2019 Nov 21.
    Microarray and mass spectrometry-based Methodology for lipid profiling of tissues and cell cultures.
    Roberto Antonio Fernández, Jone Garate, Tarson Tolentino-Cortez, Ainara Herraiz, Laura Lombardero, Fabien Ducrocq, Rafael Rodriguez-Puertas, Pierre Trifilieff, Egoitz Astigarraga, Gabriel Barreda-Gómez, Jose A Fernandez.
      The recent developments in mass spectrometry have revealed the importance of lipids as biomarkers in the context of dif-ferent diseases and as indicators of the cell's homeostasis. However, further advances are required to unveil the complex relationships between lipid classes and lipid species with proteins. Here we present a new methodology that combines micro-arrays with mass spectrometry to obtain the lipid fingerprint of samples of different nature in a standardized and fast way, with minimal sample consumption. As a proof of concept, we use the methodology to obtain the lipid fingerprint of 20 rat tissues and to create a lipid library for tissue classification. Then, we combine those results with immunohistochemistry and enzymatic assays to unveil the relationship between some lipid species and two enzymes. Finally, we demonstrate the per-formance of the methodology to explore changes in lipid composition of the nucleus accumbens from mice subjected to two lipid diets.
    DOI:  https://doi.org/10.1021/acs.analchem.9b04529
  17. Anal Chem. 2019 Nov 19.
    Statistically-driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network.
    Bobbie-Jo M Webb-Robertson, Kelly G Stratton, Jennifer E Kyle, Young-Mo Kim, Lisa M Bramer, Katrina M Waters, David Koeller, Thomas O Metz.
      Advancements in molecular separations coupled with mass spectrometry have enabled metabolome analyses for clinical co-horts. A population of interest for metabolome profiling are patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic basis, as well as mechanistic drivers of the disease and possible treatment options. We under-took the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Undiagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN patients took place over two years. We describe the study design to adjust for measurements collected over a long time-scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case-studies of interest that demonstrate the utility of metabolome profiling for rare diseases.
    DOI:  https://doi.org/10.1021/acs.analchem.9b03522
  18. Metabolites. 2019 Nov 14. pii: E280. [Epub ahead of print]9(11):
    Effects of Aging and Methionine Restriction on Rat Kidney Metabolome.
    Irene Pradas, Mariona Jové, Rosanna Cabré, Victoria Ayala, Natalia Mota-Martorell, Reinald Pamplona.
      Methionine restriction (MetR) in animal models extends maximum longevity and seems to promote renoprotection by attenuating kidney injury. MetR has also been proven to affect several metabolic pathways including lipid metabolism. However, there is a lack of studies about the effect of MetR at old age on the kidney metabolome. In view of this, a mass spectrometry-based high-throughput metabolomic and lipidomic profiling was undertaken of renal cortex samples of three groups of male rats-An 8-month-old Adult group, a 26-month-old Aged group, and a MetR group that also comprised of 26-month-old rats but were subjected to an 80% MetR diet for 7 weeks. Additionally, markers of mitochondrial stress and protein oxidative damage were analyzed by mass spectrometry. Our results showed minor changes during aging in the renal cortex metabolome, with less than 59 differential metabolites between the Adult and Aged groups, which represents about 4% of changes in the kidney metabolome. Among the compounds identified are glycerolipids and lipid species derived from arachidonic acid metabolism. MetR at old age preferentially induces lipid changes affecting glycerophospholipids, docosanoids, and eicosanoids. No significant differences were observed between the experimental groups in the markers of mitochondrial stress and tissue protein damage. More than rejuvenation, MetR seems to induce a metabolic reprogramming.
    Keywords:  aging; dietary restriction; lipidomics; mass spectrometry; protein damage; renal cortex
    DOI:  https://doi.org/10.3390/metabo9110280
  19. Mol Omics. 2019 Nov 22.
    Lipid mechanisms in hallmarks of cancer.
    J Molendijk, H Robinson, Z Djuric, M M Hill.
      Excess adiposity is a risk factor for several cancer types. This is likely due to complex mechanisms including alterations in the lipid milieu that plays a pivotal role in multiple aspects of carcinogenesis. Here we consider the direct role of lipids in regulating well-known hallmarks of cancer. Furthermore, we suggest that obesity-associated remodelling of membranes and organelles drives cancer cell proliferation and invasion. Identification of cancer-related lipid-mediated mechanisms amongst the broad metabolic disturbances due to excess adiposity is central to the identification of novel and more efficacious prevention and intervention strategies.
    DOI:  https://doi.org/10.1039/c9mo00128j
  20. Nat Commun. 2019 Nov 22. 10(1): 5291
    Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity.
    Mercedes Dávalos-Salas, Magdalene K Montgomery, Camilla M Reehorst, Rebecca Nightingale, Irvin Ng, Holly Anderton, Sheren Al-Obaidi, Analia Lesmana, Cameron M Scott, Paul Ioannidis, Hina Kalra, Shivakumar Keerthikumar, Lars Tögel, Angela Rigopoulos, Sylvia J Gong, David S Williams, Prusoth Yoganantharaja, Kim Bell-Anderson, Suresh Mathivanan, Yann Gibert, Scott Hiebert, Andrew M Scott, Matthew J Watt, John M Mariadason.
      Histone deacetylase 3 (Hdac3) regulates the expression of lipid metabolism genes in multiple tissues, however its role in regulating lipid metabolism in the intestinal epithelium is unknown. Here we demonstrate that intestine-specific deletion of Hdac3 (Hdac3IKO) protects mice from diet induced obesity. Intestinal epithelial cells (IECs) from Hdac3IKO mice display co-ordinate induction of genes and proteins involved in mitochondrial and peroxisomal β-oxidation, have an increased rate of fatty acid oxidation, and undergo marked remodelling of their lipidome, particularly a reduction in long chain triglycerides. Many HDAC3-regulated fatty oxidation genes are transcriptional targets of the PPAR family of nuclear receptors, Hdac3 deletion enhances their induction by PPAR-agonists, and pharmacological HDAC3 inhibition induces their expression in enterocytes. These findings establish a central role for HDAC3 in co-ordinating PPAR-regulated lipid oxidation in the intestinal epithelium, and identify intestinal HDAC3 as a potential therapeutic target for preventing obesity and related diseases.
    DOI:  https://doi.org/10.1038/s41467-019-13180-8
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