bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒06‒07
thirty-one papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Cancer Discov. 2020 Jun 04. pii: CD-20-0329. [Epub ahead of print]
    Alicea GM, Rebecca VW, Goldman AR, Fane ME, Douglass SM, Behera R, Webster MR, Kugel CH, Ecker BL, Caino MC, Kossenkov AV, Tang HY, Frederick DT, Flaherty KT, Xu X, Liu Q, Gabrilovich DI, Herlyn M, Blair IA, Schug ZT, Speicher DW, Weeraratna AT.
      Older melanoma patients (>50 years old) have poorer prognoses and response rates to targeted therapy compared to young patients (<50 years old), which can be driven, in part, by the aged microenvironment. Here, we show that aged dermal fibroblasts increase the secretion of neutral lipids, especially ceramides. When melanoma cells are exposed to the aged fibroblast lipid secretome, or co-cultured with aged fibroblasts, they increase the uptake of lipids, via the fatty acid transporter, fatty acid transport protein (FATP) 2, which is upregulated in melanoma cells in the aged microenvironment and known to play roles in lipid synthesis and accumulation. We show that blocking FATP2 in melanoma cells in an aged microenvironment inhibits their accumulation of lipids, and disrupts their mitochondrial metabolism. Inhibiting FATP2 overcomes age-related resistance to BRAF/MEK inhibition in animal models, ablates tumor relapse, and significantly extends survival time in older animals.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0329
  2. Talanta. 2020 Sep 01. pii: S0039-9140(20)30398-2. [Epub ahead of print]217 121107
    Segers K, Zhang W, Aourz N, Bongaerts J, Declerck S, Mangelings D, Hankemeier T, De Bundel D, Vander Heyden Y, Smolders I, Ramautar R, Van Eeckhaut A.
      Currently, a high variety of analytical techniques to perform metabolomics is available. One of these techniques is capillary electrophoresis coupled to mass spectrometry (CE-MS), which has emerged as a rather strong analytical technique for profiling polar and charged compounds. This work aims to discover with CE-MS potential metabolic consequences of evoked seizures in plasma by using a 6Hz acute corneal seizure mouse model. CE-MS is an appealing technique because of its capability to handle very small sample volumes, such as the 10 μL plasma samples obtained using capillary microsampling in this study. After liquid-liquid extraction, the samples were analyzed with CE-MS using low-pH separation conditions, followed by data analysis and biomarker identification. Both electrically induced seizures showed decreased values of methionine, lysine, glycine, phenylalanine, citrulline, 3-methyladenine and histidine in mice plasma. However, a second provoked seizure, 13 days later, showed a less pronounced decrease of the mean concentrations of these plasma metabolites, demonstrated by higher fold change ratios. Other obtained markers that can be related to seizure activities based on literature data, are isoleucine, serine, proline, tryptophan, alanine, arginine, valine and asparagine. Most amino acids showed relatively stable plasma concentrations between the basal levels (Time point 1) and after the 13-day wash-out period (Time point 3), which suggests its effectiveness. Overall, this work clearly demonstrated the possibility of profiling metabolite consequences related to seizure activities of an intrinsically low amount of body fluid using CE-MS. It would be useful to investigate and validate, in the future, the known and unknown metabolites in different animal models as well as in humans.
    Keywords:  Capillary electrophoresis; Epileptic seizures; Mass Spectrometry; Metabolomics; Volume-restricted plasma samples
    DOI:  https://doi.org/10.1016/j.talanta.2020.121107
  3. Cell Rep. 2020 Jun 02. pii: S2211-1247(20)30671-9. [Epub ahead of print]31(9): 107701
    Becker LM, O'Connell JT, Vo AP, Cain MP, Tampe D, Bizarro L, Sugimoto H, McGow AK, Asara JM, Lovisa S, McAndrews KM, Zielinski R, Lorenzi PL, Zeisberg M, Raza S, LeBleu VS, Kalluri R.
      The mechanistic contributions of cancer-associated fibroblasts (CAFs) in breast cancer progression remain to be fully understood. While altered glucose metabolism in CAFs could fuel cancer cells, how such metabolic reprogramming emerges and is sustained needs further investigation. Studying fibroblasts isolated from patients with benign breast tissues and breast cancer, in conjunction with multiple animal models, we demonstrate that CAFs exhibit a metabolic shift toward lactate and pyruvate production and fuel biosynthetic pathways of cancer cells. The depletion or suppression of the lactate production of CAFs alter the tumor metabolic profile and impede tumor growth. The glycolytic phenotype of the CAFs is in part sustained through epigenetic reprogramming of HIF-1α and glycolytic enzymes. Hypoxia induces epigenetic reprogramming of normal fibroblasts, resulting in a pro-glycolytic, CAF-like transcriptome. Our findings suggest that the glucose metabolism of CAFs evolves during tumor progression, and their breast cancer-promoting phenotype is partly mediated by oxygen-dependent epigenetic modifications.
    Keywords:  breast cancer; cancer-associated fibroblasts; epigenetic alterations; hypoxia; metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2020.107701
  4. Clin Proteomics. 2020 ;17 17
    Macklin A, Khan S, Kislinger T.
      Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
    Keywords:  Biomarker discovery; Cancer; Clinical proteomics; Mass spectrometry; Proteogenomics; Targeted assay
    DOI:  https://doi.org/10.1186/s12014-020-09283-w
  5. Pediatr Res. 2020 Jun 03.
    LaBarre JL, Miller AL, Bauer KW, Burant CF, Lumeng JC.
      BACKGROUND: Psychosocial stress in early childhood is associated with adult obesity and cardiometabolic disease. The association of psychosocial stress with the metabolome in childhood is unknown.METHOD: Low-income children (n = 28, mean age 1.8 years), recruited from the community, participated. Psychosocial stress was measured by diurnal salivary cortisol (cortisol intercept and slope) and by mother-reported chaos in the home using the Confusion, Hubbub, and Order Scale (CHAOS). At mean age 6.1 years, anthropometry was collected and fasting metabolites measured using an untargeted metabolomics and shotgun lipidomics platform.
    RESULTS: Cortisol slope was inversely associated with fatty acid (FA) 20:3, FA 20:4 and polyunsaturated fatty acids (PUFA) metabolites. A higher CHAOS score was associated with lower very long-chain PUFA metabolites and a trend towards lower long-chain PUFA containing triglycerides.
    CONCLUSIONS: Psychosocial stress in early childhood, measured with both biological markers and parent report, was associated with lower PUFAs later in childhood. Future work should examine potential mechanisms of association, including dietary intake or direct effects on polyunsaturated fatty acid levels or metabolism.
    IMPACT: In this longitudinal study, the key message is that diurnal cortisol patterns and greater parent-reported psychosocial stress exposure in early childhood are associated with lower plasma polyunsaturated fatty acid containing lipids 5 years later, potentially indicating altered dietary intake or metabolism associated with psychosocial stress.Untargeted metabolomics and lipidomics can be used to assess changes in metabolism response to psychosocial stress.Stress exposure in early childhood may be associated with the future metabolome.Future work should examine potential pathways of association, including dietary intake and direct effects on metabolism.
    DOI:  https://doi.org/10.1038/s41390-020-0989-0
  6. Mol Cancer Res. 2020 Jun 03. pii: molcanres.0364.2020. [Epub ahead of print]
    Low JY, Brennen WN, Meeker AK, Ikonen E, Simons BW, Laiho M.
      Lipid uptake occurs through caveolae, plasma membrane invaginations formed by caveolins (CAV) and caveolae-associated protein 1 (CAVIN1). Genetic alterations of CAV1N1 and CAV1 modify lipid metabolism and underpin lipodystrophy syndromes. Lipids contribute to tumorigenesis by providing fuel to cancer metabolism and supporting growth and signaling. Tumor stroma promotes tumor proliferation, invasion and metastasis but how stromal lipids influence these processes remain to be defined. Here we show that stromal CAVIN1 regulates lipid abundance in the prostate cancer microenvironment and suppresses metastasis. We show that depletion of CAVIN1 in prostate stromal cells markedly reduces their lipid droplet accumulation and increases inflammation. Stromal cells lacking CAVIN1 enhance prostate cancer cell migration and invasion. Remarkably, they increase lipid uptake and M2 inflammatory macrophage infiltration in the primary tumors and metastasis to distant sites. Our data support the concept that stromal cells contribute to prostate cancer aggressiveness by modulating lipid content and inflammation in the tumor microenvironment. Implications: This study showed that stromal CAVIN1 suppresses prostate cancer metastasis by modulating tumor microenvironment, lipid content and inflammatory response.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-20-0364
  7. J Magn Reson. 2020 May 20. pii: S1090-7807(20)30068-9. [Epub ahead of print]316 106750
    Frahm AB, Jensen PR, Ardenkjær-Larsen JH, Yigit D, Lerche MH.
      Metabolic fingerprinting is a strong tool for characterization of biological phenotypes. Classification with machine learning is a critical component in the discrimination of molecular determinants. Cellular activity can be traced using stable isotope labelling of metabolites from which information on cellular pathways may be obtained. Nuclear magnetic resonance (NMR) spectroscopy is, due to its ability to trace labelling in specific atom positions, a method of choice for such metabolic activity measurements. In this study, we used hyperpolarization in the form of dissolution Dynamic Nuclear Polarization (dDNP) NMR to measure signal enhanced isotope labelled metabolites reporting on pathway activity from four different prostate cancer cell lines. The spectra have a high signal-to-noise, with less than 30 signals reporting on 10 metabolic reactions. This allows easy extraction and straightforward interpretation of spectral data. Four metabolite signals selected using a Random Forest algorithm allowed a classification with Support Vector Machines between aggressive and indolent cancer cells with 96.9% accuracy, -corresponding to 31 out of 32 samples. This demonstrates that the information contained in the few features measured with dDNP NMR, is sufficient and robust for performing binary classification based on the metabolic activity of cultured prostate cancer cells.
    Keywords:  Dissolution dynamic nuclear polarization; Nuclear magnetic resonance; Random forest; Stable isotope resolved metabolomics; Support vector machine
    DOI:  https://doi.org/10.1016/j.jmr.2020.106750
  8. Anal Chim Acta. 2020 Jul 11. pii: S0003-2670(20)30491-8. [Epub ahead of print]1120 24-35
    Xia F, He C, Ren M, Xu FG, Wan JB.
      Eicosanoids derived from n-6 and n-3 polyunsaturated fatty acids (PUFAs), serving as important signaling molecules, are implicated in many physiological and pathological processes, including Type 2 diabetes mellitus (T2DM). However, the quantification of endogenous eicosanoids is challenged by high structural similarity, low abundance in biological sample and poor electrospray ionization efficiency. In the current study, a sensitive and accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to quantify 65 eicosanoids derived from n-6 and n-3 PUFAs in plasma samples using twin derivatization strategy with a pair of reagents, 5-(dimethylamino) naphthalene-1-sulfonyl piperazine (Dns-PP) and (diethylamino) naphthalene-1-sulfonyl piperazine (Dens-PP). Dns-PP-derivatized plasma sample was mixed with the equal volume of Dens-PP-derivatized eicosanoid internal standards for LC-MS/MS analysis in multiple reaction monitoring (MRM) mode. After Dns-PP derivatization, the ionization efficiency and separation performance were substantially improved, resulting in the enhanced sensitivity by 446- to 1009-folds compared to intact eicosanoids. The quantitative accuracy determined by twin derivatization method was found to be comparable with stable isotope labeled internal standards (SIL-IS) method. The newly proposed method was successfully employed to quantify the target eicosanoids in plasma samples from healthy controls and the patients with T2DM. N-6 PUFA-derived eicosanoids, PGF2α, PGD2, PGE2, PGA2, PGB2, 20-HETE and LTC4, significantly increased in plasma sample of T2DM patients. Oppositely, n-3 PUFA-derived eicosanoids, RvE1, 12(S)-HEPE and RvD1, remarkably decreased. Spearman's correlation analysis indicated the strong correlations between these highlighted eicosanoids and clinical parameters of T2DM. Collectively, the sensitive and reliable eicosanoid quantification method may facilitate to elucidate the characteristics of eicosanoid metabolism and understand the role of eicosanoids in the pathogenesis of T2DM and other diseases.
    Keywords:  Chemical isotope labeling; Eicosanoids; LC-MS/MS; Quantification; Twin derivatization; Type 2 diabetes mellitus
    DOI:  https://doi.org/10.1016/j.aca.2020.04.064
  9. Metabolomics. 2020 Jun 05. 16(6): 71
    Raetz M, Bonner R, Hopfgartner G.
      INTRODUCTION: While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition.OBJECTIVES: Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools.
    METHOD: Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics.
    RESULTS: DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis.
    CONCLUSIONS: Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.
    Keywords:  Data independent acquisition; LC–MS; Lipids; Metabolites; Review; SWATH
    DOI:  https://doi.org/10.1007/s11306-020-01692-0
  10. Metabolites. 2020 Jun 03. pii: E231. [Epub ahead of print]10(6):
    Aldana J, Romero-Otero A, Cala MP.
      In recent years, high-throughput lipid profiling has contributed to understand the biological, physiological and pathological roles of lipids in living organisms. Across all kingdoms of life, important cell and systemic processes are mediated by lipids including compartmentalization, signaling and energy homeostasis. Despite important advances in liquid chromatography and mass spectrometry, sample extraction procedures remain a bottleneck in lipidomic studies, since the wide structural diversity of lipids imposes a constrain in the type and amount of lipids extracted. Differences in extraction yield across lipid classes can induce a bias on down-stream analysis and outcomes. This review aims to summarize current lipid extraction techniques used for untargeted and targeted studies based on mass spectrometry. Considerations, applications, and limitations of these techniques are discussed when used to extract lipids in complex biological matrices, such as tissues, biofluids, foods, and microorganisms.
    Keywords:  extraction; lipids; targeted lipidomics; untargeted lipidomics
    DOI:  https://doi.org/10.3390/metabo10060231
  11. Nat Commun. 2020 Jun 01. 11(1): 2714
    Balsa E, Perry EA, Bennett CF, Jedrychowski M, Gygi SP, Doench JG, Puigserver P.
      Electron transport chain (ETC) defects occurring from mitochondrial disease mutations compromise ATP synthesis and render cells vulnerable to nutrient and oxidative stress conditions. This bioenergetic failure is thought to underlie pathologies associated with mitochondrial diseases. However, the precise metabolic processes resulting from a defective mitochondrial ETC that compromise cell viability under stress conditions are not entirely understood. We design a whole genome gain-of-function CRISPR activation screen using human mitochondrial disease complex I (CI) mutant cells to identify genes whose increased function rescue glucose restriction-induced cell death. The top hit of the screen is the cytosolic Malic Enzyme (ME1), that is sufficient to enable survival and proliferation of CI mutant cells under nutrient stress conditions. Unexpectedly, this metabolic rescue is independent of increased ATP synthesis through glycolysis or oxidative phosphorylation, but dependent on ME1-produced NADPH and glutathione (GSH). Survival upon nutrient stress or pentose phosphate pathway (PPP) inhibition depends on compensatory NADPH production through the mitochondrial one-carbon metabolism that is severely compromised in CI mutant cells. Importantly, this defective CI-dependent decrease in mitochondrial NADPH production pathway or genetic ablation of SHMT2 causes strong increases in inflammatory cytokine signatures associated with redox dependent induction of ASK1 and activation of stress kinases p38 and JNK. These studies find that a major defect of CI deficiencies is decreased mitochondrial one-carbon NADPH production that is associated with increased inflammation and cell death.
    DOI:  https://doi.org/10.1038/s41467-020-16423-1
  12. J Exp Med. 2020 Aug 03. pii: e20191920. [Epub ahead of print]217(8):
    Manzo T, Prentice BM, Anderson KG, Raman A, Schalck A, Codreanu GS, Nava Lauson CB, Tiberti S, Raimondi A, Jones MA, Reyzer M, Bates BM, Spraggins JM, Patterson NH, McLean JA, Rai K, Tacchetti C, Tucci S, Wargo JA, Rodighiero S, Clise-Dwyer K, Sherrod SD, Kim M, Navin NE, Caprioli RM, Greenberg PD, Draetta G, Nezi L.
      CD8+ T cells are master effectors of antitumor immunity, and their presence at tumor sites correlates with favorable outcomes. However, metabolic constraints imposed by the tumor microenvironment (TME) can dampen their ability to control tumor progression. We describe lipid accumulation in the TME areas of pancreatic ductal adenocarcinoma (PDA) populated by CD8+ T cells infiltrating both murine and human tumors. In this lipid-rich but otherwise nutrient-poor TME, access to using lipid metabolism becomes particularly valuable for sustaining cell functions. Here, we found that intrapancreatic CD8+ T cells progressively accumulate specific long-chain fatty acids (LCFAs), which, rather than provide a fuel source, impair their mitochondrial function and trigger major transcriptional reprogramming of pathways involved in lipid metabolism, with the subsequent reduction of fatty acid catabolism. In particular, intrapancreatic CD8+ T cells specifically exhibit down-regulation of the very-long-chain acyl-CoA dehydrogenase (VLCAD) enzyme, which exacerbates accumulation of LCFAs and very-long-chain fatty acids (VLCFAs) that mediate lipotoxicity. Metabolic reprogramming of tumor-specific T cells through enforced expression of ACADVL enabled enhanced intratumoral T cell survival and persistence in an engineered mouse model of PDA, overcoming one of the major hurdles to immunotherapy for PDA.
    DOI:  https://doi.org/10.1084/jem.20191920
  13. Front Oncol. 2020 ;10 776
    D'Aniello C, Patriarca EJ, Phang JM, Minchiotti G.
      Cancer cells show a formidable capacity to survive under stringent conditions, to elude mechanisms of control, such as apoptosis, and to resist therapy. Cancer cells reprogram their metabolism to support uncontrolled proliferation and metastatic progression. Phenotypic and functional heterogeneity are hallmarks of cancer cells, which endow them with aggressiveness, metastatic capacity, and resistance to therapy. This heterogeneity is regulated by a variety of intrinsic and extrinsic stimuli including those from the tumor microenvironment. Increasing evidence points to a key role for the metabolism of non-essential amino acids in this complex scenario. Here we discuss the impact of proline metabolism in cancer development and progression, with particular emphasis on the enzymes involved in proline synthesis and catabolism, which are linked to pathways of energy, redox, and anaplerosis. In particular, we emphasize how proline availability influences collagen synthesis and maturation and the acquisition of cancer cell plasticity and heterogeneity. Specifically, we propose a model whereby proline availability generates a cycle based on collagen synthesis and degradation, which, in turn, influences the epigenetic landscape and tumor heterogeneity. Therapeutic strategies targeting this metabolic-epigenetic axis hold great promise for the treatment of metastatic cancers.
    Keywords:  ALDH18A1; Budesonide; PRODH; PYCR1; collagen prolyl-hydroxylases; epigenetic remodeling; metabolic reprogramming; proline
    DOI:  https://doi.org/10.3389/fonc.2020.00776
  14. Mol Cell. 2020 May 20. pii: S1097-2765(20)30308-7. [Epub ahead of print]
    He A, Chen X, Tan M, Chen Y, Lu D, Zhang X, Dean JM, Razani B, Lodhi IJ.
      Autophagy is activated by prolonged fasting but cannot overcome the ensuing hepatic lipid overload, resulting in fatty liver. Here, we describe a peroxisome-lysosome metabolic link that restricts autophagic degradation of lipids. Acyl-CoA oxidase 1 (Acox1), the enzyme that catalyzes the first step in peroxisomal β-oxidation, is enriched in liver and further increases with fasting or high-fat diet (HFD). Liver-specific Acox1 knockout (Acox1-LKO) protected mice against hepatic steatosis caused by starvation or HFD due to induction of autophagic degradation of lipid droplets. Hepatic Acox1 deficiency markedly lowered total cytosolic acetyl-CoA levels, which led to decreased Raptor acetylation and reduced lysosomal localization of mTOR, resulting in impaired activation of mTORC1, a central regulator of autophagy. Dichloroacetic acid treatment elevated acetyl-CoA levels, restored mTORC1 activation, inhibited autophagy, and increased hepatic triglycerides in Acox1-LKO mice. These results identify peroxisome-derived acetyl-CoA as a key metabolic regulator of autophagy that controls hepatic lipid homeostasis.
    Keywords:  Acox1; Autophagy; Lipid metabolism; NAFLD; Raptor; fatty acid oxidation; lipophagy; mTOR; peroxisomes
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.007
  15. Nat Commun. 2020 Jun 03. 11(1): 2790
    Beas AO, Gordon PB, Prentiss CL, Olsen CP, Kukurugya MA, Bennett BD, Parkhurst SM, Gottschling DE.
      Age-dependent changes in metabolism can manifest as cellular lipid accumulation, but how this accumulation is regulated or impacts longevity is poorly understood. We find that Saccharomyces cerevisiae accumulate lipid droplets (LDs) during aging. We also find that over-expressing BNA2, the first Biosynthesis of NAD+ (kynurenine) pathway gene, reduces LD accumulation during aging and extends lifespan. Mechanistically, this LD accumulation during aging is not linked to NAD+ levels, but is anti-correlated with metabolites of the shikimate and aromatic amino acid biosynthesis (SA) pathways (upstream of BNA2), which produce tryptophan (the Bna2p substrate). We provide evidence that over-expressed BNA2 skews glycolytic flux from LDs towards the SA-BNA pathways, effectively reducing LDs. Importantly, we find that accumulation of LDs does not shorten lifespan, but does protect aged cells against stress. Our findings reveal how lipid accumulation impacts longevity, and how aging cell metabolism can be rewired to modulate lipid accumulation independently from longevity.
    DOI:  https://doi.org/10.1038/s41467-020-16358-7
  16. Trends Analyt Chem. 2020 Feb;pii: 115676. [Epub ahead of print]123
    Sun Q, Fan TW, Lane AN, Higashi RM.
      Metabolism is a complex network of compartmentalized and coupled chemical reactions, which often involve transfers of substructures of biomolecules, thus requiring metabolite substructures to be tracked. Stable isotope resolved metabolomics (SIRM) enables pathways reconstruction, even among chemically identical metabolites, by tracking the provenance of stable isotope-labeled substructures using NMR and ultrahigh resolution (UHR) MS. The latter can resolve and count isotopic labels in metabolites and can identify isotopic enrichment in substructures when operated in tandem MS mode. However, MS2 is difficult to implement with chromatography-based UHR-MS due to lengthy MS1 acquisition time that is required to obtain the molecular isotopologue count, which is further exacerbated by the numerous isotopologue source ions to fragment. We review here recent developments in tandem MS applications of SIRM to obtain more detailed information about isotopologue distributions in metabolites and their substructures.
    Keywords:  13C/15N positional isotopologues; Ion chromatography; data independent MS2; multiplexed stable isotope resolved metabolomics (mSIRM); nucleotides; pathway reconstruction; ultra high-resolution FT-MS
    DOI:  https://doi.org/10.1016/j.trac.2019.115676
  17. Anal Chem. 2020 Jun 05.
    Martano G, Leone M, D'oro P, Matafora V, Cattaneo A, Masseroli M, Bachi A.
      Metabolomics and lipidomics studies are becoming increasingly popular but available tools for automated data analysis are still limited. The major issue in untargeted metabolomics is linked to the lack of efficient ranking methods allowing accurate identification of metabolites. Herein, we provide a user friendly open-source software, named SMfinder, for the robust identi-fication and quantification of small molecules. The software introduces a MS2 false discovery rate approach, which is based on single spectral permutation and increases identification accuracy. SMfinder can be efficiently applied to shotgun and tar-geted analysis in metabolomics and lipidomics without requiring extensive in-house acquisition of standards as it provides accurate identification by using available MS2 libraries in instrument independent manner. The software, downloadable at www.ifom.eu/SMfinder, is suitable for untargeted, targeted and flux analysis.
    DOI:  https://doi.org/10.1021/acs.analchem.0c00585
  18. Int Rev Cell Mol Biol. 2020 ;pii: S1937-6448(20)30005-8. [Epub ahead of print]354 107-164
    Cocetta V, Ragazzi E, Montopoli M.
      Cisplatin is one of the most potent and widely used chemotherapeutic agent in the treatment of several solid tumors, despite the high toxicity and the frequent relapse of patients due to the onset of drug resistance. Resistance to chemotherapeutic agents, either intrinsic or acquired, is currently one of the major problems in oncology. Thus, understanding the biology of chemoresistance is fundamental in order to overcome this challenge and to improve the survival rate of patients. Studies over the last 30 decades have underlined how resistance is a multifactorial phenomenon not yet completely understood. Recently, tumor metabolism has gained a lot of interest in the context of chemoresistance; accumulating evidence suggests that the rearrangements of the principal metabolic pathways within cells, contributes to the sensitivity of tumor to the drug treatment. In this review, the principal metabolic alterations associated with cisplatin resistance are highlighted. Improving the knowledge of the influence of metabolism on cisplatin response is fundamental to identify new possible metabolic targets useful for combinatory treatments, in order to overcome cisplatin resistance.
    Keywords:  Cancer metabolism; Cisplatin; Drug resistance; Glutamine; Glycolysis; Lipid metabolism; Metabolic reprogramming; Metabolic targets; Mitochondria; PPP
    DOI:  https://doi.org/10.1016/bs.ircmb.2020.01.005
  19. Mol Syst Biol. 2020 Jun;16(6): e9356
    Bader JM, Geyer PE, Müller JB, Strauss MT, Koch M, Leypoldt F, Koertvelyessy P, Bittner D, Schipke CG, Incesoy EI, Peters O, Deigendesch N, Simons M, Jensen MK, Zetterberg H, Mann M.
      Neurodegenerative diseases are a growing burden, and there is an urgent need for better biomarkers for diagnosis, prognosis, and treatment efficacy. Structural and functional brain alterations are reflected in the protein composition of cerebrospinal fluid (CSF). Alzheimer's disease (AD) patients have higher CSF levels of tau, but we lack knowledge of systems-wide changes of CSF protein levels that accompany AD. Here, we present a highly reproducible mass spectrometry (MS)-based proteomics workflow for the in-depth analysis of CSF from minimal sample amounts. From three independent studies (197 individuals), we characterize differences in proteins by AD status (> 1,000 proteins, CV < 20%). Proteins with previous links to neurodegeneration such as tau, SOD1, and PARK7 differed most strongly by AD status, providing strong positive controls for our approach. CSF proteome changes in Alzheimer's disease prove to be widespread and often correlated with tau concentrations. Our unbiased screen also reveals a consistent glycolytic signature across our cohorts and a recent study. Machine learning suggests clinical utility of this proteomic signature.
    Keywords:  Alzheimer's disease; cerebrospinal fluid; mass spectrometry; neurodegeneration; proteomics
    DOI:  https://doi.org/10.15252/msb.20199356
  20. Metabolites. 2020 May 29. pii: E225. [Epub ahead of print]10(6):
    Magny R, Regazzetti A, Kessal K, Genta-Jouve G, Baudouin C, Mélik-Parsadaniantz S, Brignole-Baudouin F, Laprévote O, Auzeil N.
      Annotation of lipids in untargeted lipidomic analysis remains challenging and a systematic approach needs to be developed to organize important datasets with the help of bioinformatic tools. For this purpose, we combined tandem mass spectrometry-based molecular networking with retention time (tR) prediction to annotate phospholipid and sphingolipid species. Sixty-five standard compounds were used to establish the fragmentation rules of each lipid class studied and to define the parameters governing their chromatographic behavior. Molecular networks (MNs) were generated through the GNPS platform using a lipid standards mixture and applied to lipidomic study of an in vitro model of dry eye disease, i.e., human corneal epithelial (HCE) cells exposed to hyperosmolarity (HO). These MNs led to the annotation of more than 150 unique phospholipid and sphingolipid species in the HCE cells. This annotation was reinforced by comparing theoretical to experimental tR values. This lipidomic study highlighted changes in 54 lipids following HO exposure of corneal cells, some of them being involved in inflammatory responses. The MN approach coupled to tR prediction thus appears as a suitable and robust tool for the discovery of lipids involved in relevant biological processes.
    Keywords:  dry eye disease; hyperosmolarity; lipidomic; liquid chromatography; molecular network; tandem mass spectrometry
    DOI:  https://doi.org/10.3390/metabo10060225
  21. Nat Rev Endocrinol. 2020 Jun 03.
    Kazak L, Cohen P.
      Perturbations in metabolic processes are associated with diseases such as obesity, type 2 diabetes mellitus, certain infections and some cancers. A resurgence of interest in creatine biology is developing, with new insights into a diverse set of regulatory functions for creatine. This resurgence is primarily driven by technological advances in genetic engineering and metabolism as well as by the realization that this metabolite has key roles in cells beyond the muscle and brain. Herein, we highlight the latest advances in creatine biology in tissues and cell types that have historically received little attention in the field. In adipose tissue, creatine controls thermogenic respiration and loss of this metabolite impairs whole-body energy expenditure, leading to obesity. We also cover the various roles that creatine metabolism has in cancer cell survival and the function of the immune system. Renewed interest in this area has begun to showcase the therapeutic potential that lies in understanding how changes in creatine metabolism lead to metabolic disease.
    DOI:  https://doi.org/10.1038/s41574-020-0365-5
  22. Arch Biochem Biophys. 2020 Jun 01. pii: S0003-9861(20)30447-1. [Epub ahead of print] 108438
    Jaune-Pons E, Vasseur S.
      Cancer cells display increased oxidative stress from reactive oxygen species (ROS) and constantly have to counteract them below a tolerable threshold to avoid any toxicity due to overload of ROS. The involvement of ROS in cancer progression from precursor lesions to aggressive tumor and metastasis formation is still debated, but it is recognized that cancer cells succeed to use ROS for their own benefit in circumstances that are tumor cell-type specific. In this review we focus on amino acids' metabolic pathways that tumor cells activate as antioxidants including cysteine, methionine metabolisms and their connection with the folate, transulfuration pathways and ferroptosis. We discuss how the tumor context definitively dictates the impact of ROS on tumor progression towards a metastatic disease as well as the therapeutic approaches that target ROS to abrogate tumors or limit their aggressiveness.
    Keywords:  Amino acids; Antioxidant; Cancer metabolism; Cysteine; Oxidative stress; ROS
    DOI:  https://doi.org/10.1016/j.abb.2020.108438
  23. Anal Chim Acta. 2020 Jul 11. pii: S0003-2670(20)30494-3. [Epub ahead of print]1120 85-96
    Pickens CA, Petritis K.
      Amino acid and acylcarnitine first-tier newborn screening typically employs derivatized or non-derivatized sample preparation methods followed by FIA coupled to triple quadrupole (TQ) MS/MS. The low resolving power of TQ instruments results in difficulties distinguishing nominal isobaric metabolites, especially those with identical quantifying product ions such as malonylcarnitine (C3DC) and 4-hydroxybutylcarnitine (C4OH). Twenty-eight amino acids and acylcarnitines extracted from dried blood spots (DBS) were analyzed by direct injection (DI)-HRMS on a Q-Exactive Plus across available mass resolving powers in SIM, in PRM at 17,000 full width at half maximum (FWHM), and a developed SIM/PRM hybrid MS method. Most notably, quantitation of C3DC and C4OH was successful by HRMS in non-derivatized samples, thus, potentially eliminating sample derivatization requirements. Quantitation differed between SIM and PRM acquired data for several metabolites, and it was determined these quantitative differences were due to collision energy differences or kinetic isotope effects between the unlabeled metabolites and the corresponding labeled isotopologue internal standards. Overall quantitative data acquired by HRMS were similar to data acquired on TQ MS/MS platform. A proof-of-concept hybrid DI-HRMS and SIM/PRM/FullScan method was developed demonstrating the ability to hybridize targeted newborn screening with metabolomic screening.
    Keywords:  Amino acids and acylcarnitines; Dried blood spot; High resolution mass spectrometry; Metabolic disorders; Metabolomics; Newborn screening
    DOI:  https://doi.org/10.1016/j.aca.2020.04.067
  24. Joint Bone Spine. 2020 May 27. pii: S1297-319X(20)30091-9. [Epub ahead of print]
    Li C, Chen B, Fang Z, Leng YF, Wang DW, Chen FQ, Xiao X, Sun ZL.
      OBJECTIVE: A systematic review and analysis of data from several rheumatoid arthritis metabolomics studies attempts to determine which metabolites can be used as potential biomarkers for the diagnosis of rheumatoid arthritis and to explore the pathogenesis of rheumatoid arthritis.METHODS: We searched all the subject-related documents published by EMBASE, PubMed, Web of Science, and Cochrane Library from the database to the September 2019 publication. Two researchers independently screened the literature and extracted the data. QUADOMICS tool was used to assess the quality of studies included in this systematic review.
    RESULTS: A total of 10 studies met the inclusion criteria of systematic review, including 502 patients with Rheumatoid arthritis and 373 healthy people. Among them, the biological samples utilized for metabolomic analysis include: serum (n = 8), urine (n = 1) and synovial fluid(n = 1). Some metabolites play an important role in rheumatoid arthritis: glucose, lactic acid, citric acid, leucine, methionine, isoleucine, valine, phenylalanine, threonine, serine, proline, glutamate, histidine, alanine, cholesterol, glycerol, ribose.
    CONCLUSIONS: Metabolomics provides important new opportunities for further research in rheumatoid arthritis and is expected to elucidate the pathogenesis of rheumatoid arthritis that has not been fully understood before.
    Keywords:  Biomarker; Metabolomics; Rheumatoid arthritis; Systematic review
    DOI:  https://doi.org/10.1016/j.jbspin.2020.05.005
  25. Anal Chem. 2020 Jun 03.
    Liu KH, Nellis M, Uppal K, Ma C, Tran V, Liang Y, Walker DI, Jones DP.
      Reference standardization was developed to address quantification and harmonization challenges for high-resolution metabolomics (HRM) data collected across different studies or analytical methods. Reference standardization relies on the concurrent analysis of calibrated pooled reference samples at pre-defined intervals and enables a single-step batch correction and quantification for high-throughput metabolomics. Here, we provide quantitative measures of approximately 200 metabolites for each of three pooled reference materials (220 metabolites for Qstd3, 211 metabolites for CHEAR, 204 metabolites for NIST1950) and show application of this approach for quantification supports harmonization of metabolomics data collected from 3,677 human samples in 17 separate studies analyzed by two complementary HRM methods over a 17-month period. The results establish reference standardization as a method suitable for harmonizing large-scale metabolomics data and extending capabilities to quantify large numbers of known and unidentified metabolites detected by high-resolution mass spectrometry methods.
    DOI:  https://doi.org/10.1021/acs.analchem.0c00338
  26. Biochim Biophys Acta Mol Cell Biol Lipids. 2020 May 28. pii: S1388-1981(20)30133-5. [Epub ahead of print]1865(9): 158741
    Bayerle A, Marsching C, Rabionet M, Dworski S, Kamani MA, Chitraju C, Gluchowski NL, Gabriel KR, Herzer S, Jennemann R, Levade T, Medin JA, Sandhoff R.
      Except for epidermis and liver, little is known about endogenous expression of 1-O-acylceramides (1-OACs) in mammalian tissue. Therefore, we screened several organs (brain, lung, liver, spleen, lymph nodes, heart, kidney, thymus, small intestine, and colon) from mice for the presence of 1-OACs by LC-MS2. In most organs, low levels of about 0.25-1.3 pmol 1-OACs/mg wet weight were recorded. Higher levels were detected in liver, small and large intestines, with about 4-13 pmol 1-OACs/mg wet weight. 1-OACs were esterified mainly with palmitic, stearic, or oleic acids. Esterification with saturated very long-chain fatty acids, as in epidermis, was not observed. Western-type diet induced 3-fold increased 1-OAC levels in mice livers while ceramides were unaltered. In a mouse model of Farber disease with a decrease of acid ceramidase activity, we observed a strong, up to 50-fold increase of 1-OACs in lung, thymus, and spleen. In contrast, 1-OAC levels were reduced 0.54-fold in liver. Only in lung 1-OAC levels correlated to changes in ceramide levels - indicating tissue-specific mechanisms of regulation. Glucosylceramide synthase deficiency in liver did not cause changes in 1-OAC or ceramide levels, whereas increased ceramide levels in glucosylceramide synthase-deficient small intestine caused an increase in 1-OAC levels. Deficiency of Dgat1 in mice resulted in a reduction of 1-OACs to 30% in colon, but not in small intestine and liver, going along with constant free ceramides levels. From these data, we conclude that Dgat1 as well as lysosomal lipid metabolism contribute in vivo to homeostatic 1-OAC levels in an organ-specific manner.
    Keywords:  Acylceramides; Acyltransferases; Asah1; Brain; Ceramides; Dgat; Dgat1; Dgat2; Farber disease; Heart; Intestine; Kidney; Liver; Lung; Mammalian; Spleen; Thymus; Ugcg
    DOI:  https://doi.org/10.1016/j.bbalip.2020.158741
  27. J Lipid Res. 2020 Jun 02. pii: jlr.R120000800. [Epub ahead of print]
    Harayama T, Shimizu T.
      Polyunsaturated fatty acids (PUFAs), such as arachidonic acid and docosahexaenoic acid, are recognized as important biomolecules, but understanding their precise roles and modes of action remains challenging. PUFAs are precursors for a plethora of signaling lipids, for which knowledge about synthetic pathways and receptors has accumulated. However, due to their extreme diversity and the ambiguity concerning the identity of their cognate receptors, the roles of PUFA-derived signaling lipids require more investigation. In addition, PUFA functions cannot be explained just as lipid mediator precursors, since they are also critical for the regulation of membrane biophysical properties. The presence of PUFAs in membrane lipids also affects the functions of transmembrane proteins and peripheral membrane proteins. Although the roles of PUFAs as membrane lipid building blocks were difficult to analyze, the discovery of lysophospholipid acyltransferases, which are critical for their incorporation, advanced our understanding. Recent studies unveiled how lysophospholipid acyltransferases affect PUFA levels in membrane lipids, and their genetic manipulation became an excellent strategy to study the roles of PUFA-containing lipids. In this review, we will provide an overview of metabolic pathways regulating PUFAs as lipid mediator precursors and membrane components, and update recent progress about their functions. Some issues to be solved for future research will also be discussed.
    Keywords:  Arachidonic acid; Eicosanoids; G proteins; Membranes; Phospholipids/Biosynthesis; Phospholipids/Metabolism; Receptors; docosahexaenoic acid
    DOI:  https://doi.org/10.1194/jlr.R120000800
  28. Biochim Biophys Acta Mol Basis Dis. 2020 Jun 02. pii: S0925-4439(20)30200-3. [Epub ahead of print] 165853
    Presa N, Dominguez-Herrera A, van der Veen JN, Vance DE, Gómez-Muñoz A.
      Phosphatidylethanolamine N-methyltransferase (PEMT) is a small integral membrane protein that converts phosphatidylethanolamine (PE) into phosphatidylcholine (PC). It has been previously reported that, unexpectedly, PEMT deficiency protected from high-fat diet (HFD)-induced obesity and insulin resistance, pointing to a possible role of this enzyme in the regulation of adipose cell metabolism. Using mouse 3T3-L1 preadipocytes as a biological system, we demonstrate that PEMT expression is strongly increased during the differentiation of preadipocytes into mature adipose cells. Knockdown of PEMT reduced the expression of early and late adipogenic markers, inhibited lipid droplet formation, reduced triacylglycerol content and decreased the levels of leptin release from the adipocytes, suggesting that PEMT is a novel and relevant regulator of adipogenesis. Investigation into the mechanisms whereby PEMT regulates adipocyte differentiation revealed that extracellularly regulated kinases (ERK1/2) and AKT are essential factors in this process. Specifically, the activities of ERK1/2 and AKT, which are decreased during adipocyte differentiation, were elevated upon Pemt knockdown. Moreover, treatment of cells with exogenous ceramide 1-phosphate (C1P), which we reported to be a negative regulator of adipogenesis, decreased PEMT expression, suggesting that PEMT is also a relevant factor in the anti-adipogenic action of C1P. Altogether, the data presented here identify PEMT as a novel regulator of adipogenesis and a mediator of the anti-adipogenic action of C1P.
    Keywords:  Adipogenesis; Ceramide 1-phosphate; Phosphatidylcholine; Sphingolipids
    DOI:  https://doi.org/10.1016/j.bbadis.2020.165853
  29. Talanta. 2020 Sep 01. pii: S0039-9140(20)30365-9. [Epub ahead of print]217 121074
    Koch E, Mainka M, Dalle C, Ostermann AI, Rund KM, Kutzner L, Froehlich LF, Bertrand-Michel J, Gladine C, Schebb NH.
      Oxidized unsaturated fatty acids - i.e. eicosanoids and other oxylipins - are lipid mediators involved in the regulation of numerous physiological functions such as inflammation, blood coagulation, vascular tone and endothelial permeability. They have raised strong interest in clinical lipidomics in order to understand their role in health and diseases and their use as biomarkers. However, before the clinical translation, it is crucial to validate the analytical reliability of oxylipins. This notably requires to assess the putative artificial formation or degradation of oxylipins by (unsuitable) blood handling during plasma generation, storage and sample preparation. Using a liquid chromatography-mass spectrometry method covering 133 oxylipins we comprehensively analyzed the total (free + esterified) oxylipin profile in plasma and investigated the influence of i) addition of additives during sample preparation, ii) different storage times and temperatures during the transitory stage of plasma generation and iii) long-term storage of plasma samples at -80 °C. Addition of radical scavenger butylated hydroxytoluene reduced the apparent concentrations of hydroxy-PUFA and thus should be added to the samples at the beginning of sample preparation. The concentrations of all oxylipin classes remained stable (within analytical variance of 20%) during the transitory stage of plasma generation up to 24 h at 4 °C or 4 h at 20 °C before centrifugation of EDTA-whole blood and up to 5 days at -20 °C after plasma separation. The variations in oxylipin concentrations did not correlate with storage time, storage temperature or stage of plasma generation. A significant increase of potentially lipoxygenase derived hydroxy-PUFA compared to immediate processing was only detected when samples were stored for longer times before centrifugation, plasma separation as well as freezing of plasma revealing residual enzymatic activity. Autoxidative rather than enzymatic processes led to a slightly increased concentration of 9-HETE when plasma samples were stored at -80 °C for 15 months. Overall, we demonstrate that total plasma oxylipins are robust regarding delays during plasma generation and long-term storage at -80 °C supporting the application of oxylipin profiling in clinical research.
    Keywords:  Blood sampling; Eicosanoids; LC-MS/MS; Lipid mediators
    DOI:  https://doi.org/10.1016/j.talanta.2020.121074
  30. Cancers (Basel). 2020 May 31. pii: E1419. [Epub ahead of print]12(6):
    Sangineto M, Villani R, Cavallone F, Romano A, Loizzi D, Serviddio G.
      : Metabolic reprogramming is critically involved in the development and progression of cancer. In particular, lipid metabolism has been investigated as a source of energy, micro-environmental adaptation, and cell signalling in neoplastic cells. However, the specific role of lipid metabolism dysregulation in hepatocellular carcinoma (HCC) has not been widely described yet. Alterations in fatty acid synthesis, β-oxidation, and cellular lipidic composition contribute to initiation and progression of HCC. The aim of this review is to elucidate the mechanisms by which lipid metabolism is involved in hepatocarcinogenesis and tumour adaptation to different conditions, focusing on the transcriptional aberrations with new insights in lipidomics and lipid zonation. This will help detect new putative therapeutic approaches in the second most frequent cause of cancer-related death.
    Keywords:  fatty acid β-oxidation; hepatocellular carcinoma; lipid metabolism; lipidomics; non-alcoholic fatty liver disease; tumour progression
    DOI:  https://doi.org/10.3390/cancers12061419
  31. ACS Omega. 2020 May 26. 5(20): 11314-11323
    Xu C, Song D, Holck AL, Zhou Y, Liu R.
      Oleic acid (OA), one of the most important monounsaturated fatty acids, possesses protective properties against chronic liver disease (CLD) development, but the underlying metabolic metabolism remains unknown. HPLC-MS-based lipidomics was utilized to identify and quantify the endogenously altered lipid metabolites when hepatocytes were exposed to OA administration. The identified lipids could be grouped into 22 lipid classes; of which, 10 classes were significantly influenced by the OA treatment: lysophosphatidylcholine (LPC), phosphatidylglycerol (PG), ceramides (Cer), hexosylceramides (Hex1Cer), dihexosylceramides (Hex2Cer), cholesterol ester (ChE), and coenzyme (Co) were decreased, while diglyceride (DG), triglyceride (TG), and acyl carnitine (AcCa) were increased. In addition, as the variable importance in projection (VIP) list (VIP > 1.0 and P < 0.05) showed, 478 lipid species showed significant difference with OA administration, and these molecules could be potential biomarkers in conjunction with OA administration. In summary, our results provided a novel perspective to understand the influences of OA administration by investigating endogenous altered levels of lipid metabolites via lipidomics.
    DOI:  https://doi.org/10.1021/acsomega.9b04402