bims-mascan 2021-12-26 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–12–26
twenty-one papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh

Cancer metabolism and dietary interventions.
A reversed phase ultra-high-performance liquid chromatography-data independent mass spectrometry method for the rapid identification of mycobacterial lipids.
Metabolomics Work Flow and Analytics in Systems Biology.
Deep Profiling of Aminophospholipids Reveals a Dysregulated Desaturation Pattern in Breast Cancer Cell Lines.
Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.
A pilot study optimizing metabolomic and lipidomic acquisition in serum for biomarker discovery in nonalcoholic fatty liver disease.
Hyaluronic acid fuels pancreatic cancer cell growth.
Stability of lipids in plasma and serum: Effects of temperature-related storage conditions on the human lipidome.
Metformin Treatment or PRODH/POX-Knock out Similarly Induces Apoptosis by Reprograming of Amino Acid Metabolism, TCA, Urea Cycle and Pentose Phosphate Pathway in MCF-7 Breast Cancer Cells.
Is Current Practice Adhering to Guidelines Proposed for Metabolite Identification in LC-MS Untargeted Metabolomics? A Meta-Analysis of the Literature.
Dimethylcysteine (DiCys)/o-Phthalaldehyde Derivatization for Chiral Metabolite Analyses: Cross-Comparison of Six Chiral Thiols.
Multi-Omic Metabolic Enrichment Network Analysis reveals metabolite-protein physical interaction subnetworks altered in cancer.
Lipidomic and Metabolomic Signature of Progression of Chronic Kidney Disease in Patients with Severe Obesity.
Amino acid transporters as modulators of glucose homeostasis.
LINT-Web: A Web-Based Lipidomic Data Mining Tool Using Intra-Omic Integrative Correlation Strategy.
Dinner is served, sir: Fighting cancer with the right diet.
Hydrogen/Deuterium Exchange Aiding Metabolite Identification in Single-Cell Nanospray High-Resolution Mass Spectrometry Analysis.
Optimized Workflow for On-Line Derivatization for Targeted Metabolomics Approach by Gas Chromatography-Mass Spectrometry.
DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia.
Small molecule targeting of chromatin writers in cancer.
Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity.

Cancer Biol Med. 2021 Dec 22. pii: j.issn.2095-3941.2021.0461. [Epub ahead of print]

Cancer metabolism and dietary interventions.

Lin Qian, Fan Zhang, Miao Yin, Qunying Lei.

  Metabolic remodeling is a key feature of cancer development. Knowledge of cancer metabolism has greatly expanded since the first observation of abnormal metabolism in cancer cells, the so-called Warburg effect. Malignant cells tend to modify cellular metabolism to favor specialized fermentation over the aerobic respiration usually used by most normal cells. Thus, targeted cancer therapies based on reprogramming nutrient or metabolite metabolism have received substantial attention both conceptually and in clinical practice. In particular, the management of nutrient availability is becoming more attractive in cancer treatment. In this review, we discuss recent findings on tumor metabolism and potential dietary interventions based on the specific characteristics of tumor metabolism. First, we present a comprehensive overview of changes in macronutrient metabolism. Carbohydrates, amino acids, and lipids, are rewired in the cancer microenvironment individually or systematically. Second, we summarize recent progress in cancer interventions applying different types of diets and specific nutrient restrictions in pre-clinical research or clinical trials.

Keywords:  Cancer metabolism; amino acid; carbohydrate; diet intervention; lipid

DOI:  https://doi.org/10.20892/j.issn.2095-3941.2021.0461
J Chromatogr A. 2021 Dec 08. pii: S0021-9673(21)00861-X. [Epub ahead of print]1662 462739

A reversed phase ultra-high-performance liquid chromatography-data independent mass spectrometry method for the rapid identification of mycobacterial lipids.

Isin T Sakallioglu, Amith S Maroli, Aline De Lima Leite, Robert Powers.

  A rapid reversed-phase ultra-high-performance liquid chromatography-high resolution mass spectrometry based mycobacterial lipidomics approach is described. This method enables the separation of various lipid classes including lipids specific to mycobacterial, such as methoxy mycolic acid and α-mycolic acid. Lipid separation occurs during a relatively short runtime of 14 min on a charged surface hybrid C18 column. A high-resolution quadrupole-time of flight mass spectrometer and a data independent acquisition mode allowed for the simultaneous acquisition of the full scan and collision induced dissociation fragmentation. The proposed method provides lipid detection results equivalent to or better than existing methods, but with a faster throughput and an overall higher sensitivity. The reversed-phase ultra-high-performance liquid chromatography-high resolution mass spectrometry method was shown to obtain structural information for lipids extracted from Mycobacterium smegmatis, but the method is applicable to the analysis of lipids from various bacterial and mammalian cell lines.

Keywords:  Lipidomics; Liquid chromatography; Mass spectrometry; Mycobacteria; Mycolic acid

DOI:  https://doi.org/10.1016/j.chroma.2021.462739
Curr Mol Med. 2021 Dec 16.

Metabolomics Work Flow and Analytics in Systems Biology.

Sanoj Chacko, Yumna B Haseeb, Sohaib Haseeb.

  Metabolomics is an omics approach of systems biology that involves the development and assessment of large-scale, comprehensive biochemical analysis tools for metabolites in biological systems. This review describes the metabolomics workflow and provides an overview of current analytic tools used for the quantification of metabolic profiles. We explain analytic tools such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, ionization techniques, and approaches for data extraction and analysis.

Keywords:  Biomarker; NMR spectroscopy; liquid chromatography; mass spectrometry; metabolomics; proteome

DOI:  https://doi.org/10.2174/1566524022666211217102105
Anal Chem. 2021 Dec 21.

Deep Profiling of Aminophospholipids Reveals a Dysregulated Desaturation Pattern in Breast Cancer Cell Lines.

Qiaohong Lin, Pengyun Li, Mengxuan Fang, Donghui Zhang, Yu Xia.

Phosphatidylethanolamines (PEs), ether-PEs, and phosphatidylserines (PSs) are glycerophospholipids harboring a primary amino group in their headgroups. They are key components of mammalian cell membranes and play pivotal roles in cell signaling and apoptosis. In this study, a liquid chromatography-mass spectrometry (LC-MS) workflow for deep profiling of PEs, ether-PEs, and PSs has been developed by integrating two orthogonal derivatizations: (1) derivatization of the primary amino group by 4-trimethylammoniumbutyryl-N-hydroxysuccinimide (TMAB-NHS) for enhanced LC separation and MS detection and (2) the Paternò-Büchi (PB) reaction for carbon-carbon double bond (C═C) derivatization and localization. Significant improvement of the limit of identification down to the C═C location has been achieved for the standards of PSs (3 nM) and ether-PEs (20 nM). This workflow facilitates an identification of more than 200 molecular species of aminophospholipids in the porcine brain, two times more than those identified without TMAB-NHS derivatization. Importantly, we discovered that the n-10 isomers in C16:1 and C18:1 of aminophospholipids showed elevated contribution among other isomers, which correlated well with an increased transcription of the corresponding desaturase (FADS2) in the human breast cancer cell line (MDA-MB-231) relative to that in the normal cell line (HMEC). The abovementioned data suggest that lipid reprograming via forming different C═C location isomers might be an alternative mechanism in cancer cells.

DOI: https://doi.org/10.1021/acs.analchem.1c03494
Elife. 2021 Dec 23. pii: e72593. [Epub ahead of print]10

Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.

Dylan Gerard Ryan, Ming Yang, Hiran A Prag, Giovanny Rodriguez Blanco, Efterpi Nikitopoulou, Marc Segarra-Mondejar, Christopher A Powell, Tim Young, Nils Burger, Jan Lj Miljkovic, Michal Minczuk, Michael P Murphy, Alex von Kriegsheim, Christian Frezza.

  The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.

Keywords:  biochemistry; cell biology; chemical biology; mouse

DOI:  https://doi.org/10.7554/eLife.72593
J Mass Spectrom Adv Clin Lab. 2021 Nov;22 17-25

A pilot study optimizing metabolomic and lipidomic acquisition in serum for biomarker discovery in nonalcoholic fatty liver disease.

Dandan He, Yang Su, Duanyue Meng, Xinmiao Wang, Jun Wang, Hui Ye.

   Background: The worldwide prevalence of non-alcoholic fatty liver disease (NAFLD) has stimulated work to identify biomarkers and develop effective treatments. Metabolomics is an emerging tool that has been widely applied to discover biomarkers and simultaneously uncover pathological mechanisms. Here, we aim to optimize metabolomic acquisition with the goal of obtaining a systemic metabolic profile to unravel the potential link between dysregulated metabolism and NAFLD.
Methods: We analyzed serum samples collected from healthy subjects (n = 8) and NAFLD patients (n = 8) via an integrative analytical workflow using two orthogonal separation modes with T3 and amide columns and two ionization polarity modes on a UPLC-ESI-Q/TOF. Data dependent acquisition was employed for data acquisition. Differentially expressed metabolites and lipids were identified by comparing the collected metabolic and lipidomic profiles between the healthy subjects and NAFLD patients.
Results: The integrative LC-MS/MS analytical workflow employed here features an improved coverage of metabolites and lipids, which leads to the identification of 20 potential biomarkers of NAFLD, including lipids, acylcarnitines, and organic acids.
Conclusions: This pilot study has identified potential biomarkers for NAFLD and revealed corresponding dysregulated metabolic pathways related to NAFLD's occurrence and progression, establishing a molecular basis for NAFLD diagnosis and therapeutic intervention.

Keywords:  ACN, acetonitrile; Acylcarnitines; DGs, diacylglycerols; EICs, extracted ion chromatograms; ESI− and ESI+, ionization polarity modes; FA, Formic acid; FC, fold change; HCC, hepatocellular carcinoma; HFD, high-fat diet; HILIC, hydrophilic interaction chromatography; LE, Leucine enkephalin; LPC, lysophosphatidylcholine; Lipids; MCD, methionine-choline-deficient; MGs, monoacylglycerols; MS, mass spectrometry; Metabolic biomarkers; Metabolomics; NAFLD; NAFLD, non-alcoholic fatty liver disease; NASH, non-alcoholic steatohepatitis; OPLS-DA, orthogonal partial least square discriminant analysis; PCs, phosphorylcholines; PEs, phosphatidylethanolamines; PKC∊, protein kinase C∊; ROC, receiver operating characteristic; RPLC, reversed-phase liquid chromatography; T3-neg, T3 column-based reverse phase separation plus the negative ion mode; T3-pos, T3 column-based reverse phase separation plus the positive ion mode; TIC, total ion chromatogram; VIP, variable importance; amide-neg, amide column-based HILIC separation plus the negative ion mode; amide-pos, amide column-based HILIC separation plus the positive ion mode

DOI:  https://doi.org/10.1016/j.jmsacl.2021.10.001
Elife. 2021 Dec 24. pii: e62645. [Epub ahead of print]10

Hyaluronic acid fuels pancreatic cancer cell growth.

Peter K Kim, Christopher J Halbrook, Samuel A Kerk, Megan Radyk, Stephanie Wisner, Daniel M Kremer, Peter Sajjakulnukit, Anthony Andren, Sean W Hou, Ayush Trivedi, Galloway Thurston, Abhinav Anand, Liang Yan, Lucia Salamanca-Cardona, Samuel D Welling, Li Zhang, Matthew R Pratt, Kayvan R Keshari, Haoqiang Ying, Costas Lyssiotis.

  Rewired metabolism is a hallmark of pancreatic ductal adenocarcinomas (PDA). Previously, we demonstrated that PDA cells enhance glycosylation precursor biogenesis through the hexosamine biosynthetic pathway (HBP) via activation of the rate limiting enzyme, glutamine-fructose 6-phosphate amidotransferase 1 (GFAT1). Here, we genetically ablated GFAT1 in human PDA cell lines, which completely blocked proliferation in vitro and led to cell death. In contrast, GFAT1 knockout did not preclude the growth of human tumor xenografts in mice, suggesting that cancer cells can maintain fidelity of glycosylation precursor pools by scavenging nutrients from the tumor microenvironment. We found that hyaluronic acid (HA), an abundant carbohydrate polymer in pancreatic tumors composed of repeating N-acetyl-glucosamine (GlcNAc) and glucuronic acid sugars, can bypass GFAT1 to refuel the HBP via the GlcNAc salvage pathway. Together, these data show HA can serve as a nutrient fueling PDA metabolism beyond its previously appreciated structural and signaling roles.

Keywords:  cancer biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.62645
J Mass Spectrom Adv Clin Lab. 2021 Nov;22 34-42

Stability of lipids in plasma and serum: Effects of temperature-related storage conditions on the human lipidome.

Gregory B Reis, Jon C Rees, Anna A Ivanova, Zsuzsanna Kuklenyik, Nathan M Drew, James L Pirkle, John R Barr.

  Large epidemiological studies often require sample transportation and storage, presenting unique considerations when applying advanced lipidomics techniques. The goal of this study was to acquire lipidomics data on plasma and serum samples stored at potential preanalytical conditions (e.g., thawing, extracting, evaporating), systematically monitoring lipid species for a period of one month. Split aliquots of 10 plasma samples and 10 serum samples from healthy individuals were kept in three temperature-related environments: refrigerator, laboratory benchtop, or heated incubator. Samples were analyzed at six different time points over 28 days using a Bligh & Dyer lipid extraction protocol followed by direct infusion into a lipidomics platform using differential mobility with tandem mass spectrometry. The observed concentration changes over time were evaluated relative to method and inter-individual biological variability. In addition, to evaluate the effect of lipase enzyme levels on concentration changes during storage, we compared corresponding fasting and post-prandial plasma samples collected from 5 individuals. Based on our data, a series of low abundance free fatty acid (FFA), diacylglycerol (DAG), and cholesteryl ester (CE) species were identified as potential analytical markers for degradation. These FFA and DAG species are typically produced by endogenous lipases from numerous triacylglycerols (TAGs), and certain high abundance phosphatidylcholines (PCs). The low concentration CEs, which appeared to increase several fold, were likely mass-isobars from oxidation of other high concentration CEs. Although the concentration changes of the high abundant TAG, PC, and CE precursors remained within method variability, the concentration trends of FFA, DAG, and oxidized CE products should be systematically monitored over time to inform analysts about possible pre-analytical biases due to degradation in the study sample sets.

Keywords:  15-Hp-PGD2, 15-hydroperoxy-prostaglandin D2; CE, Cholesteryl ester; CER, Ceramide; Cholesteryl Ester; DAG, Diacylglycerol; Degradation; FFA, Free Fatty Acid; Fatty Acids; HpETE, hydroperoxyeicosatetraenoic acid; HpODE, hydroperoxyoctadecadienoic acid; Hydrolysis; LPC, Lysophosphatidylcholine; LPE, Lysophosphatidylethanolamine; Lipidomics; LysoPL, Lysophospholipid; Oxidation; PC, Phosphatidylcholine; PE, Phosphatidylethanolamine; PGD2, prostaglandin D2; PL, Phospholipid; PLA1, phospholipase A1; PLA2, phospholipase A2; SM, Sphingomyelin; Stability; TAG, Triacylglycerol; Triglycerides

DOI:  https://doi.org/10.1016/j.jmsacl.2021.10.002
Biomolecules. 2021 Dec 15. pii: 1888. [Epub ahead of print]11(12):

Metformin Treatment or PRODH/POX-Knock out Similarly Induces Apoptosis by Reprograming of Amino Acid Metabolism, TCA, Urea Cycle and Pentose Phosphate Pathway in MCF-7 Breast Cancer Cells.

Thi Yen Ly Huynh, Ilona Oscilowska, Jorge Sáiz, Magdalena Nizioł, Weronika Baszanowska, Coral Barbas, Jerzy Palka.

  It has been considered that proline dehydrogenase/proline oxidase (PRODH/POX) is involved in antineoplastic activity of metformin (MET). The aim of this study is identification of key metabolites of glycolysis, pentose phosphate pathway (PPP), tricarboxylic acids (TCA), urea cycles (UC) and some amino acids in MET-treated MCF-7 cells and PRODH/POX-knocked out MCF-7 (MCF-7crPOX) cells. MCF-7crPOX cells were generated by using CRISPR-Cas9. Targeted metabolomics was performed by LC-MS/MS/QqQ. Expression of pro-apoptotic proteins was evaluated by Western blot. In the absence of glutamine, MET treatment or PRODH/POX-knock out of MCF-7 cells contributed to similar inhibition of glycolysis (drastic increase in intracellular glucose and pyruvate) and increase in the utilization of phospho-enol-pyruvic acid, glucose-6-phosphate and some metabolites of TCA and UC, contributing to apoptosis. However, in the presence of glutamine, MET treatment or PRODH/POX-knock out of MCF-7 cells contributed to utilization of some studied metabolites (except glucose), facilitating pro-survival phenotype of MCF-7 cells in these conditions. It suggests that MET treatment or PRODH/POX-knock out induce similar metabolic effects (glucose starvation) and glycolysis is tightly linked to glutamine metabolism in MCF-7 breast cancer cells. The data provide insight into mechanism of anticancer activity of MET as an approach to further studies on experimental breast cancer therapy.

Keywords:  MCF-7crPOX cells; PRODH/POX; glutamine; lactic acid; metformin; proline

DOI:  https://doi.org/10.3390/biom11121888
J Proteome Res. 2021 Dec 20.

Is Current Practice Adhering to Guidelines Proposed for Metabolite Identification in LC-MS Untargeted Metabolomics? A Meta-Analysis of the Literature.

Dritan Kodra, Petros Pousinis, Panagiotis A Vorkas, Katerina Kademoglou, Theodoros Liapikos, Alexandros Pechlivanis, Christina Virgiliou, Ian D Wilson, Helen Gika, Georgios Theodoridis.

  Metabolite identification remains a bottleneck and a still unregulated area in untargeted LC-MS metabolomics. The metabolomics research community and, in particular, the metabolomics standards initiative (MSI) proposed minimum reporting standards for metabolomics including those for reporting metabolite identification as long ago as 2007. Initially, four levels were proposed ranging from level 1 (unambiguously identified analyte) to level 4 (unidentified analyte). This scheme was expanded in 2014, by independent research groups, to give five levels of confidence. Both schemes provided guidance to the researcher and described the logical steps that had to be made to reach a confident reporting level. These guidelines have been presented and discussed extensively, becoming well-known to authors, editors, and reviewers for academic publications. Despite continuous promotion within the metabolomics community, the application of such guidelines is questionable. The scope of this meta-analysis was to systematically review the current LC-MS-based literature and effectively determine the proportion of papers following the proposed guidelines. Also, within the scope of this meta-analysis was the measurement of the actual identification levels reported in the literature, that is to find how many of the published papers really reached full metabolite identification (level 1) and how many papers did not reach this level.

Keywords:  biomarker discovery; liquid chromatography; mass spectrometry; metabolic profiling; metabolite annotation; metabonomics; unknown metabolites

DOI:  https://doi.org/10.1021/acs.jproteome.1c00841
Molecules. 2021 Dec 07. pii: 7416. [Epub ahead of print]26(24):

Dimethylcysteine (DiCys)/o-Phthalaldehyde Derivatization for Chiral Metabolite Analyses: Cross-Comparison of Six Chiral Thiols.

Ankhbayar Lkhagva, Hwan-Ching Tai.

  Metabolomics profiling using liquid chromatography-mass spectrometry (LC-MS) has become an important tool in biomedical research. However, resolving enantiomers still represents a significant challenge in the metabolomics study of complex samples. Here, we introduced N,N-dimethyl-l-cysteine (dimethylcysteine, DiCys), a chiral thiol, for the o-phthalaldehyde (OPA) derivatization of enantiomeric amine metabolites. We took interest in DiCys because of its potential for multiplex isotope-tagged quantification. Here, we characterized the usefulness of DiCys in reversed-phase LC-MS analyses of chiral metabolites, compared against five commonly used chiral thiols: N-acetyl-l-cysteine (NAC); N-acetyl-d-penicillamine (NAP); isobutyryl-l-cysteine (IBLC); N-(tert-butoxycarbonyl)-l-cysteine methyl ester (NBC); and N-(tert-butylthiocarbamoyl)-l-cysteine ethyl ester (BTCC). DiCys and IBLC showed the best overall performance in terms of chiral separation, fluorescence intensity, and ionization efficiency. For chiral separation of amino acids, DiCys/OPA also outperformed Marfey's reagents: 1-fluoro-2-4-dinitrophenyl-5-l-valine amide (FDVA) and 1-fluoro-2-4-dinitrophenyl-5-l-alanine amide (FDAA). As proof of principle, we compared DiCys and IBLC for detecting chiral metabolites in aqueous extracts of rice. By LC-MS analyses, both methods detected twenty proteinogenic l-amino acids and seven d-amino acids (Ala, Arg, Lys, Phe, Ser, Tyr, and Val), but DiCys showed better analyte separation. We conclude that DiCys/OPA is an excellent amine-derivatization method for enantiomeric metabolite detection in LC-MS analyses.

Keywords:  chiral metabolomics; d-amino acids; dimethyl labeling; enantiomer separation; rice water

DOI:  https://doi.org/10.3390/molecules26247416
Mol Cell Proteomics. 2021 Dec 18. pii: S1535-9476(21)00161-4. [Epub ahead of print] 100189

Multi-Omic Metabolic Enrichment Network Analysis reveals metabolite-protein physical interaction subnetworks altered in cancer.

Benjamin C Blum, Weiwei Lin, Matthew L Lawton, Qian Liu, Julian Kwan, Isabella Turcinovic, Ryan Hekman, Pingzhao Hu, Andrew Emili.

  Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce MOMENTA, an integrative multi-omic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.

Keywords:  Cancer; Multi-omic; Networks; Proteomics; Systems Biology

DOI:  https://doi.org/10.1016/j.mcpro.2021.100189
Metabolites. 2021 Dec 03. pii: 836. [Epub ahead of print]11(12):

Lipidomic and Metabolomic Signature of Progression of Chronic Kidney Disease in Patients with Severe Obesity.

Borja Lanzon, Marina Martin-Taboada, Victor Castro-Alves, Rocio Vila-Bedmar, Ignacio González de Pablos, Daniel Duberg, Pilar Gomez, Elias Rodriguez, Matej Orešič, Tuulia Hyötyläinen, Enrique Morales, Francisco J Ruperez, Gema Medina-Gomez.

  Severe obesity is a major risk for chronic kidney disease (CKD). Early detection and careful monitoring of renal function are critical for the prevention of CKD during obesity, since biopsies are not performed in patients with CKD and diagnosis is dependent on the assessment of clinical parameters. To explore whether distinct lipid and metabolic signatures in obesity may signify early stages of pathogenesis toward CKD, liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-high resolution accurate mass-mass spectrometry (GC-HRAM-MS) analyses were performed in the serum and the urine of severely obese patients with and without CKD. Moreover, the impact of bariatric surgery (BS) in lipid and metabolic signature was also studied, through LC-MS and GC-HRAM-MS analyses in the serum and urine of patients with severe obesity and CKD before and after undergoing BS. Regarding patients with severe obesity and CKD compared to severely obese patients without CKD, serum lipidome analysis revealed significant differences in lipid signature. Furthermore, serum metabolomics profile revealed significant changes in specific amino acids, with isoleucine and tyrosine, increased in CKD patients compared with patients without CKD. LC-MS and GC-HRAM-MS analysis in serum of patients with severe obesity and CKD after BS showed downregulation of levels of triglycerides (TGs) and diglycerides (DGs) as well as a decrease in branched-chain amino acid (BCAA), lysine, threonine, proline, and serine. In addition, BS removed most of the correlations in CKD patients against biochemical parameters related to kidney dysfunction. Concerning urine analysis, hippuric acid, valine and glutamine were significantly decreased in urine from CKD patients after surgery. Interestingly, bariatric surgery did not restore all the lipid species, some of them decreased, hence drawing attention to them as potential targets for early diagnosis or therapeutic intervention. Results obtained in this study would justify the use of comprehensive mass spectrometry-based lipidomics to measure other lipids aside from conventional lipid profiles and to validate possible early markers of risk of CKD in patients with severe obesity.

Keywords:  CKD; bariatric surgery; lipidomics; metabolomics; severe obesity

DOI:  https://doi.org/10.3390/metabo11120836
Trends Endocrinol Metab. 2021 Dec 16. pii: S1043-2760(21)00267-8. [Epub ahead of print]

Amino acid transporters as modulators of glucose homeostasis.

Stefan Bröer.

  Amino acids modulate glucose homeostasis. Cytosolic levels of amino acids are regulated by amino acid transporters, modulating insulin release, protein synthesis, cell proliferation, cell fate, and metabolism. In β-cells, amino acid transporters modulate incretin-stimulated insulin release. In the liver, amino acid transporters provide glutamine and alanine for gluconeogenesis. Intestinal amino acid transporters facilitate the intake of amino acids causing protein restriction when inactive. Adipocyte development is regulated by amino acid transporters through activation of mechanistic target of rapamycin (mTORC1) and amino acid-related metabolites. The accumulation and metabolism of branched-chain amino acids (BCAAs) in muscle depends on transporters. The integration between amino acid metabolism and transport is critical for the maintenance and function of tissues and cells involved in glucose homeostasis.

Keywords:  GCN2; adipocytes; gluconeogenesis; solute carrier; β-cell

DOI:  https://doi.org/10.1016/j.tem.2021.11.004
Small Methods. 2021 Sep;5(9): e2100206

LINT-Web: A Web-Based Lipidomic Data Mining Tool Using Intra-Omic Integrative Correlation Strategy.

Fengsheng Li, Jia Song, Yingkun Zhang, Shuaikang Wang, Jinhui Wang, Li Lin, Chaoyong Yang, Peng Li, He Huang.

  Lipidomics is a younger member of the "omics" family. It aims to profile lipidome alterations occurring in biological systems. Similar to the other "omics", lipidomic data is highly dimensional and contains a massive amount of information awaiting deciphering and data mining. Currently, the available bioinformatic tools targeting lipidomic data processing and lipid pathway analysis are limited. A few tools designed for lipidomic analysis perform only basic statistical analyses, and lipid pathway analyses rely heavily on public databases (KEGG, Reactome, and HMDB). Due to the inadequate understanding of lipid signaling and metabolism, the use of public databases for lipid pathway analysis can be biased and misleading. Instead of using public databases to interpret lipidomic ontology, the authors introduce an intra-omic integrative correlation strategy for lipidomic data mining. Such an intra-omic strategy allows researchers to unscramble and predict lipid biological functions from correlated genomic ontological results using statistical approaches. To simplify and improve the lipidomic data processing experience, they designed an interactive web-based tool: LINT-web (http://www.lintwebomics.info/) to perform the intra-omic analysis strategy, and validated the functions of LINT-web using two biological systems. Users without sophisticated statistical experience can easily process lipidomic datasets and predict the potential lipid biological functions using LINT-web.

Keywords:  lipidomics; online tools; systems biology; transcriptomics

DOI:  https://doi.org/10.1002/smtd.202100206
Cell. 2021 Dec 22. pii: S0092-8674(21)01386-6. [Epub ahead of print]184(26): 6226-6228

Dinner is served, sir: Fighting cancer with the right diet.

Andrés Méndez-Lucas, Mariia Yuneva.

Altered metabolism of tumors offers an opportunity to use metabolic interventions as a therapeutic strategy. Lien et al. demonstrate that understanding how specific diets with different carbohydrate and fat composition affect tumor metabolism is essential in order to use this opportunity efficiently.

DOI: https://doi.org/10.1016/j.cell.2021.11.036
Anal Chem. 2021 Dec 21.

Hydrogen/Deuterium Exchange Aiding Metabolite Identification in Single-Cell Nanospray High-Resolution Mass Spectrometry Analysis.

Changzhi Shi, Hetian Jia, Sisi Chen, Juan Huang, Yue'e Peng, Wei Guo.

The identification of metabolites in single-cell or small-volume tissue samples using single-cell mass spectrometry (MS) is challenging. In this study, hydrogen/deuterium (H/D) exchange was combined with microsampling nanospray high-resolution mass spectrometry (HRMS) to improve the efficiency and confidence level of metabolite identification in a single cell using commercial software. A nanospray ion source showed an improved reaction depth of 8% for H/D exchange compared with an electrospray ion source. In total, 273 metabolites were identified in Allium cepa L. single cells by searching commercial databases. Generally, more than one candidate is given for a precursor ion by MS or tandem MS (MS2) databases such as ChemSpider, MetDNA, MassBank, and mzCloud. With the help of the H/D exchange technique, the number of candidates decreased and reduction of the search space by a factor of 8 was achieved. In addition, two enzymolysis products of isoalliin, the transient intermediate and its isomer, were tracked at the single-cell level using the proposed method.

DOI: https://doi.org/10.1021/acs.analchem.1c02057
Metabolites. 2021 Dec 18. pii: 888. [Epub ahead of print]11(12):

Optimized Workflow for On-Line Derivatization for Targeted Metabolomics Approach by Gas Chromatography-Mass Spectrometry.

Raphaela Fritsche-Guenther, Yoann Gloaguen, Anna Bauer, Tobias Opialla, Stefan Kempa, Christina A Fleming, Henry Paul Redmond, Jennifer A Kirwan.

  Using manual derivatization in gas chromatography-mass spectrometry samples have varying equilibration times before analysis which increases technical variability and limits the number of potential samples analyzed. By contrast, automated derivatization methods can derivatize and inject each sample in an identical manner. We present a fully automated (on-line) derivatization method used for targeted analysis of different matrices. We describe method optimization and compare results from using off-line and on-line derivatization protocols, including the robustness and reproducibility of the methods. Our final parameters for the derivatization process were 20 µL of methoxyamine (MeOx) in pyridine for 60 min at 30 °C followed by 80 µL N-Methyl-N-trimethylsilyltrifluoracetamide (MSTFA) for 30 min at 30 °C combined with 4 h of equilibration time. The repeatability test in plasma and liver revealed a median relative standard deviation (RSD) of 16% and 10%, respectively. Serum samples showed a consistent intra-batch median RSD of 20% with an inter-batch variability of 27% across three batches. The direct comparison of on-line versus off-line demonstrated that on-line was fit for purpose and improves repeatability with a measured median RSD of 11% compared to 17% using the same method off-line. In summary, we recommend that optimized on-line methods may improve results for metabolomics and should be used where available.

Keywords:  automated derivatization; gas-chromatography mass spectrometry; metabolomics; on-line derivatization; optimization; quality assurance (QA); quality control (QC); validation

DOI:  https://doi.org/10.3390/metabo11120888
Mol Cell Proteomics. 2021 Dec 15. pii: S1535-9476(21)00159-6. [Epub ahead of print] 100187

DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia.

Wei Liu, Yaoting Sun, Weigang Ge, Fangfei Zhang, Lin Gan, Yi Zhu, Tiannan Guo, Kexin Liu.

  Drug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia (CML). To understand the underlying resistance mechanisms in response to imatinib (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for two months to generate derivative cells with mild, intermediate and severe resistance to the drugs as defined by their increasing resistance index (RI). PulseDIA-based quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7082 proteotypic proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin Signaling Pathway was found to be significantly enriched in both ADR- and IMA-resistant K562 cells. In particular, IDH2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated IDH2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.

Keywords:  DIA; Drug-resistance; IHD2; adriamycin; imatinib

DOI:  https://doi.org/10.1016/j.mcpro.2021.100187
Nat Chem Biol. 2021 Dec 24.

Small molecule targeting of chromatin writers in cancer.

Andrew R Conery, Jennifer L Rocnik, Patrick Trojer.

More than a decade after the launch of DNA methyltransferase and histone deacetylase inhibitors for the treatment of cancer, 2020 heralded the approval of the first histone methyltransferase inhibitor, revitalizing the concept that targeted manipulation of the chromatin regulatory landscape can have profound therapeutic impact. Three chromatin regulatory pathways-DNA methylation, histone acetylation and methylation-are frequently implicated in human cancer but hundreds of potentially druggable mechanisms complicate identification of key targets for therapeutic intervention. In addition to human genetics and functional screening, chemical biology approaches have proven critical for the discovery of key nodes in these pathways and in an ever-increasing complexity of molecularly defined human cancer contexts. This review introduces small molecule targeting approaches, showcases chemical probes and drug candidates for epigenetic writer enzymes, illustrates molecular features that may represent epigenetic dependencies and suggests translational strategies to maximize their impact in cancer therapy.

DOI: https://doi.org/10.1038/s41589-021-00920-5
Nat Metab. 2021 Dec;3(12): 1596-1607

Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity.

Herbert Tilg, Timon E Adolph, Michael Dudek, Percy Knolle.

Non-alcoholic fatty liver disease (NAFLD) has emerged pandemically across the globe and particularly affects patients with obesity and type 2 diabetes. NAFLD is a complex systemic disease that is characterised by hepatic lipid accumulation, lipotoxicity, insulin resistance, gut dysbiosis and inflammation. In this review, we discuss how metabolic dysregulation, the gut microbiome, innate and adaptive immunity and their interplay contribute to NAFLD pathology. Lipotoxicity has been shown to instigate liver injury, inflammation and insulin resistance. Synchronous metabolic dysfunction, obesity and related nutritional perturbation may alter the gut microbiome, in turn fuelling hepatic and systemic inflammation by direct activation of innate and adaptive immune responses. We review evidence suggesting that, collectively, these unresolved exogenous and endogenous cues drive liver injury, culminating in liver fibrosis and advanced sequelae of this disorder such as liver cirrhosis and hepatocellular carcinoma. Understanding NAFLD as a complex interplay between metabolism, gut microbiota and the immune response will challenge the clinical perception of NAFLD and open new therapeutic avenues.

DOI: https://doi.org/10.1038/s42255-021-00501-9