bims-mascan 2020-03-15 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2020‒03‒15
twenty papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research

SLC25A32 sustains cancer cell proliferation by regulating flavin adenine nucleotide (FAD) metabolism.
Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer.
A lipidomic workflow capable of resolving sn- and C[double bond, length as m-dash]C location isomers of phosphatidylcholines.
MaxQuant software for ion mobility enhanced shotgun proteomics.
Cancer associated fibroblast FAK regulates malignant cell metabolism.
The Quiescent Metabolic Phenotype of Glioma Stem Cells.
Metabolic Profiling of Formalin-Fixed Paraffin-Embedded Tissues Discriminates Normal Colon from Colorectal Cancer.
Tumor-derived exosomes in the regulation of macrophage polarization.
ANGPTL3 deficiency alters the lipid profile and metabolism of cultured hepatocytes and human lipoproteins.
AIG1 and ADTRP are endogenous hydrolases of fatty acid esters of hydroxy fatty acids (FAHFAs) in mice.
mTOR complex 2 is an integrator of cancer metabolism and epigenetics.
lipidr: a software tool for data mining and analysis of lipidomics datasets.
A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis.
LC-HRMS based approach to identify novel sphingolipid biomarkers in breast cancer patients.
Software tools, databases and resources in metabolomics: updates from 2018 to 2019.
Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations.
Lipid peroxidation and ferroptosis: The role of GSH and GPx4.
Glutaminase-1 (GLS1) inhibition limits metastatic progression in osteosarcoma.
Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines.
Autophagy-Dependent Ferroptosis: Machinery and Regulation.

Oncotarget. 2020 Feb 25. 11(8): 801-812

SLC25A32 sustains cancer cell proliferation by regulating flavin adenine nucleotide (FAD) metabolism.

Valeria Santoro, Ilya Kovalenko, Kim Vriens, Stefan Christen, Andreas Bernthaler, Andrea Haegebarth, Sarah-Maria Fendt, Sven Christian.

  SLC25A32 is a member of the solute carrier 25 family of mitochondrial transporters. SLC25A32 transports tetrahydrofolate (THF) as well as FAD into mitochondria and regulates mitochondrial one-carbon metabolism and redox balance. While it is known that cancer cells require one-carbon and FAD-dependent mitochondrial metabolism to sustain cell proliferation, the role of SLC25A32 in cancer cell growth remains unexplored. Our results indicate that the SLC25A32 gene is highly amplified in different tumors and that amplification correlates with increased mRNA expression and reduced patients´ survival. siRNA-mediated knock-down and CRISPR-mediated knock-out of SLC25A32 in cancer cells of different origins, resulted in the identification of cell lines sensitive and resistant to SLC25A32 inhibition. Mechanistically, tracing of deuterated serine revealed that SLC25A32 knock-down does not affect the mitochondrial/cytosolic folate flux as measured by Liquid Chromatography coupled Mass Spectrometry (LC-MS). Instead, SLC25A32 inhibition results in a respiratory chain dysfunction at the FAD-dependent complex II enzyme, induction of Reactive Oxygen Species (ROS) and depletion of reduced glutathione (GSH), which impairs cancer cell proliferation. Moreover, buthionine sulfoximine (BSO) treatment further sensitizes cells to ROS-mediated inhibition of cell proliferation upon SLC25A32 knock-down. Treatment of cells with the FAD precursor riboflavin and with GSH rescues cancer cell proliferation upon SLC25A32 down-regulation. Our results indicate that the reduction of mitochondrial FAD concentrations by targeting SLC25A32 has potential clinical applications as a single agent or in combination with approved cancer drugs that lead to increased oxidative stress and reduced tumor growth.

Keywords:  FAD; ROS; metabolism; mitochondria; transporter

DOI:  https://doi.org/10.18632/oncotarget.27486
Br J Cancer. 2020 Mar 09.

Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer.

Wenting Dai, Guan Wang, Jason Chwa, Myung Eun Oh, Tharindumala Abeywardana, Yanzhong Yang, Qiong A Wang, Lei Jiang.

BACKGROUND: Previous studies suggested that mdivi-1 (mitochondrial division inhibitor), a putative inhibitor of dynamin-related protein (DRP1), decreased cancer cell proliferation through inducing mitochondrial fusion and altering oxygen consumption. However, the metabolic reprogramming underlying the DRP1 inhibition is still unclear in cancer cells.METHODS: To better understand the metabolic effect of DRP1 inhibition, [U-13C]glucose isotope tracing was employed to assess mdivi-1 effects in several cancer cell lines, DRP1-WT (wild-type) and DRP1-KO (knockout) H460 lung cancer cells and mouse embryonic fibroblasts (MEFs).
RESULTS: Mitochondrial staining confirmed that mdivi-1 treatment and DRP1 deficiency induced mitochondrial fusion. Surprisingly, metabolic isotope tracing found that mdivi-1 decreased mitochondrial oxidative metabolism in the lung cancer cell lines H460, A549 and the colon cancer cell line HCT116. [U-13C]glucose tracing studies also showed that the TCA cycle intermediates had significantly lower enrichment in mdivi-1-treated cells. In comparison, DRP1-WT and DRP1-KO H460 cells had similar oxidative metabolism, which was decreased by mdivi-1 treatment. Furthermore, mdivi-1-mediated effects on oxidative metabolism were independent of mitochondrial fusion.
CONCLUSIONS: Our data suggest that, in cancer cells, mdivi-1, a putative inhibitor of DRP1, decreases oxidative metabolism to impair cell proliferation.

DOI: https://doi.org/10.1038/s41416-020-0778-x
Chem Sci. 2019 Dec 14. 10(46): 10740-10748

A lipidomic workflow capable of resolving sn- and C[double bond, length as m-dash]C location isomers of phosphatidylcholines.

Xue Zhao, Wenpeng Zhang, Donghui Zhang, Xinwei Liu, Wenbo Cao, Qinhua Chen, Zheng Ouyang, Yu Xia.

As a major class of mammalian lipids, phosphatidylcholines (PCs) often contain mixtures of structural isomers, resulting from different lipogenesis pathways. Profiling PCs at the isomer level, however, remains challenging in lipidomic settings, especially for characterizing the positions of fatty acyls on the glycerol backbone (sn-positions) and the locations of carbon-carbon double bonds (C[double bond, length as m-dash]Cs) in unsaturated acyl chains. In this work, we have developed a workflow for profiling PCs down to sn- and C[double bond, length as m-dash]C locations at high coverage and sensitivity. This capability is enabled by radical-directed fragmentation, forming sn-1 specific fragment ions upon collision-induced dissociation (CID) of bicarbonate anion adducts of PCs ([M + HCO3]-) inside a mass spectrometer. This new tandem mass spectrometry (MS/MS) method can be simply incorporated into liquid chromatography by employing ammonium bicarbonate in the mobile phase without any instrument modification needed. It is also compatible with the online Paternò-Büchì reaction and subsequent MS/MS for the assignment of C[double bond, length as m-dash]C locations in sn-1 fatty acyl chains of unsaturated PCs. The analytical performance of the workflow is manifested by identification of 82 distinct PC molecular species from the polar extract of bovine liver, including quantification of 19 pairs of sn-isomers. Finally, we demonstrate that five pairs of PC sn-isomers show significant compositional changes in tissue samples of human breast cancer relative to controls, suggesting a potential for monitoring PC sn-isomers for biomedical applications.

DOI: https://doi.org/10.1039/c9sc03521d
Mol Cell Proteomics. 2020 Mar 10. pii: mcp.TIR119.001720. [Epub ahead of print]

MaxQuant software for ion mobility enhanced shotgun proteomics.

Nikita Prianichnikov, Heiner Koch, Scarlet Koch, Markus Lubeck, Raphael Heilig, Sven Brehmer, Roman Fischer, Jürgen Cox.

  Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

Keywords:  Bioinformatics; Bioinformatics software; Label-free quantification; Mass Spectrometry; Quantification

DOI:  https://doi.org/10.1074/mcp.TIR119.001720
Nat Commun. 2020 Mar 10. 11(1): 1290

Cancer associated fibroblast FAK regulates malignant cell metabolism.

Fevzi Demircioglu, Jun Wang, Juliana Candido, Ana S H Costa, Pedro Casado, Beatriz de Luxan Delgado, Louise E Reynolds, Jesus Gomez-Escudero, Emma Newport, Vinothini Rajeeve, Ann-Marie Baker, Marina Roy-Luzarraga, Trevor A Graham, Julie Foster, Yu Wang, James J Campbell, Rajinder Singh, Penglie Zhang, Thomas J Schall, Frances R Balkwill, Jane Sosabowski, Pedro R Cutillas, Christian Frezza, Patricia Sancho, Kairbaan Hodivala-Dilke.

Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through pathways under the control of FAK. In breast and pancreatic cancer patients we find that low FAK expression, specifically in the stromal compartment, predicts reduced overall survival. In mice, depletion of FAK in a subpopulation of CAFs regulates paracrine signals that increase malignant cell glycolysis and tumour growth. Proteomic and phosphoproteomic analysis in our mouse model identifies metabolic alterations which are reflected at the transcriptomic level in patients with low stromal FAK. Mechanistically we demonstrate that FAK-depletion in CAFs increases chemokine production, which via CCR1/CCR2 on cancer cells, activate protein kinase A, leading to enhanced malignant cell glycolysis. Our data uncover mechanisms whereby stromal fibroblasts regulate cancer cell metabolism independent of genetic mutations in cancer cells.

DOI: https://doi.org/10.1038/s41467-020-15104-3
J Proteomics Bioinform. 2019 ;12(6): 96-103

The Quiescent Metabolic Phenotype of Glioma Stem Cells.

Elizabeth I Spehalski, Jennifer A Lee, Cord Peters, Philip Tofilon, Kevin Camphausen.

  Introduction: Glioblastoma (GBM) is the most common primary malignant brain tumor in humans and, even with aggressive treatment that includes surgical resection, radiation (IR), and chemotherapy administration, prognosis is poor due to tumor recurrence. There is evidence that within GBMs a small number of glioma stem-like cells (GSLCs) exist, which are thought to be therapy resistant and are thus capable of repopulating a tumor after treatment. Like most cancers, GBMs largely employ aerobic glycolysis to create ATP, a phenomenon known as the Warburg Effect. There is no consensus on the metabolic characteristics of cancer stem cells. GSLCs have been shown to rely more heavily on oxidative phosphorylation, but there is also evidence that cancer stem cells can adapt their metabolism by fluctuating between energy pathways or acquiring intermediate metabolic phenotypes. We hypothesized that the metabolism of GSLCs differs from that of differentiated GBM tumor cell lines, and that the steady state metabolism would be differentially altered following radiation treatment.Materials and Methods: We evaluated the oxygen consumption rate, extracellular acidification rate, and metabolic enzyme levels of GBM cell lines and GSLCs before and after irradiation using extracellular flux assays. We also measured absolute metabolite levels in these cells via mass spectroscopy with and without radiation treatment.
Results: GSLCs were found to be significantly more quiescent in comparison to adherent GBM cell lines, highlighted by lower glycolytic and maximal respiratory capacities as well as lower oxygen consumption and extracellular acidification rates. Analysis of individual metabolite concentrations revealed lower total metabolite concentrations overall but also elevated levels of metabolites in different energy pathways for GSLCs compared to GBM cell lines. Additionally, the metabolism of both GSLCs and GBM cell lines were found to be altered by IR.
Conclusions: While there is not one metabolic alteration that distinguishes irradiated GSLC metabolism from that of GBM cell lines, therapies targeting more metabolically quiescent tumor cells and thus the resistant GSLC population may increase a cancer's sensitivity to radiotherapy.

Keywords:  glioblastoma; glioma stem cells; radiation sensitivity; tumor metabolism

DOI:  https://doi.org/10.35248/0974-276x.19.12.502
Mol Cancer Res. 2020 Mar 12. pii: molcanres.1091.2019. [Epub ahead of print]

Metabolic Profiling of Formalin-Fixed Paraffin-Embedded Tissues Discriminates Normal Colon from Colorectal Cancer.

Kota Arima, Mai Chan Lau, Melissa Zhao, Koichiro Haruki, Keisuke Kosumi, Kosuke Mima, Mancang Gu, Juha P Väyrynen, Tyler S Twombly, Yoshifumi Baba, Kenji Fujiyoshi, Junko Kishikawa, Chunguang Guo, Hideo Baba, William G Richards, Andrew T Chan, Reiko Nishihara, Jeffrey A Meyerhardt, Jonathan A Nowak, Marios Giannakis, Charles S Fuchs, Shuji Ogino.

Accumulating evidence suggests that metabolic reprogramming has a critical role in carcinogenesis and tumor progression. The usefulness of formalin-fixed paraffin-embedded (FFPE) tissue material for metabolomics analysis as compared with fresh frozen tissue material remains unclear. Liquid chromatography tandem mass spectrometry-based metabolomics analysis was performed on 11 pairs of matched tumor and normal tissues in both FFPE and fresh frozen tissue materials from colorectal carcinoma patients. Permutation t-test was applied to identify metabolites with differential abundance between tumor and normal tissues. A total of 200 metabolites were detected in the FFPE samples and 536 in the fresh frozen samples. The preservation of metabolites in FFPE samples was diverse according to classes and chemical characteristics, ranging from 78% (energy) to 0% (peptides). Compared with the normal tissues, 34 (17%) and 174 (32%) metabolites were either accumulated or depleted in the tumor tissues derived from FFPE and fresh frozen samples, respectively. Among them, 15 metabolites were common in both FFPE and fresh frozen samples. Notably, branched chain amino acids were highly accumulated in tumor tissues. Using KEGG pathway analyses, glyoxylate and dicarboxylate metabolism, arginine and proline, glycerophospholipid, and glycine, serine and threonine metabolism pathways distinguishing tumor from normal tissues were found in both FFPE and fresh frozen samples. This study demonstrates that informative data of metabolic profiles can be retrieved from FFPE tissue materials. Implications: Our findings suggest potential value of metabolic profiling using FFPE tumor tissues and may help to shape future translational studies through developing treatment strategies targeting metabolites.

DOI: https://doi.org/10.1158/1541-7786.MCR-19-1091
Inflamm Res. 2020 Mar 11.

Tumor-derived exosomes in the regulation of macrophage polarization.

Mirza S Baig, Anjali Roy, Sajjan Rajpoot, Dongfang Liu, Rajkumar Savai, Sreeparna Banerjee, Manabu Kawada, Syed M Faisal, Rohit Saluja, Uzma Saqib, Tomokazu Ohishi, Kishore K Wary.

  BACKGROUND: This review focuses on exosomes derived from various cancer cells. The review discusses the possibility of differentiating macrophages in alternatively activated anti-inflammatory pro-tumorigenic M2 macrophage phenotypes and classically activated pro-inflammatory, anti-tumorigenic M1 macrophage phenotypes in the tumor microenvironment (TME). The review is divided into two main parts, as follows: (1) role of exosomes in alternatively activating M2-like macrophages-breast cancer-derived exosomes, hepatocellular carcinoma (HCC) cell-derived exosomes, lung cancer-derived exosomes, prostate cancer-derived exosomes, Oral squamous cell carcinoma (OSCC)-derived exosomes, epithelial ovarian cancer (EOC)-derived exosomes, Glioblastoma (GBM) cell-derived exosomes, and colorectal cancer-derived exosomes, (2) role of exosomes in classically activating M1-like macrophages, oral squamous cell carcinoma-derived exosomes, breast cancer-derived exosomes, Pancreatic-cancer derived modified exosomes, and colorectal cancer-derived exosomes, and (3) exosomes and antibody-dependent cellular cytotoxicity (ADCC). This review addresses the following subjects: (1) crosstalk between cancer-derived exosomes and recipient macrophages, (2) the role of cancer-derived exosome payload(s) in modulating macrophage fate of differentiation, and (3) intracellular signaling mechanisms in macrophages regarding the exosome's payload(s) upon its uptake and regulation of the TME.EVIDENCE: Under the electron microscope, nanoscale exosomes appear as specialized membranous vesicles that emerge from the endocytic cellular compartments. Exosomes harbor proteins, growth factors, cytokines, lipids, miRNA, mRNA, and DNAs. Exosomes are released by many cell types, including reticulocytes, dendritic cells, B-lymphocytes, platelets, mast cells, and tumor cells. It is becoming clear that exosomes can impinge upon signal transduction pathways, serve as a mediator of signaling crosstalk, thereby regulating cell-to-cell wireless communications.
CONCLUSION: Based on the vesicular cargo, the molecular constituents, the exosomes have the potential to change the fate of macrophage phenotypes, either M1, classically activated macrophages, or M2, alternatively activated macrophages. In this review, we discuss and describe the ability of tumor-derived exosomes in the mechanism of macrophage activation and polarization.

Keywords:  Exosomes; Inflammatory response; M1 macrophages; M2 macrophages; Tumor

DOI:  https://doi.org/10.1007/s00011-020-01318-0
Biochim Biophys Acta Mol Cell Biol Lipids. 2020 Mar 06. pii: S1388-1981(20)30071-8. [Epub ahead of print] 158679

ANGPTL3 deficiency alters the lipid profile and metabolism of cultured hepatocytes and human lipoproteins.

Hanna Ruhanen, P A Nidhina Haridas, Ilenia Minicocci, Juuso H Taskinen, Francesco Palmas, Alessia di Costanzo, Laura D'Erasmo, Jari Metso, Jennimari Partanen, Jesmond Dalli, You Zhou, Marcello Arca, Matti Jauhiainen, Reijo Käkelä, Vesa M Olkkonen.

  Loss-of-function (LOF) mutations in ANGPTL3, an inhibitor of lipoprotein lipase (LPL), cause a drastic reduction of serum lipoproteins and protect against the development of atherosclerotic cardiovascular disease. Therefore, ANGPTL3 is a promising therapy target. We characterized the impacts of ANGPTL3 depletion on the immortalized human hepatocyte (IHH) transcriptome, lipidome and human plasma lipoprotein lipidome. The transcriptome of ANGPTL3 knock-down (KD) cells showed altered expression of several pathways related to lipid metabolism. Accordingly, ANGPTL3 depleted IHH displayed changes in cellular overall fatty acid (FA) composition and in the lipid species composition of several lipid classes, characterized by abundant n-6 and n-3 polyunsaturated FAs (PUFAs). This PUFA increase coincided with an elevation of lipid mediators, among which there were species relevant for resolution of inflammation, protection from lipotoxic and hypoxia-induced ER stress, hepatic steatosis and insulin resistance or for the recovery from cardiovascular events. Cholesterol esters were markedly reduced in ANGPTL3 KD IHH, coinciding with suppression of the SOAT1 mRNA and protein. ANGPTL3 LOF caused alterations in plasma lipoprotein FA and lipid species composition. All lipoprotein fractions of the ANGPTL3 LOF subjects displayed a marked drop of 18:2n-6, while several highly unsaturated triacylglycerol (TAG) species were enriched. The present work reveals distinct impacts of ANGPTL3 depletion on the hepatocellular lipidome, transcriptome and lipid mediators, as well as on the lipidome of lipoproteins isolated from plasma of ANGPTL3-deficient human subjects. It is important to consider these lipidomics and transcriptomics findings when targeting ANGPTL3 for therapy and translating it to the human context.

Keywords:  Angiopoietin like 3; Cholesterol ester; Lipid metabolism; Lipidomics; Lipoprotein lipase; Polyunsaturated fatty acid

DOI:  https://doi.org/10.1016/j.bbalip.2020.158679
J Biol Chem. 2020 Mar 09. pii: jbc.RA119.012145. [Epub ahead of print]

AIG1 and ADTRP are endogenous hydrolases of fatty acid esters of hydroxy fatty acids (FAHFAs) in mice.

Meric Erikci Ertunc, Bernard P Kok, William H Parsons, Justin G Wang, Dan Tan, Cynthia J Donaldson, Antonio F M Pinto, Joan M Vaughan, Nhi Ngo, Kenneth M Lum, Cassandra L Henry, Aundrea R Coppola, Micah J Niphakis, Benjamin F Cravatt, Enrique Saez, Alan Saghatelian.

  Fatty acid esters of hydroxy fatty acids (FAHFAs) are a newly discovered class of signaling lipids with anti-inflammatory and anti-diabetic properties. However, the endogenous regulation of FAHFAs remains a pressing but unanswered question. Here, using MS-based FAHFA hydrolysis assays, LC-MS-based lipidomics analyses, and activity-based protein profiling, we found that androgen-induced gene 1 (AIG1) and androgen-dependent TFPI-regulating protein (ADTRP), two threonine hydrolases, control FAHFA levels in vivo in both genetic and pharmacologic mouse models. Tissues from mice lacking ADTRP (Adtrp-KO) or both AIG1 and ADTRP (DKO) had higher concentrations of FAHFAs particularly isomers with the ester bond at the 9th carbon due to decreased FAHFA hydrolysis activity. The levels of other lipids were unaltered indicating that AIG1 and ADTRP specifically hydrolyze FAHFAs. Complementing these genetic studies, we also identified a dual AIG1/ADTRP inhibitor, ABD-110207, that is active in vivo Acute treatment of wild-type mice with ABD-110207 resulted in elevated FAHFA levels, further supporting the notion that AIG1 and ADTRP activity control endogenous FAHFA levels. However, loss of AIG1/ADTRP did not mimic the changes associated with pharmacologically administered FAHFAs on circulating and tissue FAHFA levels, glucose tolerance or insulin sensitivity in mice, indicating that therapeutic strategies should continue to focus on FAHFA administration. Together, these findings identify AIG1 and ADTRP as the first endogenous FAHFA hydrolases identified and provide critical genetic and chemical tools for further characterization of these enzymes and endogenous FAHFAs to unravel their physiological functions and roles in health and disease.

Keywords:  androgen induced gene 1 (AIG1); androgen-dependent TFPI-regulating protein (ADTRP); diabetes; enzyme inhibitor; fatty acid ester of hydroxy fatty acid (FAHFA); glucose metabolism; lipid ester; lipid signaling; metabolism; threonine hydrolase

DOI:  https://doi.org/10.1074/jbc.RA119.012145
Cancer Lett. 2020 Mar 04. pii: S0304-3835(20)30118-X. [Epub ahead of print]

mTOR complex 2 is an integrator of cancer metabolism and epigenetics.

Kenta Masui, Mio Harachi, Webster K Cavenee, Paul S Mischel, Noriyuki Shibata.

  Metabolic reprogramming is a central hallmark of cancer and is driven by abnormalites of oncogenes and tumor suppressors. This enables tumor cells to obtain the macromolecular precursors and energy needed for rapid tumor growth. Accelerated metabolism also translates into cancer cell aggression through epigenetic changes. The aberrant signaling cascades activated by oncogenes coordinate metabolic reprogramming with epigenetic shifts and subsequent global transcriptional changes through the dysregulation of rate-limiting metabolic enzymes as well as by facilitating the production of intermediary metabolites. As the landscape of cancer cell metabolism has been elucidated, it is now time for this knowledge to be translated into benefit for patients. Here we review the recently identified central regulatory role for mechanistic/mammalian target of rapamycin complex 2 (mTORC2), a downstream effector of many cancer-causing mutations, in reprogramming the metabolic and epigenetic landscape. This leads to tumor cell survival and cancer drug resistance.

Keywords:  histone acetylation; iron metabolism; mTOR complex; metabolic reprogramming; microenvironment

DOI:  https://doi.org/10.1016/j.canlet.2020.03.001
J Proteome Res. 2020 Mar 13.

lipidr: a software tool for data mining and analysis of lipidomics datasets.

Ahmed Mohamed, Jeffrey Molendijk, Michelle M Hill.

The rapid evolution of mass spectrometry (MS)-based lipidomics has enabled the simultaneous measurement of numerous lipid classes. With lipidomics datasets becoming increasingly available, lipidomic-focused software tools are required to facilitate data analysis as well as mining of public datasets, integrating lipidomics-unique molecular information, such as lipid class, chain length and unsaturation. To address this need, we developed lipidr, an open-source R/Bioconductor package for data mining and analysis of lipidomics datasets. lipidr implements a comprehensive lipidomic-focused analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports and Metabolomics Workbench files directly into R, automatically inferring lipid class and chain information from lipid names. Through integration with the Metabolomics Workbench API, users can search, download and reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, uni- and multivariate analyses, displaying results as interactive visualizations. To enable interpretation of lipid class, chain length and total unsaturation data, we also developed and implemented a novel Lipid Set Enrichment Analysis. A companion online guide with two live example datasets is presented at https://www.lipidr.org/.We expect that the ease of use and innovative features of lipidr allow the lipidomics research community to gain novel detailed insights from lipidomics data.

DOI: https://doi.org/10.1021/acs.jproteome.0c00082
J Pathol. 2020 Mar 10.

A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis.

Fabian Coscia, Sophia Doll, Jacob Mathias Bech, Lisa Schweizer, Andreas Mund, Ernst Lengyel, Jan Lindebjerg, Gunvor Iben Madsen, José M A Moreira, Matthias Mann.

  Formalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Here, we describe an MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from histopathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including low-input cancer tissue isolated by laser microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner. This article is protected by copyright. All rights reserved.

Keywords:  Adenoma; Biobank samples; FFPE tissue; High-throughput, Protocol, Biomarker discovery; Mass spectrometry; Proteomics

DOI:  https://doi.org/10.1002/path.5420
Sci Rep. 2020 Mar 13. 10(1): 4668

LC-HRMS based approach to identify novel sphingolipid biomarkers in breast cancer patients.

Priyanka Bhadwal, Divya Dahiya, Dhananjay Shinde, Kim Vaiphei, Raviswamy G H Math, Vinay Randhawa, Navneet Agnihotri.

Perturbations in lipid metabolic pathways to meet the bioenergetic and biosynthetic requirements is a principal characteristic of cancer cells. Sphingolipids (SPLs) are the largest class of bioactive lipids associated to various aspects of tumorigenesis and have been extensively studied in cancer cell lines and experimental models. The clinical relevance of SPLs in human malignancies however is still poorly understood and needs further investigation. In the present study, we adopted a UHPLC-High resolution (orbitrap) Mass spectrometry (HRMS) approach to identify various sphingolipid species in breast cancer patients. A total of 49 SPLs falling into 6 subcategories have been identified. Further, integrating the multivariate analysis with metabolomics enabled us to identify an elevation in the levels of ceramide phosphates and sphingosine phosphates in tumor tissues as compared to adjacent normal tissues. The expression of genes involved in the synthesis of reported metabolites was also determined in local as well as TCGA cohort. A significant upregulation in the expression of CERK and SPHK1 was observed in tumor tissues in local and TCGA cohort. Sphingomyelin levels were found to be high in adjacent normal tissues. Consistent with the above findings, expression of SGMS1 in tumor tissues was downregulated in TCGA cohort only. Clinical correlations of the selected metabolites and their performance as biomarkers was also evaluated. Significant ROC and positive correlation with Ki67 index highlight the diagnostic potential and clinical relevance of ceramide phosphates in breast cancer.

DOI: https://doi.org/10.1038/s41598-020-61283-w
Metabolomics. 2020 Mar 07. 16(3): 36

Software tools, databases and resources in metabolomics: updates from 2018 to 2019.

Keiron O'Shea, Biswapriya B Misra.

  Metabolomics has evolved as a discipline from a discovery and functional genomics tool, and is now a cornerstone in the era of big data-driven precision medicine. Sample preparation strategies and analytical technologies have seen enormous growth, and keeping pace with data analytics is challenging, to say the least. This review introduces and briefly presents around 100 metabolomics software resources, tools, databases, and other utilities that have surfaced or have improved in 2019. Table 1 provides the computational dependencies of the tools, categorizes the resources based on utility and ease of use, and provides hyperlinks to webpages where the tools can be downloaded or used. This review intends to keep the community of metabolomics researchers up to date with all the software tools, resources, and databases developed in 2019, in one place.

Keywords:  Annotation; Database; In silico; Metabolite; Metabolomics; Program; Resource; Software; Tool

DOI:  https://doi.org/10.1007/s11306-020-01657-3
J Proteomics Bioinform. 2019 ;12(3): 48-55

Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations.

Sudhir Srivastava, Michael Merchant, Anil Rai, Shesh N Rai.

  Introduction: The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values and data heterogeneity from technical variability. We considered a proteomics data set generated from human kidney biopsy material to investigate the technical effects of sample preparation and the quantitative MS.Methods: We studied the effect of tissue storage methods (TSMs) and tissue extraction methods (TEMs) on data analysis. There are two TSMs: frozen (FR) and FFPE (formalin-fixed paraffin embedded); and three TEMs: MAX, TX followed by MAX and SDS followed by MAX. We assessed the impact of different strategies to analyze the data while considering heterogeneity and MVs. We have used analysis of variance (ANOVA) model to study the effects due to various sources of variability.
Results and Conclusion: We found that the FFPE TSM is better than the FR TSM. We also found that the one-step TEM (MAX) is better than those of two-steps TEMs. Furthermore, we found the imputation method is a better approach than excluding the proteins with MVs or using unbalanced design.

Keywords:  ANOVA; Imputation; Proteins; Technical variability; Tissue extraction; Tissue storage

DOI:  https://doi.org/10.35248/0974-276x.19.12.496
Free Radic Biol Med. 2020 Mar 09. pii: S0891-5849(19)32437-2. [Epub ahead of print]

Lipid peroxidation and ferroptosis: The role of GSH and GPx4.

Fulvio Ursini, Matilde Maiorino.

  Ferroptosis (FPT) is a form of cell death due to missed control of membrane lipid peroxidation (LPO). According to the axiomatic definition of non-accidental cell death, LPO takes place in a scenario of altered homeostasis. FPT, differently from apoptosis, occurs in the absence of any known specific genetically encoded death pathway or specific agonist, and thus must be rated as a regulated, although not "programmed", death pathway. It follows that LPO is under a homeostatic metabolic control and is only permitted when indispensable constraints are satisfied and the antiperoxidant machinery collapses. The activity of the selenoperoxidase Glutathione Peroxidase 4 (GPx4) is the cornerstone of the antiperoxidant defence. Converging evidence on both mechanism of LPO and GPx4 enzymology indicates that LPO is initiated by alkoxyl radicals produced by ferrous iron from the hydroperoxide derivatives of lipids (LOOH), traces of which are the unavoidable drawback of aerobic metabolism. FPT takes place when a threshold has been exceeded. This occurs when the major conditions are satisfied: i) oxygen metabolism leading to the continuous formation of traces of LOOH from phospholipid-containing polyunsaturated fatty acids; ii) missed enzymatic reduction of LOOH; iii) availability of ferrous iron from the labile iron pool. Although the effectors impacting on homeostasis and leading to FPT in physiological conditions are not known, from the available knowledge on LPO and GPx4 enzymology we propose that it is aerobic life itself that, while supporting bioenergetics, is also a critical requisite of FPT. Yet, when the homeostatic control of the steady state between LOOH formation and reduction is lost, LPO is activated and FPT is executed.

Keywords:  GPx4; GSH; Lipid hydroperoxide; Lipid peroxidation; Oxygen toxicity; Selenium; cell death; ferroptosis

DOI:  https://doi.org/10.1016/j.freeradbiomed.2020.02.027
Cancer Metab. 2020 ;8 4

Glutaminase-1 (GLS1) inhibition limits metastatic progression in osteosarcoma.

L Ren, V Ruiz-Rodado, T Dowdy, S Huang, S H Issaq, J Beck, H Wang, C Tran Hoang, A Lita, M Larion, A K LeBlanc.

  Background: Osteosarcoma (OS) is a malignant bone tumor that often develops during the period of rapid growth associated with adolescence. Despite successful primary tumor control accompanied by adjuvant chemotherapy, death from pulmonary metastases occurs in approximately 30% of patients within 5 years. As overall survival in patients remains unchanged over the last 30 years, urgent needs for novel therapeutic strategies exist. Cancer metastasis is characterized by complex molecular events which result from alterations in gene and protein expression/function. Recent studies suggest that metabolic adaptations, or "metabolic reprogramming," may similarly contribute to cancer metastasis. The goal of this study was to specifically interrogate the metabolic vulnerabilities of highly metastatic OS cell lines in a series of in vitro and in vivo experiments, in order to identify a tractable metabolically targeted therapeutic strategy for patients.Methods: Nutrient deprivation and drug treatment experiments were performed in MG63.3, 143B, and K7M2 OS cell lines to identify the impact of glutaminase-1 (GLS1) inhibition and metformin treatment on cell proliferation. We functionally validated the impact of drug treatment with extracellular flux analysis, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. 13C-glucose and 13C-glutamine tracing was employed to identify specific contributions of these nutrients to the global metabolic profiles generated with GLS1 inhibition and metformin treatment in vivo.
Results: Highly metastatic OS cell lines require glutamine for proliferation, and exposure to CB-839, in combination with metformin, induces both primary tumor growth inhibition and a distinct reduction in metastatic outgrowth in vivo. Further, combination-treated OS cells showed a reduction in cellular mitochondrial respiration, while NMR confirmed the pharmacodynamic effects of glutaminase inhibition in tumor tissues. We observed global decreases in glycolysis and tricarboxylic acid (TCA) cycle functionality, alongside an increase in fatty acid oxidation and pyrimidine catabolism.
Conclusions: This data suggests combination-treated cells cannot compensate for metformin-induced electron transport chain inhibition by upregulating glutaminolysis to generate TCA cycle intermediates required for cell proliferation, translating into significant reductions in tumor growth and metastatic progression. This therapeutic approach could be considered for future clinical development for OS patients presenting with or at high risk of developing metastasis.

Keywords:  Glutaminase; Metabolism; Metastasis; Metformin; Osteosarcoma

DOI:  https://doi.org/10.1186/s40170-020-0209-8
Nat Commun. 2020 Mar 13. 11(1): 1393

Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines.

Ruben Boon, Manoj Kumar, Tine Tricot, Ilaria Elia, Laura Ordovas, Frank Jacobs, Jennifer One, Jonathan De Smedt, Guy Eelen, Matthew Bird, Philip Roelandt, Ginevra Doglioni, Kim Vriens, Matteo Rossi, Marta Aguirre Vazquez, Thomas Vanwelden, François Chesnais, Adil El Taghdouini, Mustapha Najimi, Etienne Sokal, David Cassiman, Jan Snoeys, Mario Monshouwer, Wei-Shou Hu, Christian Lange, Peter Carmeliet, Sarah-Maria Fendt, Catherine M Verfaillie.

Predicting drug-induced liver injury in a preclinical setting remains challenging, as cultured primary human hepatocytes (PHHs), pluripotent stem cell-derived hepatocyte-like cells (HLCs), and hepatoma cells exhibit poor drug biotransformation capacity. We here demonstrate that hepatic functionality depends more on cellular metabolism and extracellular nutrients than on developmental regulators. Specifically, we demonstrate that increasing extracellular amino acids beyond the nutritional need of HLCs and HepG2 cells induces glucose independence, mitochondrial function, and the acquisition of a transcriptional profile that is closer to PHHs. Moreover, we show that these high levels of amino acids are sufficient to drive HLC and HepG2 drug biotransformation and liver-toxin sensitivity to levels similar to those in PHHs. In conclusion, we provide data indicating that extracellular nutrient levels represent a major determinant of cellular maturity and can be utilized to guide stem cell differentiation to the hepatic lineage.

DOI: https://doi.org/10.1038/s41467-020-15058-6
Cell Chem Biol. 2020 Mar 03. pii: S2451-9456(20)30069-6. [Epub ahead of print]

Autophagy-Dependent Ferroptosis: Machinery and Regulation.

Jiao Liu, Feimei Kuang, Guido Kroemer, Daniel J Klionsky, Rui Kang, Daolin Tang.

  Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved cellular process capable of degrading various biological molecules (e.g., protein, glycogen, lipids, DNA, and RNA) and organelles (e.g., mitochondria, endoplasmic reticulum [ER] ribosomes, lysosomes, and micronuclei) via the lysosomal pathway. Ferroptosis is a type of oxidative stress-dependent regulated cell death associated with iron accumulation and lipid peroxidation. The recently discovered role of autophagy, especially selective types of autophagy (e.g., ferritinophagy, lipophagy, clockophagy, and chaperone-mediated autophagy), in driving cells toward ferroptotic death motivated us to explore the functional interactions between metabolism, immunity, and cell death. Here, we describe types of selective autophagy and discuss the regulatory mechanisms and signaling pathways of autophagy-dependent ferroptosis. We also summarize chemical modulators that are currently available for triggering or blocking autophagy-dependent ferroptosis and that may be developed for therapeutic interventions in human diseases.

Keywords:  autophagy; ferroptosis; network; regulated cell death; selective autophagy

DOI:  https://doi.org/10.1016/j.chembiol.2020.02.005