bims-mascan 2021-08-15 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021‒08‒15
27 papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

Metabolic reprogramming of cancer-associated fibroblasts and its effect on cancer cell reprogramming.
Molecular Characterization of Advanced Colorectal Cancer Using Serum Proteomics and Metabolomics.
Prostate Cancer Progression: as a Matter of Fats.
Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions.
A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows.
Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins.
Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution.
Metabolic profiles of human brain parenchyma and glioma for rapid tissue diagnosis by targeted desorption electrospray ionization mass spectrometry.
Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations.
Targeted and Untargeted Mass Spectrometry Reveals the Impact of High-Fat Diet on Peripheral Amino Acid Regulation in a Mouse Model of Alzheimer's Disease.
GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis.
Histone Methylation Connects DNA Repair to Metabolism in Cancer Cells.
Non-alcoholic fatty liver disease Stratification by Liver Lipidomics.
IceR improves proteome coverage and data completeness in global and single-cell proteomics.
Sensitive and quantitative determination of short-chain fatty acids in human serum using liquid chromatography mass spectrometry.
Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters.
Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.
The pathogenesis of mesothelioma is driven by a dysregulated translatome.
Metabolic orchestration of the wound healing response.
Novel MYC-Targeting Drug Is Effective in Mouse Prostate Cancer Models.
Developing a SWATH capillary LC-MS/MS method for simultaneous therapeutic drug monitoring and untargeted metabolomics analysis of neonatal plasma.
A proteomic and phosphoproteomic landscape of KRAS mutant cancers identifies combination therapies.
Proline metabolism in cancer.
Structural Analysis of Lipid Hydroperoxides Using Mass Spectrometry with Alkali Metals.
Histamine signaling and metabolism identify potential biomarkers and therapies for lymphangioleiomyomatosis.
Selective and sensitive UHPLC-ESI-Orbitrap MS method to quantify protein oxidation markers.
Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition.

Theranostics. 2021 ;11(17): 8322-8336

Metabolic reprogramming of cancer-associated fibroblasts and its effect on cancer cell reprogramming.

Zhenzhen Li, Chanjun Sun, Zhihai Qin.

  Cancer cells are well-known for adapting their metabolism to maintain high proliferation rates and survive in unfavorable environments with low oxygen and nutritional deficiency. Metabolic reprogramming most commonly arises from the tumor microenvironment (TME). The events of metabolic pathways include the Warburg effect, shift in Krebs cycle metabolites, and increase rate of oxidative phosphorylation that provides the energy for the development and invasion of cancer cells. The TME and shift in tumor metabolism shows a close relationship through bidirectional signaling pathways between the stromal and tumor cells. Cancer-associated fibroblasts (CAFs) are the main type of stromal cells in the TME and consist of a heterogeneous and plastic population that play key roles in tumor growth and metastatic capacity. Emerging evidence suggests that CAFs act as major regulators in shaping tumor metabolism especially through the dysregulation of several metabolic pathways, including glucose, amino acid, and lipid metabolism. The arrangement of these metabolic switches is believed to shape distinct CAF behavior and change tumor cell behavior by the CAFs. The crosstalk between cancer cells and CAFs is associated with cell metabolic reprogramming that contributes to cancer cell growth, progression, and evasion from cancer therapies. But the mechanism and process of this interaction remain unclear. This review aimed to highlight the metabolic couplings between tumor cells and CAFs. We reviewed the recent literature supporting an important role of CAFs in the regulation of cancer cell metabolism, and the relevant pathways, which may serve as targets for therapeutic interventions.

Keywords:  Cancer; Cancer-associated fibroblasts; Metabolic reprogramming; Tumor microenvironment

DOI:  https://doi.org/10.7150/thno.62378
Front Mol Biosci. 2021 ;8 687229

Molecular Characterization of Advanced Colorectal Cancer Using Serum Proteomics and Metabolomics.

Jun Rao, Xianghui Wan, Fangfang Tou, Qinsi He, Aihua Xiong, Xinyi Chen, Wenhao Cui, Zhi Zheng.

  Colorectal cancer (CRC) is a growing public health concern due to its high mortality rate. Currently, there is a lack of valid diagnostic biomarkers and few therapeutic strategies are available for CRC treatment, especially for advanced CRC whose underlying pathogenic mechanisms remain poorly understood. In the present study, we investigated the serum samples from 20 patients with stage III or IV advanced CRC using data-independent acquisition (DIA)-based proteomics and ultra-performance liquid chromatography coupled to time-of-flight tandem mass spectrometry (UPLC-TOF-MS/MS) metabolomics techniques. Overall, 551 proteins and 719 metabolites were identified. Hierarchical clustering analysis revealed that the serum proteomes of advanced CRC are more diversified than the metabolomes. Ten biochemical pathways associated with cancer cell metabolism were enriched in the detected proteins and metabolites, including glycolysis/gluconeogenesis, biosynthesis of amino acids, glutathione metabolism, and arachidonic acid metabolism, etc. A protein-protein interaction network in advanced CRC serum was constructed with 80 proteins and 21 related metabolites. Correlation analysis revealed conserved roles of lipids and lipid-like molecules in a regulatory network of advanced CRC. Three metabolites (hydroquinone, leucenol and sphingomyelin) and two proteins (coagulation factor XIII A chain and plasma kallikrein) were selected to be potential biomarkers for advanced CRC, which are positively and significantly correlated with CEA and/or CA 19-9. Altogether, the results expanded our understanding of the physiopathology of advanced CRC and discovered novel potential biomarkers for further validation and application to improve the diagnosis and monitoring of advanced CRC.

Keywords:  DIA-MS; UPLC/Q-TOF-MS/MS; biomarker; colorectal cancer; correlation analysis

DOI:  https://doi.org/10.3389/fmolb.2021.687229
Front Oncol. 2021 ;11 719865

Prostate Cancer Progression: as a Matter of Fats.

Natalia Scaglia, Yesica Romina Frontini-López, Giorgia Zadra.

  Advanced prostate cancer (PCa) represents the fifth cause of cancer death worldwide. Although survival has improved with second-generation androgen signaling and Parp inhibitors, the benefits are not long-lasting, and new therapeutic approaches are sorely needed. Lipids and their metabolism have recently reached the spotlight with accumulating evidence for their role as promoters of PCa development, progression, and metastasis. As a result, interest in targeting enzymes/transporters involved in lipid metabolism is rapidly growing. Moreover, the use of lipogenic signatures to predict prognosis and resistance to therapy has been recently explored with promising results. Despite the well-known association between obesity with PCa lethality, the underlying mechanistic role of diet/obesity-derived metabolites has only lately been unveiled. Furthermore, the role of lipids as energy source, building blocks, and signaling molecules in cancer cells has now been revisited and expanded in the context of the tumor microenvironment (TME), which is heavily influenced by the external environment and nutrient availability. Here, we describe how lipids, their enzymes, transporters, and modulators can promote PCa development and progression, and we emphasize the role of lipids in shaping TME. In a therapeutic perspective, we describe the ongoing efforts in targeting lipogenic hubs. Finally, we highlight studies supporting dietary modulation in the adjuvant setting with the purpose of achieving greater efficacy of the standard of care and of synthetic lethality. PCa progression is "a matter of fats", and the more we understand about the role of lipids as key players in this process, the better we can develop approaches to counteract their tumor promoter activity while preserving their beneficial properties.

Keywords:  castration resistance; fatty acids; lipid metabolism; lipidomics; microenvironment; obesity; prostate cancer

DOI:  https://doi.org/10.3389/fonc.2021.719865
Methods Mol Biol. 2021 ;2351 251-274

Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions.

Luciano Nicosia, Tiziana Bonaldi.

  In this chapter, we describe the proteomic approach named "Native Chromatin Proteomics" (N-ChroP) that couples a modified Chromatin ImmunoPrecipitation (ChIP) protocol with the mass spectrometry (MS) analysis of immunoprecipitated proteins to study the combinatorial enrichment or exclusion of histone post-translational modifications (PTMs) at specific genomic regions, such as promoters or enhancers. We describe the protocol steps from the digestion of chromatin and nucleosome immunoprecipitation to histone digestion and peptide enrichment prior to MS analysis, up to the MS raw data analysis. We also discuss current challenges and offer suggestions based on the direct hands-on experience acquired during the method setup.

Keywords:  Chromatin; Chromatin immunoprecipitation; Genomic regions; Histone post-translational modifications; Label-free quantification; Mass spectrometry; Proteomics

DOI:  https://doi.org/10.1007/978-1-0716-1597-3_14
J Proteome Res. 2021 Aug 12.

A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows.

Aivett Bilbao, Bryson C Gibbons, Sarah M Stow, Jennifer E Kyle, Kent J Bloodsworth, Samuel H Payne, Richard D Smith, Yehia M Ibrahim, Erin S Baker, John C Fjeldsted.

  The ability to improve the data quality of ion mobility-mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.

Keywords:  data-independent acquisition; ion mobility spectrometry; lipid annotation; mass spectrometry; preprocessing software; time-of-flight detector saturation

DOI:  https://doi.org/10.1021/acs.jproteome.1c00425
Curr Opin Chem Biol. 2021 Aug 04. pii: S1367-5931(21)00096-X. [Epub ahead of print]

Recent advancements in mass spectrometry-based tools to investigate newly synthesized proteins.

Wouter van Bergen, Albert J R Heck, Marc P Baggelaar.

  Tight regulation of protein translation drives the proteome to undergo changes under influence of extracellular or intracellular signals. Despite mass spectrometry-based proteomics being an excellent method to study differences in protein abundance in complex proteomes, analyzing minute or rapid changes in protein synthesis and abundance remains challenging. Therefore, several dedicated techniques to directly detect and quantify newly synthesized proteins have been developed, notably puromycin-based, bio-orthogonal noncanonical amino acid tagging-based, and stable isotope labeling by amino acids in cell culture-based methods, combined with mass spectrometry. These techniques have enabled the investigation of perturbations, stress, or stimuli on protein synthesis. Improvements of these methods are still necessary to overcome various remaining limitations. Recent improvements include enhanced enrichment approaches and combinations with various stable isotope labeling techniques, which allow for more accurate analysis and comparison between conditions on shorter timeframes and in more challenging systems. Here, we aim to review the current state in this field.

Keywords:  Bio-orthogonal noncanonical amino acid tagging (BONCAT); Mass spectrometry; Newly synthesized proteins; Protein dynamics; Protein synthesis; Proteomics; Puromycin; Stable isotope labeling by amino acids in cell culture (SILAC)

DOI:  https://doi.org/10.1016/j.cbpa.2021.07.001
J Am Soc Mass Spectrom. 2021 Aug 10.

Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution.

Michael J Taylor, Andrey Liyu, Akos Vertes, Christopher R Anderton.

  Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging method that has the potential to transform the field of metabolomics. This is in part due to LAESI-MS being an ambient ionization method that requires minimal sample preparation and uses (endogenous) water for in situ analysis. This application note details the employment of the "LAESI microscope" source to perform spatially resolved MS analysis of cells and MS imaging (MSI) of tissues at high spatial resolution. This source configuration utilizes a long-working-distance reflective objective that permits both visualization of the sample and a smaller LAESI laser beam profile than conventional LAESI setups. Here, we analyzed 200 single cells of Allium cepa (red onion) and imaged Fittonia argyroneura (nerve plant) in high spatial resolution using this source coupled to a Fourier transform mass spectrometer for high-mass-resolution and high-mass-accuracy metabolomics.

Keywords:  LAESI; mass spectrometry imaging; metabolomics; native analysis; spatial metabolomics

DOI:  https://doi.org/10.1021/jasms.1c00149
Anal Bioanal Chem. 2021 Aug 09.

Metabolic profiles of human brain parenchyma and glioma for rapid tissue diagnosis by targeted desorption electrospray ionization mass spectrometry.

Rong Chen, Hannah Marie Brown, R Graham Cooks.

  Desorption electrospray ionization mass spectrometry (DESI-MS) is well suited for intraoperative tissue analysis since it requires little sample preparation and offers rapid and sensitive molecular diagnostics. Currently, intraoperative assessment of the tumor cell percentage of glioma biopsies can be made by measuring a single metabolite, N-acetylaspartate (NAA). The inclusion of additional biomarkers will likely improve the accuracy when distinguishing brain parenchyma from glioma by DESI-MS. To explore this possibility, mass spectra were recorded for extracts from 32 unmodified human brain samples with known pathology. Statistical analysis of data obtained from full-scan and multiple reaction monitoring (MRM) profiles identified discriminatory metabolites, namely gamma-aminobutyric acid (GABA), creatine, glutamic acid, carnitine, and hexane-1,2,3,4,5,6-hexol (abbreviated as hexol), as well as the established biomarker NAA. Brain parenchyma was readily differentiated from glioma based on these metabolites as measured both in full-scan mass spectra and by the intensities of their characteristic MRM transitions. New DESI-MS methods (5 min acquisition using full scans and MS/MS), developed to measure ion abundance ratios among these metabolites, were tested using smears of 29 brain samples. Ion abundance ratios based on signals for GABA, creatine, carnitine, and hexol all had sensitivities > 90%, specificities > 80%, and accuracies > 85%. Prospectively, the implementation of diagnostic ion abundance ratios should strengthen the discriminatory power of individual biomarkers and enhance method robustness against signal fluctuations, resulting in an improved DESI-MS method of glioma diagnosis.

Keywords:  Ambient ionization; Biomarker; Glioma; Metabolomics; Multiple reaction monitoring; Tandem mass spectrometry

DOI:  https://doi.org/10.1007/s00216-021-03593-0
Anal Chem. 2021 Aug 10.

Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations.

Premy Shanthamoorthy, Adamo Young, Hannes Röst.

Targeted, untargeted, and data-independent acquisition (DIA) metabolomics workflows are often hampered by ambiguous identification based on either MS1 information alone or relatively few MS2 fragment ions. While DIA methods have been popularized in proteomics, it is less clear whether they are suitable for metabolomics workflows due to their large precursor isolation windows and complex coisolation patterns. Here, we quantitatively investigate the conditions necessary for unique metabolite detection in complex backgrounds using precursor and fragment ion mass-to-charge (m/z) separation, comparing three benchmarked mass spectrometry (MS) methods [MS1, MRM (multiple reaction monitoring), and DIA]. Our simulations show that DIA outperformed MS1-only and MRM-based methods with regards to specificity by factors of ∼2.8-fold and ∼1.8-fold, respectively. Additionally, we show that our results are not dependent on the number of transitions used or the complexity of the background matrix. Finally, we show that collision energy is an important factor in unambiguous detection and that a single collision energy setting per compound cannot achieve optimal pairwise differentiation of compounds. Our analysis demonstrates the power of using both high-resolution precursor and high-resolution fragment ion m/z for unambiguous compound detection. This work also establishes DIA as an emerging MS acquisition method with high selectivity for metabolomics, outperforming both data-dependent acquisition (DDA) and MRM with regards to unique compound identification potential.

DOI: https://doi.org/10.1021/acs.analchem.1c01204
J Proteome Res. 2021 Aug 12.

Targeted and Untargeted Mass Spectrometry Reveals the Impact of High-Fat Diet on Peripheral Amino Acid Regulation in a Mouse Model of Alzheimer's Disease.

Amelia L Taylor, Don E Davis, Simona G Codreanu, Fiona E Harrison, Stacy D Sherrod, John A McLean.

  Recent research regarding amino acid metabolism has shown that there may be a link between obesity and Alzheimer's disease (AD). This work reports a metabolomics study using targeted and untargeted mass spectrometry-based metabolomic strategies to investigate this link. Targeted hydrophilic interaction liquid chromatography-triple quadrupole mass spectrometry and untargeted reversed-phase liquid chromatography-high resolution tandem mass spectrometry assays were developed to analyze the metabolic changes that occur in AD and obesity. APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice (to represent familial or early-onset AD) and wild-type littermate controls were fed either a high-fat diet (HFD, 60% kcal from lard) or a low-fat diet (LFD, 10% kcal from lard) from 2 months of age or a reversal diet (HFD, followed by LFD from 9.5 months). For targeted analyses, we applied the guidelines outlined in the Clinical and Laboratory Standards Institute (CLSI) LC-MS C62-A document and the U.S. Food and Drug Administration (FDA) bioanalytical method validation guidance for industry to evaluate the figures of merit of the assays. Our targeted and untargeted metabolomics results suggest that numerous peripheral pathways, specifically amino acid metabolism and fatty acid metabolism, were significantly affected by AD and diet. Multiple amino acids (including alanine, glutamic acid, leucine, isoleucine, and phenylalanine), carnitines, and members of the fatty acid oxidation pathway were significantly increased in APP/PSEN1 mice on HFD compared to those on LFD. More substantial effects and changes were observed in the APP/PSEN1 mice than in the WT mice, suggesting that they were more sensitive to an HFD. These dysregulated peripheral pathways include numerous amino acid pathways and fatty acid beta oxidation and suggest that obesity combined with AD further enhances cognitive impairment, possibly through aggravated mitochondrial dysfunction. Furthermore, partial reversibility of many altered pathways was observed, which highlights that diet change can mitigate the metabolic effects of AD. The same trends in individual amino acids were observed in both strategies, highlighting the biological validity of the results.

Keywords:  Alzheimer’s disease; amino acid metabolism; high-fat diet; low-fat diet; mass spectrometry; metabolomics; mitochondrial dysfunction; reversal diet

DOI:  https://doi.org/10.1021/acs.jproteome.1c00344
Nat Commun. 2021 08 11. 12(1): 4860

GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis.

Daniel M Kremer, Barbara S Nelson, Lin Lin, Emily L Yarosz, Christopher J Halbrook, Samuel A Kerk, Peter Sajjakulnukit, Amy Myers, Galloway Thurston, Sean W Hou, Eileen S Carpenter, Anthony C Andren, Zeribe C Nwosu, Nicholas Cusmano, Stephanie Wisner, Nneka E Mbah, Mengrou Shan, Nupur K Das, Brian Magnuson, Andrew C Little, Milan R Savani, Johanna Ramos, Tina Gao, Stephen A Sastra, Carmine F Palermo, Michael A Badgley, Li Zhang, John M Asara, Samuel K McBrayer, Marina Pasca di Magliano, Howard C Crawford, Yatrik M Shah, Kenneth P Olive, Costas A Lyssiotis.

Cancer metabolism is rewired to support cell survival in response to intrinsic and environmental stressors. Identification of strategies to target these adaptions is an area of active research. We previously described a cytosolic aspartate aminotransaminase (GOT1)-driven pathway in pancreatic cancer used to maintain redox balance. Here, we sought to identify metabolic dependencies following GOT1 inhibition to exploit this feature of pancreatic cancer and to provide additional insight into regulation of redox metabolism. Using pharmacological methods, we identify cysteine, glutathione, and lipid antioxidant function as metabolic vulnerabilities following GOT1 withdrawal. We demonstrate that targeting any of these pathways triggers ferroptosis, an oxidative, iron-dependent form of cell death, in GOT1 knockdown cells. Mechanistically, we reveal that GOT1 inhibition represses mitochondrial metabolism and promotes a catabolic state. Consequently, we find that this enhances labile iron availability through autophagy, which potentiates the activity of ferroptotic stimuli. Overall, our study identifies a biochemical connection between GOT1, iron regulation, and ferroptosis.

DOI: https://doi.org/10.1038/s41467-021-24859-2
Cancer Discov. 2020 Aug;10(8): OF7

Histone Methylation Connects DNA Repair to Metabolism in Cancer Cells.

Metabolites produced in cancer cells interfered with resolution of DNA double-strand breaks.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2020-089
J Lipid Res. 2021 Aug 09. pii: S0022-2275(21)00086-9. [Epub ahead of print] 100104

Non-alcoholic fatty liver disease Stratification by Liver Lipidomics.

Olga Vvedenskaya, Tim Daniel Rose, Oskar Knittelfelder, Alessandra Palladini, Judith Andrea Heidrun Wodke, Kai Schumann, Jacobo Miranda Ackerman, Yuting Wang, Canan Has, Mario Brosch, Veera Raghavan Thangapandi, Stephan Buch, Thomas Züllig, Jürgen Hartler, Harald C Köfeler, Christoph Röcken, Ünal Coskun, Edda Klipp, Witigo von Schoenfels, Justus Gross, Clemens Schafmayer, Jochen Hampe, Josch Konstantin Pauling, Andrej Shevchenko.

  Non-alcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including non-steatotic patients with normal or excessive weight, patients diagnosed with NAFL (non-alcoholic fatty liver) or NASH (non-alcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and tri- acylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of non-steatoic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.

Keywords:  NAFL; NAFLD; NASH; biclustering analysis; lipid biomarkers; liver biopsies; liver lipidome; shotgun lipidomics; sphingomyelins; steatosis

DOI:  https://doi.org/10.1016/j.jlr.2021.100104
Nat Commun. 2021 08 09. 12(1): 4787

IceR improves proteome coverage and data completeness in global and single-cell proteomics.

Mathias Kalxdorf, Torsten Müller, Oliver Stegle, Jeroen Krijgsveld.

Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly quantification workflow that combines high identification rates of data-dependent acquisition with low missing value rates similar to data-independent acquisition. Specifically, IceR uses ion current information for a hybrid peptide identification propagation approach with superior quantification precision, accuracy, reliability and data completeness compared to other quantitative workflows. Applied to plasma and single-cell proteomics data, IceR enhanced the number of reliably quantified proteins, improved discriminability between single-cell populations, and allowed reconstruction of a developmental trajectory. IceR will be useful to improve performance of large scale global as well as low-input proteomics applications, facilitated by its availability as an easy-to-use R-package.

DOI: https://doi.org/10.1038/s41467-021-25077-6
Anal Bioanal Chem. 2021 Aug 11.

Sensitive and quantitative determination of short-chain fatty acids in human serum using liquid chromatography mass spectrometry.

Armaghan Shafaei, Veronica Vamathevan, Jessica Pandohee, Nathan G Lawler, David Broadhurst, Mary C Boyce.

  Short-chain fatty acids (SCFAs) are increasingly being monitored to elucidate the link between gut health and disease. These metabolites are routinely measured in faeces, but their determination in serum is more challenging due to their low concentrations. A method for the determination of eight SCFAs in serum is described here. High-resolution mass spectrometry and gas chromatography were used to identify the presence of isomeric interferences, which were then overcome through a combination of chromatographic separation and judicious choice of MS fragment ion. The SCFAs were derivatised to form 3-nitrophenylhydrazones before being separated on a reversed-phase column and then detected using liquid chromatography tandem mass spectrometry (LC-QQQ-MS). The LODs and LOQs of SCFAs using this method were in the range 1 to 7 ng mL-1 and 3 to 19 ng mL-1, respectively. The recovery of the SCFAs in serum ranged from 94 to 114% over the three concentration ranges tested.

Keywords:  High-resolution mass spectrometry; LC-MS/MS; SCFA; Serum

DOI:  https://doi.org/10.1007/s00216-021-03589-w
Nat Commun. 2021 08 12. 12(1): 4905

Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate esters.

Seth J Parker, Joel Encarnación-Rosado, Kate E R Hollinshead, David M Hollinshead, Leonard J Ash, Juan A K Rossi, Elaine Y Lin, Albert S W Sohn, Mark R Philips, Drew R Jones, Alec C Kimmelman.

α-ketoglutarate (KG), also referred to as 2-oxoglutarate, is a key intermediate of cellular metabolism with pleiotropic functions. Cell-permeable esterified analogs are widely used to study how KG fuels bioenergetic and amino acid metabolism and DNA, RNA, and protein hydroxylation reactions, as cellular membranes are thought to be impermeable to KG. Here we show that esterified KG analogs rapidly hydrolyze in aqueous media, yielding KG that, in contrast to prevailing assumptions, imports into many cell lines. Esterified KG analogs exhibit spurious KG-independent effects on cellular metabolism, including extracellular acidification, arising from rapid hydrolysis and de-protonation of α-ketoesters, and significant analog-specific inhibitory effects on glycolysis or mitochondrial respiration. We observe that imported KG decarboxylates to succinate in the cytosol and contributes minimally to mitochondrial metabolism in many cell lines cultured in normal conditions. These findings demonstrate that nuclear and cytosolic KG-dependent reactions may derive KG from functionally distinct subcellular pools and sources.

DOI: https://doi.org/10.1038/s41467-021-25228-9
Nat Commun. 2021 08 10. 12(1): 4814

Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.

Clément Bodineau, Mercedes Tomé, Sarah Courtois, Ana S H Costa, Marco Sciacovelli, Benoit Rousseau, Elodie Richard, Pierre Vacher, Carlos Parejo-Pérez, Emilie Bessede, Christine Varon, Pierre Soubeyran, Christian Frezza, Piedad Del Socorro Murdoch, Victor H Villar, Raúl V Durán.

Glutamoptosis is the induction of apoptotic cell death as a consequence of the aberrant activation of glutaminolysis and mTORC1 signaling during nutritional imbalance in proliferating cells. The role of the bioenergetic sensor AMPK during glutamoptosis is not defined yet. Here, we show that AMPK reactivation blocks both the glutamine-dependent activation of mTORC1 and glutamoptosis in vitro and in vivo. We also show that glutamine is used for asparagine synthesis and the GABA shunt to produce ATP and to inhibit AMPK, independently of glutaminolysis. Overall, our results indicate that glutamine metabolism is connected with mTORC1 activation through two parallel pathways: an acute alpha-ketoglutarate-dependent pathway; and a secondary ATP/AMPK-dependent pathway. This dual metabolic connection between glutamine and mTORC1 must be considered for the future design of therapeutic strategies to prevent cell growth in diseases such as cancer.

DOI: https://doi.org/10.1038/s41467-021-25079-4
Nat Commun. 2021 Aug 13. 12(1): 4920

The pathogenesis of mesothelioma is driven by a dysregulated translatome.

Stefano Grosso, Alberto Marini, Katarina Gyuraszova, Johan Vande Voorde, Aristeidis Sfakianos, Gavin D Garland, Angela Rubio Tenor, Ryan Mordue, Tanya Chernova, Nobu Morone, Marco Sereno, Claire P Smith, Leah Officer, Pooyeh Farahmand, Claire Rooney, David Sumpton, Madhumita Das, Ana Teodósio, Catherine Ficken, Maria Guerra Martin, Ruth V Spriggs, Xiao-Ming Sun, Martin Bushell, Owen J Sansom, Daniel Murphy, Marion MacFarlane, John P C Le Quesne, Anne E Willis.

Malignant mesothelioma (MpM) is an aggressive, invariably fatal tumour that is causally linked with asbestos exposure. The disease primarily results from loss of tumour suppressor gene function and there are no 'druggable' driver oncogenes associated with MpM. To identify opportunities for management of this disease we have carried out polysome profiling to define the MpM translatome. We show that in MpM there is a selective increase in the translation of mRNAs encoding proteins required for ribosome assembly and mitochondrial biogenesis. This results in an enhanced rate of mRNA translation, abnormal mitochondrial morphology and oxygen consumption, and a reprogramming of metabolic outputs. These alterations delimit the cellular capacity for protein biosynthesis, accelerate growth and drive disease progression. Importantly, we show that inhibition of mRNA translation, particularly through combined pharmacological targeting of mTORC1 and 2, reverses these changes and inhibits malignant cell growth in vitro and in ex-vivo tumour tissue from patients with end-stage disease. Critically, we show that these pharmacological interventions prolong survival in animal models of asbestos-induced mesothelioma, providing the basis for a targeted, viable therapeutic option for patients with this incurable disease.

DOI: https://doi.org/10.1038/s41467-021-25173-7
Cell Metab. 2021 Aug 09. pii: S1550-4131(21)00362-4. [Epub ahead of print]

Metabolic orchestration of the wound healing response.

Sabine A Eming, Peter J Murray, Edward J Pearce.

Wound healing requires cooperation between different cell types, among which macrophages play a central role. In particular, inflammatory macrophages are engaged in the initial response to wounding, and alternatively activated macrophages are essential for wound closure and the resolution of tissue repair. The links between temporal activation-induced changes in the metabolism of such macrophages and the influence this has on their functional states, along with the realization that metabolites play both intrinsic and extrinsic roles in the cells that produce them, has focused attention on the metabolism of wound healing. Here, we discuss macrophage metabolism during distinct stages of normal healing and its related pathologic processes, such as during cancer and fibrosis. Further, we frame these insights in a broader context of the current understanding of macrophage metabolic reprogramming linked to cellular activation and function. Finally, we discuss parallels between the metabolism of macrophages and fibroblasts, the latter being a key stromal cell type in wound healing, and consider the importance of the metabolic interplay between different cell types in the wound microenvironment.

DOI: https://doi.org/10.1016/j.cmet.2021.07.017
Cancer Discov. 2020 Jan;10(1): 15

Novel MYC-Targeting Drug Is Effective in Mouse Prostate Cancer Models.

A new MYC inhibitor reduced tumor growth in mouse prostate cancer models.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2019-167
J Chromatogr B Analyt Technol Biomed Life Sci. 2021 Jul 27. pii: S1570-0232(21)00346-9. [Epub ahead of print]1179 122865

Developing a SWATH capillary LC-MS/MS method for simultaneous therapeutic drug monitoring and untargeted metabolomics analysis of neonatal plasma.

Jingcheng Xiao, Jian Shi, Ruiting Li, Lucy Her, Xinwen Wang, Jiapeng Li, Matthew J Sorensen, Varsha Bhatt-Mehta, Hao-Jie Zhu.

  Most medications prescribed to neonatal patients are off-label uses. The pharmacokinetics and pharmacodynamics of drugs differ significantly between neonates and adults. Therefore, personalized pharmacotherapy guided by therapeutic drug monitoring (TDM) and drug response biomarkers are particularly beneficial to neonatal patients. Herein, we developed a capillary LC-MS/MS metabolomics method using a SWATH-based data-independent acquisition strategy for simultaneous targeted and untargeted metabolomics analysis of neonatal plasma samples. We applied the method to determine the global plasma metabolomics profiles and quantify the plasma concentrations of five drugs commonly used in neonatal intensive care units, including ampicillin, caffeine, fluconazole, vancomycin, and midazolam and its active metabolite α-hydroxymidazolam, in neonatal patients. The method was successfully validated and found to be suitable for the TDM of the drugs of interest. Moreover, the global metabolomics analysis revealed plasma metabolite features that could differentiate preterm and full-term neonates. This study demonstrated that the SWATH-based capillary LC-MS/MS metabolomics approach could be a powerful tool for simultaneous TDM and the discovery of neonatal plasma metabolite biomarkers.

Keywords:  Data-independent acquisition; SWATH; Therapeutic drug monitoring; Untargeted metabolomics

DOI:  https://doi.org/10.1016/j.jchromb.2021.122865
Mol Cell. 2021 Jul 30. pii: S1097-2765(21)00590-6. [Epub ahead of print]

A proteomic and phosphoproteomic landscape of KRAS mutant cancers identifies combination therapies.

Zhiwei Liu, Yingluo Liu, Lili Qian, Shangwen Jiang, Xiameng Gai, Shu Ye, Yuehong Chen, Xiaomin Wang, Linhui Zhai, Jun Xu, Congying Pu, Jing Li, Fuchu He, Min Huang, Minjia Tan.

  KRAS mutant cancer, characterized by the activation of a plethora of phosphorylation signaling pathways, remains a major challenge for cancer therapy. Despite recent advancements, a comprehensive profile of the proteome and phosphoproteome is lacking. This study provides a proteomic and phosphoproteomic landscape of 43 KRAS mutant cancer cell lines across different tissue origins. By integrating transcriptomics, proteomics, and phosphoproteomics, we identify three subsets with distinct biological, clinical, and therapeutic characteristics. The integrative analysis of phosphoproteome and drug sensitivity information facilitates the identification of a set of drug combinations with therapeutic potentials. Among them, we demonstrate that the combination of DOT1L and SHP2 inhibitors is an effective treatment specific for subset 2 of KRAS mutant cancers, corresponding to a set of TCGA clinical tumors with the poorest prognosis. Together, this study provides a resource to better understand KRAS mutant cancer heterogeneity and identify new therapeutic possibilities.

Keywords:  DOT1L; KRAS mutation; SHP2; cancer; drug sensitivity; heterogeneity; phosphoproteomics; proteomics; subtype; therapy

DOI:  https://doi.org/10.1016/j.molcel.2021.07.021
Amino Acids. 2021 Aug 14.

Proline metabolism in cancer.

Pengyu Geng, Wangshu Qin, Guowang Xu.

  Cancer cells often change their metabolism to support uncontrolled proliferation. Proline is the only proteogenic secondary amino acid that is abundant in the body. Recent studies have shown that proline metabolism plays an important role in metabolic reprogramming and affects the occurrence and development of cancer. Proline metabolism is related to ATP production, protein and nucleotide synthesis, and redox homeostasis in tumor cells. Proline can be synthesized by aldehyde dehydrogenase family 18 member A1 (ALDH18A1) and delta1-pyrroline-5-carboxylate reductase (PYCR), up-regulating ALDH18A1 and PYCR can promote the proliferation and invasion of cancer cells. As the main storage of proline, collagen can influence cancer cells proliferation, invasion, and metastasis. Its synthesis depends on the hydroxylation of proline catalyzed by prolyl 4-hydroxylases (P4Hs), which will affect the plasticity and metastasis of cancer cells. The degradation of proline occurs in the mitochondria and involves an oxidation step catalyzed by proline dehydrogenase/proline oxidase (PRODH/POX). Proline catabolism has a dual role in cancer, linking apoptosis with the survival and metastasis of cancer cells. In addition, it has been demonstrated that the regulation of proline metabolic enzymes at the genetic and post-translational levels is related to cancer. This article reviews the role of proline metabolic enzymes in cancer proliferation, apoptosis, metastasis, and development. Research on proline metabolism may provide a new strategy for cancer treatment.

Keywords:  ALDH18A1; Cancer; P4Hs; PRODH/POX; PYCR; Proline metabolism

DOI:  https://doi.org/10.1007/s00726-021-03060-1
J Am Soc Mass Spectrom. 2021 Aug 12.

Structural Analysis of Lipid Hydroperoxides Using Mass Spectrometry with Alkali Metals.

Shunji Kato, Naoki Shimizu, Yusuke Ogura, Yurika Otoki, Junya Ito, Masayoshi Sakaino, Takashi Sano, Shigefumi Kuwahara, Susumu Takekoshi, Jun Imagi, Kiyotaka Nakagawa.

  Lipid oxidation is involved in various biological phenomena (e.g., oxylipin generation and oxidative stress). Of oxidized lipid structures, the hydroperoxyl group position of lipid hydroperoxides (LOOHs) is a critical factor in determining their biological roles. Despite such interest, current methods to determine hydroperoxyl group positions possess some drawbacks such as selectivity. While we previously reported mass spectrometric methods using Na+ for the highly selective determination of hydroperoxyl group positions, nothing was known except for the fact that sodiated LOOHs (mainly linoleate) provide specific fragment ions. Thus, this study was aimed to investigate the effects of different alkali metals on the fragmentation of LOOHs, assuming its further application to analysis of other complex LOOHs. From the analysis of PC 16:0/18:2;OOH (phosphatidylcholine) and FA 18:2;OOH (fatty acid), we found that fragmentation pathways and ion intensities largely depend on the binding position and type of alkali metals (i.e., Li+, Hock fragmentation; Na+ and K+, α-cleavage (Na+ > K+); Rb+ and Cs+, no fragmentation). Furthermore, we proved that this method can be applied to determine the hydroperoxyl group position of esterified lipids (e.g., phospholipids and cholesterol esters) as well as polyunsaturated fatty acids (PUFAs) including n-3, n-6, and n-9 FA. We anticipate that the insights described in this study provide additional unique insights to conventional lipid oxidation research.

Keywords:  alkali metals; hydroperoxide isomers; lipid hydroperoxides; mass spectrometry; oxidative stress

DOI:  https://doi.org/10.1021/jasms.1c00039
EMBO Mol Med. 2021 Aug 11. e13929

Histamine signaling and metabolism identify potential biomarkers and therapies for lymphangioleiomyomatosis.

Carmen Herranz, Francesca Mateo, Alexandra Baiges, Gorka Ruiz de Garibay, Alexandra Junza, Simon R Johnson, Suzanne Miller, Nadia García, Jordi Capellades, Antonio Gómez, August Vidal, Luis Palomero, Roderic Espín, Ana I Extremera, Eline Blommaert, Eva Revilla-López, Berta Saez, Susana Gómez-Ollés, Julio Ancochea, Claudia Valenzuela, Tamara Alonso, Piedad Ussetti, Rosalía Laporta, Antoni Xaubet, José A Rodríguez-Portal, Ana Montes-Worboys, Carlos Machahua, Jaume Bordas, Javier A Menendez, Josep M Cruzado, Roser Guiteras, Christophe Bontoux, Concettina La Motta, Aleix Noguera-Castells, Mario Mancino, Enrique Lastra, Raúl Rigo-Bonnin, Jose C Perales, Francesc Viñals, Alvaro Lahiguera, Xiaohu Zhang, Daniel Cuadras, Coline H M van Moorsel, Joanne J van der Vis, Marian J R Quanjel, Harilaos Filippakis, Razq Hakem, Chiara Gorrini, Marc Ferrer, Aslihan Ugun-Klusek, Ellen Billett, Elżbieta Radzikowska, Álvaro Casanova, María Molina-Molina, Antonio Roman, Oscar Yanes, Miquel A Pujana.

  Inhibition of mTOR is the standard of care for lymphangioleiomyomatosis (LAM). However, this therapy has variable tolerability and some patients show progressive decline of lung function despite treatment. LAM diagnosis and monitoring can also be challenging due to the heterogeneity of symptoms and insufficiency of non-invasive tests. Here, we propose monoamine-derived biomarkers that provide preclinical evidence for novel therapeutic approaches. The major histamine-derived metabolite methylimidazoleacetic acid (MIAA) is relatively more abundant in LAM plasma, and MIAA values are independent of VEGF-D. Higher levels of histamine are associated with poorer lung function and greater disease burden. Molecular and cellular analyses, and metabolic profiling confirmed active histamine signaling and metabolism. LAM tumorigenesis is reduced using approved drugs targeting monoamine oxidases A/B (clorgyline and rasagiline) or histamine H1 receptor (loratadine), and loratadine synergizes with rapamycin. Depletion of Maoa or Hrh1 expression, and administration of an L-histidine analog, or a low L-histidine diet, also reduce LAM tumorigenesis. These findings extend our knowledge of LAM biology and suggest possible ways of improving disease management.

Keywords:  biomarker; histamine; lymphangioleiomyomatosis; mTOR; therapy

DOI:  https://doi.org/10.15252/emmm.202113929
Talanta. 2021 Nov 01. pii: S0039-9140(21)00621-4. [Epub ahead of print]234 122700

Selective and sensitive UHPLC-ESI-Orbitrap MS method to quantify protein oxidation markers.

Mahesha M Poojary, Brijesh K Tiwari, Marianne N Lund.

  A targeted UHPLC-MS/MS isotopic dilution method has been developed for the simultaneous quantification of 18 different free and protein-bound aromatic amino acid oxidation products in food and biological matrices. All analytes, including critical isomeric pairs of Tyr, o-Tyr, m-Tyr, and dioxyindolylalanine diastereomers were chromatographically resolved to obtain high selectivity, without the need for derivatizing or ion pairing agents. The results of method validation showed adequate retention time reproducibility [0.1-0.6% coefficient of variation (CV) for over 224 injections], accuracy (within ±1-20% of the nominal concentration), and precision (1-17% CV) for all target analytes. The lower limit of quantification was calculated in different matrices using both the Hubaux-Vos approach and accuracy and precision data showing values in the range of 0.2-15 ng/mL. Use of stable isotope-labelled internal standards compensated errors due to matrix effects and artefactual degradation of analytes. Both acid and enzymatic hydrolyses were tested to obtain the best possible results for the quantification of protein oxidation products, demonstrating the stability of target analytes under hydrolytic conditions. The method was successfully applied to quantify target analytes in serum, tissue, milk, infant formula, pork liver pâté, chicken meat and fish. The method was also applied to assess the role of Fenton's reagent in oxidizing Trp, Phe and Tyr residues in different proteins, with results showing o-Tyr, dioxyindolylalanine diastereomers, kynurenine, dityrosine being the main oxidation products. The Fenton chemistry favored the formation of o-Tyr over m-Tyr from Phe with 2-36 folds higher yields. 3-Nitrotyrosine, a marker of protein nitration, was also detected in samples treated with Fenton's reagent.

Keywords:  Analytical method validation; Protein hydrolysis; Protein nitration; Protein oxidation; Reactive oxygen species; Tryptophan metabolism

DOI:  https://doi.org/10.1016/j.talanta.2021.122700
Science. 2021 08 13. 373(6556): 760-767

Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition.

Karol Nowicki-Osuch, Lizhe Zhuang, Sriganesh Jammula, Christopher W Bleaney, Krishnaa T Mahbubani, Ginny Devonshire, Annalise Katz-Summercorn, Nils Eling, Anna Wilbrey-Clark, Elo Madissoon, John Gamble, Massimiliano Di Pietro, Maria O'Donovan, Kerstin B Meyer, Kourosh Saeb-Parsy, Andrew D Sharrocks, Sarah A Teichmann, John C Marioni, Rebecca C Fitzgerald.

The origin of human metaplastic states and their propensity for cancer is poorly understood. Barrett's esophagus is a common metaplastic condition that increases the risk for esophageal adenocarcinoma, and its cellular origin is enigmatic. To address this, we harvested tissues spanning the gastroesophageal junction from healthy and diseased donors, including isolation of esophageal submucosal glands. A combination of single-cell transcriptomic profiling, in silico lineage tracing from methylation, open chromatin and somatic mutation analyses, and functional studies in organoid models showed that Barrett's esophagus originates from gastric cardia through c-MYC and HNF4A-driven transcriptional programs. Furthermore, our data indicate that esophageal adenocarcinoma likely arises from undifferentiated Barrett's esophagus cell types even in the absence of a pathologically identifiable metaplastic precursor, illuminating early detection strategies.

DOI: https://doi.org/10.1126/science.abd1449