bims-mascan 2023-06-11 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2023–06–11
27 papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data.
MetaPro: a web-based metabolomics application for LC-MS data batch inspection and library curation.
Fast proteomics with dia-PASEF and analytical flow-rate chromatography.
Strategies for consistent and automated quantification of HDL proteome using data-independent acquisition (DIA).
Crosstalk between arginine, glutamine, and the branched chain amino acid metabolism in the tumor microenvironment.
Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer.
Precision fermentation with mass spectrometry-based spent media analysis.
Proteome-Derived Peptide Libraries for Deep Specificity Profiling of N-terminal Modification Reagents.
Amino Acid Metabolism in Bone Metastatic Disease.
Analysis of triacylglycerol and phospholipid sn-positional isomers by liquid chromatographic and mass spectrometric methodologies.
Identification of predictive biomarkers for diagnosis and radiation sensitivity of uterine cervical cancer using wide-targeted metabolomics.
Arginine deprivation as a treatment approach targeting cancer cell metabolism and survival: A review of the literature.
Lipid metabolism in idiopathic pulmonary fibrosis: From pathogenesis to therapy.
Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.
Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots.
High-throughput quantification of microbial-derived organic acids in mucin-rich samples via reverse phase high performance liquid chromatography.
Targeting the dynamics of cancer metabolism in the era of precision oncology.
Editorial: Energy metabolism within the skeleton.
Exosomes-regulated lipid metabolism in tumorigenesis and cancer progression.
PaSTe. Blockade of the Lipid Phenotype of Prostate Cancer as Metabolic Therapy: A Theoretical Proposal.
Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking.
Validation of an LC-MS/MS method for simultaneous quantification of abiraterone, enzalutamide and darolutamide in human plasma.
The Tumor Suppressor CDKN2A Remodels the Lipidome of Glioblastoma.
Reprogramming Initiator and Nonsense Codons to Simultaneously Install Three Distinct Noncanonical Amino Acids into Proteins in E. coli.
Targeted metabolomic analysis in Parkinson's disease brain frontal cortex and putamen with relation to cognitive impairment.
Tissue and plasma free amino acid detection by LC-MS/MS method in high grade glioma patients.
Understanding glycosylation: Regulation through the metabolic flux of precursor pathways.

Biophys Rep. 2022 Dec 31. 8(5-6): 253-268

DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data.

Junjie Hou, Jifeng Wang, Fuquan Yang, Tao Xu.

  Identifying peptides directly from data-independent acquisition (DIA) data remains challenging due to the highly multiplexed MS/MS spectra. Spectral library-based peptide detection is sensitive, but it is limited to the depth of the library and mutes the discovery potential of DIA data. We present here, DIA-MS2pep, a library-free framework for comprehensive peptide identification from DIA data. DIA-MS2pep uses a data-driven algorithm for MS/MS spectrum demultiplexing using the fragments data without the need of a precursor. With a large precursor mass tolerance database search, DIA-MS2pep can identify the peptides and their modified forms. We demonstrate the performance of DIA-MS2pep by comparing it to conventional library-free tools in accuracy and sensitivity of peptide identifications using publicly available DIA datasets of varying samples, including HeLa cell lysates, phosphopeptides, plasma, etc. Compared with data-dependent acquisition-based spectral libraries, spectral libraries built directly from DIA data with DIA-MS2pep improve the accuracy and reproducibility of the quantitative proteome.

Keywords:  DIA-MS; Large precursor mass tolerance; Mass spectrometry; Spectral library-free; Spectrum demultiplexing

DOI:  https://doi.org/10.52601/bpr.2022.220011
Metabolomics. 2023 Jun 08. 19(6): 57

MetaPro: a web-based metabolomics application for LC-MS data batch inspection and library curation.

Shaowei An, Ruimin Wang, Miaoshan Lu, Chao Zhang, Huafen Liu, Jinyin Wang, Cong Xie, Changbin Yu.

   INTRODUCTION: Metabolomics analysis based on liquid chromatography-mass spectrometry (LC-MS) has been a prevalent method in the metabolic field. However, accurately quantifying all the metabolites in large metabolomics sample cohorts is challenging. The analysis efficiency is restricted by the abilities of software in many labs, and the lack of spectra for some metabolites also hinders metabolite identification.
OBJECTIVES: Develop software that performs semi-targeted metabolomics analysis with an optimized workflow to improve quantification accuracy. The software also supports web-based technologies and increases laboratory analysis efficiency. A spectral curation function is provided to promote the prosperity of homemade MS/MS spectral libraries in the metabolomics community.
METHODS: MetaPro is developed based on an industrial-grade web framework and a computation-oriented MS data format to improve analysis efficiency. Algorithms from mainstream metabolomics software are integrated and optimized for more accurate quantification results. A semi-targeted analysis workflow is designed based on the concept of combining artificial judgment and algorithm inference.
RESULTS: MetaPro supports semi-targeted analysis workflow and functions for fast QC inspection and self-made spectral library curation with easy-to-use interfaces. With curated authentic or high-quality spectra, it can improve identification accuracy using different peak identification strategies. It demonstrates practical value in analyzing large amounts of metabolomics samples.
CONCLUSION: We offer MetaPro as a web-based application characterized by fast batch QC inspection and credible spectral curation towards high-throughput metabolomics data. It aims to resolve the analysis difficulty in semi-targeted metabolomics.

Keywords:  Database; Mass spectrometry; Metabolite identification; Metabolomics; Quality assurance; Quality control; Software; Spectral library; Web-based; Workflow

DOI:  https://doi.org/10.1007/s11306-023-02018-6
Proteomics. 2023 Jun 07. e2300100

Fast proteomics with dia-PASEF and analytical flow-rate chromatography.

Lukasz Szyrwiel, Christoph Gille, Michael Mülleder, Vadim Demichev, Markus Ralser.

  Increased throughput in proteomic experiments can improve accessibility of proteomic platforms, reduce costs, and facilitate new approaches in systems biology and biomedical research. Here we propose combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and data analysis with the DIA-NN software suite, to achieve high-quality proteomic experiments from limited sample amounts, at a throughput of up to 400 samples per day. For instance, when benchmarking our workflow using a 500-μL/min flow rate and 3-min chromatographic gradients, we report the quantification of 5211 proteins from 2 μg of a mammalian cell-line standard at high quantitative accuracy and precision. We further used this platform to analyze blood plasma samples from a cohort of COVID-19 inpatients, using a 3-min chromatographic gradient and alternating column regeneration on a dual pump system. The method delivered a comprehensive view of the COVID-19 plasma proteome, allowing classification of the patients according to disease severity and revealing plasma biomarker candidates.

Keywords:  alternating column regeneration; analytical flow-rate chromatography; dia-PASEF; high-throughput proteomics; plasma proteomics

DOI:  https://doi.org/10.1002/pmic.202300100
J Lipid Res. 2023 Jun 05. pii: S0022-2275(23)00070-6. [Epub ahead of print] 100397

Strategies for consistent and automated quantification of HDL proteome using data-independent acquisition (DIA).

Douglas Ricardo Souza Junior, Amanda Ribeiro Martins Silva, Graziella Eliza Ronsein.

  The introduction of mass spectrometry-based proteomics has revolutionized HDL field, with the description, characterization and implication of HDL-associated proteins in an array of pathologies. However, acquiring robust, reproducible data is still a challenge in the quantitative assessment of HDL proteome. Data-independent acquisition (DIA) is a mass spectrometry methodology that allows the acquisition of reproducible data, but data analysis remains a challenge in the field. Up to date, there is no consensus in how to process DIA-derived data for HDL proteomics. Here, we developed a pipeline aiming to standardize HDL proteome quantification. We optimized instrument parameters, and compared the performance of four freely available, user-friendly software tools (DIA-NN, EncyclopeDIA, MaxDIA and Skyline) in processing DIA data. Importantly, pooled samples were used as quality controls throughout our experimental setup. A carefully evaluation of precision, linearity, and detection limits, first using E. coli background for HDL proteomics, and second using HDL proteome and synthetic peptides, was undertaken. Finally, as a proof of concept, we employed our optimized and automated pipeline to quantify the proteome of HDL and apolipoprotein B (APOB)-containing lipoproteins. Our results show that determination of precision is key to confidently and consistently quantify HDL proteins. Taking this precaution, any of the available software tested here would be appropriate for quantification of HDL proteome, although their performance varied considerably.

Keywords:  HDL; apolipoproteins; data-independent acquisition; high-density lipoprotein; lipoproteins; proteomics; quantitative proteomics

DOI:  https://doi.org/10.1016/j.jlr.2023.100397
Front Oncol. 2023 ;13 1186539

Crosstalk between arginine, glutamine, and the branched chain amino acid metabolism in the tumor microenvironment.

Tanner J Wetzel, Sheila C Erfan, Lucas D Figueroa, Leighton M Wheeler, Elitsa A Ananieva.

  Arginine, glutamine, and the branched chain amino acids (BCAAs) are a focus of increased interest in the field of oncology due to their importance in the metabolic reprogramming of cancer cells. In the tumor microenvironment (TME), these amino acids serve to support the elevated biosynthetic and energy demands of cancer cells, while simultaneously maintaining the growth, homeostasis, and effector function of tumor-infiltrating immune cells. To escape immune destruction, cancer cells utilize a variety of mechanisms to suppress the cytotoxic activity of effector T cells, facilitating T cell exhaustion. One such mechanism is the ability of cancer cells to overexpress metabolic enzymes specializing in the catabolism of arginine, glutamine, and the BCAAs in the TME. The action of such enzymes supplies cancer cells with metabolic intermediates that feed into the TCA cycle, supporting energy generation, or providing precursors for purine, pyrimidine, and polyamine biosynthesis. Armed with substantial metabolic flexibility, cancer cells redirect amino acids from the TME for their own advantage and growth, while leaving the local infiltrating effector T cells deprived of essential nutrients. This review addresses the metabolic pressure that cancer cells exert over immune cells in the TME by up-regulating amino acid metabolism, while discussing opportunities for targeting amino acid metabolism for therapeutic intervention. Special emphasis is given to the crosstalk between arginine, glutamine, and BCAA metabolism in affording cancer cells with metabolic dominance in the TME.

Keywords:  TME; arginine; glutamine; isoleucine; leucine; metabolism; valine

DOI:  https://doi.org/10.3389/fonc.2023.1186539
J Proteome Res. 2023 Jun 09.

Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer.

Mukul K Midha, Charu Kapil, Michal Maes, David H Baxter, Seamus R Morrone, Timothy J Prokop, Robert L Moritz.

  By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide molecular ions by the electrospray source. To maximize the transfer of peptides from the liquid to gaseous phase and allow molecular ions to enter the mass spectrometer at microspray flow rates, an efficient electrospray process is required. Here we describe the superior performance of newly design vacuum insulated probe heated electrospray ionization (VIP-HESI) source coupled to a Bruker timsTOF PRO mass spectrometer operated in microspray mode. VIP-HESI significantly improves chromatography signals in comparison to electrospray ionization (ESI) and nanospray ionization using the captivespray (CS) source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient of variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that the Slice-PASEF VIP-HESI mode is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with microflow rate chromatography achieves a higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications. Data and spectral libraries are available via ProteomeXchange (PXD040497).

Keywords:  captivespray (CS); data-independent acquisition-parallel accumulation and serial fragmentation (dia-PASEF); electrospray ionization (ESI); microflow liquid chromatography (μLC); slice-parallel accumulation and serial fragmentation (Slice-PASEF); vacuum insulated probe heated electrospray ionization (VIP-HESI) source

DOI:  https://doi.org/10.1021/acs.jproteome.3c00305
Biotechnol Bioeng. 2023 Jun 05.

Precision fermentation with mass spectrometry-based spent media analysis.

Hardik Dodia, Avinash Vellore Sunder, Yogen Borkar, Pramod P Wangikar.

  Optimization and monitoring of bioprocesses requires the measurement of several process parameters and quality attributes. Mass spectrometry (MS)-based techniques such as those coupled to gas chromatography (GCMS) and liquid Chromatography (LCMS) enable the simultaneous measurement of hundreds of metabolites with high sensitivity. When applied to spent media, such metabolome analysis can help determine the sequence of substrate uptake and metabolite secretion, consequently facilitating better design of initial media and feeding strategy. Furthermore, the analysis of metabolite diversity and abundance from spent media will aid the determination of metabolic phases of the culture and the identification of metabolites as surrogate markers for product titer and quality. This review covers the recent advances in metabolomics analysis applied to the development and monitoring of bioprocesses. In this regard, we recommend a stepwise workflow and guidelines that a bioprocesses engineer can adopt to develop and optimize a fermentation process using spent media analysis. Finally, we show examples of how the use of MS can revolutionize the design and monitoring of bioprocesses.

Keywords:  bioprocess development; exo-metabolomics; mass spectrometry; productivity markers; spent media analysis

DOI:  https://doi.org/10.1002/bit.28450
Curr Protoc. 2023 Jun;3(6): e798

Proteome-Derived Peptide Libraries for Deep Specificity Profiling of N-terminal Modification Reagents.

Haley N Bridge, Amy M Weeks.

  Protein and peptide N termini are important targets for selective modification with chemoproteomics reagents and bioconjugation tools. The N-terminal ⍺-amine occurs only once in each polypeptide chain, making it an attractive target for protein bioconjugation. In cells, new N termini can be generated by proteolytic cleavage and captured by N-terminal modification reagents that enable proteome-wide identification of protease substrates through tandem mass spectrometry (LC-MS/MS). An understanding of the N-terminal sequence specificity of the modification reagents is critical for each of these applications. Proteome-derived peptide libraries in combination with LC-MS/MS are powerful tools for profiling the sequence specificity of N-terminal modification reagents. These libraries are highly diverse, and LC-MS/MS enables analysis of the modification efficiencies of tens of thousands of sequences in a single experiment. Proteome-derived peptide libraries are a powerful tool for profiling the sequence specificities of enzymatic and chemical peptide labeling reagents. Subtiligase, an enzymatic modification reagent, and 2-pyridinecarboxaldehyde (2PCA), a chemical modification reagent, are two reagents that have been developed for selective N-terminal peptide modification and can be studied using proteome-derived peptide libraries. This protocol outlines the steps for generating N-terminally diverse proteome-derived peptide libraries and for applying these libraries to profile the specificity of N-terminal modification reagents. Although we detail the steps for profiling the specificity of 2PCA and subtiligase in Escherichia coli and human cells, these protocols can easily be adapted to alternative proteome sources and other N-terminal peptide labeling reagents. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of N-terminally diverse proteome-derived peptide libraries from E. coli Alternate Protocol: Generation of N-terminally diverse proteome-derived peptide libraries from human cells Basic Protocol 2: Characterizing the specificity of 2-pyridinecarboxaldehyde using proteome-derived peptide libraries Basic Protocol 3: Characterizing the specificity of subtiligase using proteome-derived peptide libraries.

Keywords:  2-pyridinecarboxaldehyde; N terminomics; protein N terminus; proteome-derived peptide libraries; subtiligase

DOI:  https://doi.org/10.1002/cpz1.798
Curr Osteoporos Rep. 2023 Jun 06.

Amino Acid Metabolism in Bone Metastatic Disease.

Deanna N Edwards.

   PURPOSE OF REVIEW: Breast and prostate tumors frequently metastasize to the bone, but the underlying mechanisms for osteotropism remain elusive. An emerging feature of metastatic progression is metabolic adaptation of cancer cells to new environments. This review will summarize the recent advances on how cancer cells utilize amino acid metabolism during metastasis, from early dissemination to interactions with the bone microenvironment.
RECENT FINDINGS: Recent studies have suggested that certain metabolic preferences for amino acids may be associated with bone metastasis. Once in the bone microenvironment, cancer cells encounter a favorable microenvironment, where a changing nutrient composition of the tumor-bone microenvironment may alter metabolic interactions with bone-resident cells to further drive metastatic outgrowth. Enhanced amino acid metabolic programs are associated with bone metastatic disease and may be further augmented by the bone microenvironment. Additional studies are necessary to fully elucidate the role of amino acid metabolism on bone metastasis.

Keywords:  Amino acids; Bone; Cancer; Metabolism; Metastasis; Microenvironment

DOI:  https://doi.org/10.1007/s11914-023-00797-4
Mass Spectrom Rev. 2023 Jun 06.

Analysis of triacylglycerol and phospholipid sn-positional isomers by liquid chromatographic and mass spectrometric methodologies.

Mikael Fabritius, Baoru Yang.

  Analysis of triacylglycerol (TG) and phospholipid sn-positional isomers can be divided into two main categories: (a) direct separation by chromatography or other means such as ion mobility mass spectrometry and (b) quantification of regioisomer ratios by structurally informative fragment ions with mass spectrometric methods. Due to long retention times and limited performance, researchers are moving away from direct chromatographic separation of isomers, using mass spectrometry instead. Many established analytical methods are targeting specific isomers of interest instead of untargeted analysis of comprehensive profiles of regioisomers. Challenges remain arising from the large number of isobaric and isomeric lipid species in natural samples, often overlapping chromatographically and sharing structurally informative fragment ions. Further, fragmentation of glycerolipids is influenced by the nature of the attached fatty acids, and the lack of available regiopure standards is still an obstacle for establishing calibration curves required for accurate quantification of regioisomers. Additionally, throughput of many methods is still quite limited. Optimization algorithms and fragmentation models are useful especially for analysis of TG regioisomers, as identification using calibration curves alone without proper separation is difficult with complex samples.

Keywords:  liquid chromatography; mass spectrometry; phospholipid; regioisomer; triacylglycerol

DOI:  https://doi.org/10.1002/mas.21853
J Obstet Gynaecol Res. 2023 Jun 09.

Identification of predictive biomarkers for diagnosis and radiation sensitivity of uterine cervical cancer using wide-targeted metabolomics.

Eiji Hishinuma, Muneaki Shimada, Naomi Matsukawa, Bin Li, Ikuko N Motoike, Tatsuya Hagihara, Shogo Shigeta, Hideki Tokunaga, Daisuke Saigusa, Kengo Kinoshita, Seizo Koshiba, Nobuo Yaegashi.

   AIM: Uterine cervical cancer (UCC) is the fourth most common cancer in women, responsible for more than 300 000 deaths worldwide. Its early detection, by cervical cytology, and prevention, by vaccinating against human papilloma virus, greatly contribute to reducing cervical cancer mortality in women. However, penetration of the effective prevention of UCC in Japan remains low. Plasma metabolome analysis is widely used for biomarker discovery and the identification of cancer-specific metabolic pathways. Here, we aimed to identify predictive biomarkers for the diagnosis and radiation sensitivity of UCC using wide-targeted plasma metabolomics.
METHODS: We analyzed 628 metabolites in plasma samples obtained from 45 patients with UCC using ultra-high-performance liquid chromatography with tandem mass spectrometry.
RESULTS: The levels of 47 metabolites were significantly increased and those of 75 metabolites were significantly decreased in patients with UCC relative to healthy controls. Increased levels of arginine and ceramides, and decreased levels of tryptophan, ornithine, glycosylceramides, lysophosphatidylcholine, and phosphatidylcholine were characteristic of patients with UCC. Comparison of metabolite profiles in groups susceptible and non-susceptible to radiation therapy, a treatment for UCC, revealed marked variations in polyunsaturated fatty acid, nucleic acid, and arginine metabolism in the group not susceptible to treatment.
CONCLUSIONS: Our findings suggest that the metabolite profile of patients with UCC may be an important indicator for distinguishing these patients from healthy cohorts, and may also be useful for predicting sensitivity to radiotherapy.

Keywords:  mass spectrometry; metabolome; radiation tolerance; tumor biomarker; uterine cervical neoplasm

DOI:  https://doi.org/10.1111/jog.15709
Eur J Pharmacol. 2023 Jun 03. pii: S0014-2999(23)00341-2. [Epub ahead of print] 175830

Arginine deprivation as a treatment approach targeting cancer cell metabolism and survival: A review of the literature.

Ghaith Assi, Wissam H Faour.

  Amino acid requirement of metabolically active cells is a key element in cellular survival. Of note, cancer cells were shown to have an abnormal metabolism and high-energy requirements including the high amino acid requirement needed for growth factor synthesis. Thus, amino acid deprivation is considered a novel approach to inhibit cancer cell proliferation and offer potential treatment prospects. Accordingly, arginine was proven to play a significant role in cancer cell metabolism and therapy. Arginine depletion induced cell death in various types of cancer cells. Also, the various mechanisms of arginine deprivation, e.g., apoptosis and autophagy were summarized. Finally, the adaptive mechanisms of arginine were also investigated. Several malignant tumors had high amino acid metabolic requirements to accommodate their rapid growth. Antimetabolites that prevent the production of amino acids were also developed as anticancer therapies and are currently under clinical investigation. The aim of this review is to provide a concise literature on arginine metabolism and deprivation, its effects in different tumors, its different modes of action, as well as the related cancerous escape mechanisms.

Keywords:  Apoptosis; Arginine depraving factors; Arginine deprivation; Autophagy; Cancer therapy; Escape mechanisms

DOI:  https://doi.org/10.1016/j.ejphar.2023.175830
J Mol Med (Berl). 2023 Jun 08.

Lipid metabolism in idiopathic pulmonary fibrosis: From pathogenesis to therapy.

Ranxun Chen, Jinghong Dai.

  Idiopathic pulmonary fibrosis (IPF) is a chronic irreversible interstitial lung disease characterized by a progressive decline in lung function. The etiology of IPF is unknown, which poses a significant challenge to the treatment of IPF. Recent studies have identified a strong association between lipid metabolism and the development of IPF. Qualitative and quantitative analysis of small molecule metabolites using lipidomics reveals that lipid metabolic reprogramming plays a role in the pathogenesis of IPF. Lipids such as fatty acids, cholesterol, arachidonic acid metabolites, and phospholipids are involved in the onset and progression of IPF by inducing endoplasmic reticulum stress, promoting cell apoptosis, and enhancing the expression of pro-fibrotic biomarkers. Therefore, targeting lipid metabolism can provide a promising therapeutic strategy for pulmonary fibrosis. This review focuses on lipid metabolism in the pathogenesis of pulmonary fibrosis.

Keywords:  Cholesterol; Fatty acids; Idiopathic pulmonary fibrosis; Lipid metabolism

DOI:  https://doi.org/10.1007/s00109-023-02336-1
BMC Bioinformatics. 2023 Jun 06. 24(1): 239

Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.

Jeff Jones, Elliot J MacKrell, Ting-Yu Wang, Brett Lomenick, Michael L Roukes, Tsui-Fen Chou.

   BACKGROUND: The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approachable standardized post-processing analyses such as sample group statistics, quantitative variation and even data filtering. We developed tidyproteomics to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object.
RESULTS: The R package tidyproteomics was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such, tidyproteomics allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms.
CONCLUSIONS: Tidyproteomics aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in tidyproteomics are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.

Keywords:  Analysis; Annotation enrichment; Imputation; Normalization; Pipeline; Protein expression; Proteomics; Quantitative; Workflow

DOI:  https://doi.org/10.1186/s12859-023-05360-7
Biochem Mol Biol Educ. 2023 Jun 07.

Using MetaboAnalyst to introduce undergraduates to lipidomic analysis and lipid remodeling in barley roots.

Mercedes Reyna, Micaela Peppino Margutti, Ana Carolina Vilchez, Ana Laura Villasuso.

  Lipidomics is a discipline that focuses on the identification and quantification of lipids. Although a part of the larger omics field, lipidomics requires specific approaches for the analysis and biological interpretation of datasets. This article presents a series of activities for introducing undergraduate microbiology students to lipidomic analysis through tools from the web-based platform MetaboAnalyst. The students perform a complete lipidomic workflow, which includes experiment design, data processing, data normalization, and statistical analysis of molecular phospholipid species obtained from barley roots exposed to Fusarium macroconidia. The input data are provided by the teacher, but students also learn about the methods through which they were originally obtained (untargeted liquid chromatography coupled with mass spectrometry). The ultimate aim is for students to understand the biological significance of phosphatidylcholine acyl editing. The chosen methodology allows users who are not proficient in statistics to make a comprehensive analysis of quantitative lipidomic datasets. We strongly believe that virtual activities based on the analysis of such datasets should be incorporated more often into undergraduate courses, in order to improve students' data-handling skills for omics sciences.

Keywords:  Fusarium; MetaboAnalyst; acyl editing of phospholipids; lipidomic workflow; omics sciences

DOI:  https://doi.org/10.1002/bmb.21755
J Med Microbiol. 2023 Jun;72(6):

High-throughput quantification of microbial-derived organic acids in mucin-rich samples via reverse phase high performance liquid chromatography.

Alex R Villarreal, Sarah K Lucas, Joshua R Fletcher, Ryan C Hunter.

  Organic acids (short chain fatty acids, amino acids, etc.) are common metabolic byproducts of commensal bacteria of the gut and oral cavity in addition to microbiota associated with chronic infections of the airways, skin, and soft tissues. A ubiquitous characteristic of these body sites in which mucus-rich secretions often accumulate in excess, is the presence of mucins; high molecular weight (HMW), glycosylated proteins that decorate the surfaces of non-keratinized epithelia. Owing to their size, mucins complicate quantification of microbial-derived metabolites as these large glycoproteins preclude use of 1D and 2D gel approaches and can obstruct analytical chromatography columns. Standard approaches for quantification of organic acids in mucin-rich samples typically rely on laborious extractions or outsourcing to laboratories specializing in targeted metabolomics. Here we report a high-throughput sample preparation process that reduces mucin abundance and an accompanying isocratic reverse phase high performance liquid chromatography (HPLC) method that enables quantification of microbial-derived organic acids. This approach allows for accurate quantification of compounds of interest (0.01 mM - 100 mM) with minimal sample preparation, a moderate HPLC method run time, and preservation of both guard and analytical column integrity. This approach paves the way for further analyses of microbial-derived metabolites in complex clinical samples.

Keywords:  amino acids; glycoproteins; high performance liquid chromatography; mucin; organic acids; reverse phase liquid chromatography; targeted metabolomics

DOI:  https://doi.org/10.1099/jmm.0.001708
Metabolism. 2023 Jun 05. pii: S0026-0495(23)00219-6. [Epub ahead of print] 155615

Targeting the dynamics of cancer metabolism in the era of precision oncology.

Peijie Zheng, Zihao Lin, Yuemin Ding, Shiwei Duan.

  Cancer metabolic reprogramming is a promising target for cancer therapy. The progression of tumors, including their growth, development, metastasis, and spread, is a dynamic process that varies over time and location. This means that the metabolic state of tumors also fluctuates. A recent study found that energy production efficiency is lower in solid tumors but increases significantly in tumor metastasis. Despite its importance for targeted tumor metabolism therapy, few studies have described the dynamic metabolic changes of tumors. In this commentary, we discuss the limitations of past targeted tumor metabolism therapy and the key findings of this study. We also summarize its immediate clinical implications for dietary intervention and explore future research directions for understanding the dynamic changes in tumor metabolic reprogramming.

Keywords:  ATP; Biological rhythms; Cancer; Dietary therapy; Metabolic reprogramming; Tumor

DOI:  https://doi.org/10.1016/j.metabol.2023.155615
Front Physiol. 2023 ;14 1205435

Editorial: Energy metabolism within the skeleton.

Bram C J van der Eerden, Ryan C Riddle, Steve Stegen, Michaela Tencerova.



Keywords:  amino acids; bone cells; energy metabolism; fatty acids; glucose

DOI:  https://doi.org/10.3389/fphys.2023.1205435
Cytokine Growth Factor Rev. 2023 May 24. pii: S1359-6101(23)00022-9. [Epub ahead of print]

Exosomes-regulated lipid metabolism in tumorigenesis and cancer progression.

Leiguang Ye, Yingpu Li, Sifan Zhang, Jinsong Wang, Bo Lei.

  Increasing evidence highlights the role of lipid metabolism in tumorigenesis and tumor progression. Targeting the processes of lipid metabolism, including lipogenesis, lipid uptake, fatty acid oxidation, and lipolysis, is an optimal strategy for anti-cancer therapy. Beyond cell-cell membrane surface interaction, exosomes are pivotal factors that transduce intercellular signals in the tumor microenvironment (TME). Most research focuses on the role of lipid metabolism in regulating exosome biogenesis and extracellular matrix (ECM) remodeling. The mechanisms of exosome and ECM-mediated reprogramming of lipid metabolism are currently unclear. We summarize several mechanisms associated with the regulation of lipid metabolism in cancer, including transport of exosomal carriers and membrane receptors, activation of the PI3K pathway, ECM ligand-receptor interactions, and mechanical stimulation. This review aims to highlight the significance of these intercellular factors in TME and to deepen the understanding of the functions of exosomes and ECM in the regulation of lipid metabolism.

Keywords:  CD36; ECM; Exosome; Lipid metabolism; Mechanotransduction; TME

DOI:  https://doi.org/10.1016/j.cytogfr.2023.05.002
Curr Med Chem. 2023 Jun 07.

PaSTe. Blockade of the Lipid Phenotype of Prostate Cancer as Metabolic Therapy: A Theoretical Proposal.

Adriana Romo-Perez, Guadalupe Domínguez-Gómez, Alma Chávez-Blanco, Aurora González-Fierro, José Correa-Basurto, Alfonso Dueñas-González.

   BACKGROUND: Prostate cancer is the most frequently diagnosed malignancy in 112 countries and is the leading cause of death in eighteen. In addition to continuing research on prevention and early diagnosis, improving treatments and making them more affordable is imperative. In this sense, the therapeutic repurposing of low-cost and widely available drugs could reduce global mortality from this disease. The malignant metabolic phenotype is becoming increasingly important due to its therapeutic implications. Cancer generally is characterized by hyperactivation of glycolysis, glutaminolysis, and fatty acid synthesis. However, prostate cancer is particularly lipidic; it exhibits increased activity in the pathways for synthesizing fatty acids, cholesterol, and fatty acid oxidation (FAO).
OBJECTIVE: Based on a literature review, we propose the PaSTe regimen (Pantoprazole, Simvastatin, Trimetazidine) as a metabolic therapy for prostate cancer. Pantoprazole and simvastatin inhibit the enzymes fatty acid synthase (FASN) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), therefore, blocking the synthesis of fatty acids and cholesterol, respectively. In contrast, trimetazidine inhibits the enzyme 3-b-Ketoacyl-CoA thiolase (3-KAT), an enzyme that catalyzes the oxidation of fatty acids (FAO). It is known that the pharmacological or genetic depletion of any of these enzymes has antitumor effects in prostatic cancer.
RESULTS: Based on this information, we hypothesize that the PaSTe regimen will have increased antitumor effects and may impede the metabolic reprogramming shift. Existing knowledge shows that enzyme inhibition occurs at molar concentrations achieved in plasma at standard doses of these drugs.
CONCLUSION: We conclude that this regimen deserves to be preclinically evaluated because of its clinical potential for the treatment of prostate cancer.

Keywords:  cancer drug repurposing; de novo fatty-acid synthesis; fatty-acid oxidation.; metabolic blockade; mevalonate pathway; prostate cancer

DOI:  https://doi.org/10.2174/0929867330666230607104441
Plant J. 2023 Jun 05.

Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking.

Leonardo Perez de Souza, Elena Bitocchi, Roberto Papa, Takayuki Tohge, Alisdair R Fernie.

  The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.

Keywords:  Phaseolus vulgaris; common bean; domestication; metabolomics; molecular networking; specialized metabolites

DOI:  https://doi.org/10.1111/tpj.16277
J Chromatogr B Analyt Technol Biomed Life Sci. 2023 May 26. pii: S1570-0232(23)00162-9. [Epub ahead of print]1225 123752

Validation of an LC-MS/MS method for simultaneous quantification of abiraterone, enzalutamide and darolutamide in human plasma.

Stefan A J Buck, Peter de Bruijn, Inge M Ghobadi-Moghaddam-Helmantel, Mei H Lam, Ronald de Wit, Stijn L W Koolen, Ron H J Mathijssen.

  Currently, several oral androgen receptor signalling inhibitors are available for the treatment of advanced prostate cancer. Quantification of plasma concentrations of these drugs is highly relevant for various purposes, such as Therapeutic Drug Monitoring (TDM) in oncology. Here, we report a liquid chromatography/tandem mass spectrometric (LC-MS/MS) method for the simultaneous quantification of abiraterone, enzalutamide, and darolutamide. The validation was performed according to the requirements of the U.S. Food and Drug Administration and European Medicine Agency. We also demonstrate the clinical applicability of the quantification of enzalutamide and darolutamide in patients with metastatic castration-resistant prostate cancer.

Keywords:  Abiraterone; Darolutamide; Enzalutamide; Human plasma; LC-MS/MS

DOI:  https://doi.org/10.1016/j.jchromb.2023.123752
Cancer Discov. 2023 Jun 09. OF1

The Tumor Suppressor CDKN2A Remodels the Lipidome of Glioblastoma.

CDKN2A loss remodels the glioblastoma lipidome and sensitizes cells to lipid peroxidation and ferroptosis.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2023-089
Methods Mol Biol. 2023 ;2676 101-116

Reprogramming Initiator and Nonsense Codons to Simultaneously Install Three Distinct Noncanonical Amino Acids into Proteins in E. coli.

Han-Kai Jiang, Jeffery M Tharp.

  Multiple noncanonical amino acids can be installed into proteins in E. coli using mutually orthogonal aminoacyl-tRNA synthetase and tRNA pairs. Here we describe a protocol for simultaneously installing three distinct noncanonical amino acids into proteins for site-specific bioconjugation at three sites. This method relies on an engineered, UAU-suppressing, initiator tRNA, which is aminoacylated with a noncanonical amino acid by Methanocaldococcus jannaschii tyrosyl-tRNA synthetase. Using this initiator tRNA/aminoacyl-tRNA synthetase pair, together with the pyrrolysyl-tRNA synthetase/tRNAPyl pairs from Methanosarcina mazei and Ca. Methanomethylophilus alvus, three noncanonical amino acids can be installed into proteins in response to the UAU, UAG, and UAA codons.

Keywords:  Bioorthogonal chemistry; Genetic code expansion; Non-canonical amino acids; Pyrrolysyl-tRNA synthetase; Synthetic biology

DOI:  https://doi.org/10.1007/978-1-0716-3251-2_7
NPJ Parkinsons Dis. 2023 Jun 03. 9(1): 84

Targeted metabolomic analysis in Parkinson's disease brain frontal cortex and putamen with relation to cognitive impairment.

Karel Kalecký, Teodoro Bottiglieri.

We performed liquid chromatography tandem mass spectrometry analysis with the targeted metabolomic kit Biocrates MxP Quant 500, in human brain cortex (Brodmann area 9) and putamen, to reveal metabolic changes characteristic of Parkinson's disease (PD) and PD-related cognitive decline. This case-control study involved 101 subjects (33 PD without dementia, 32 PD with dementia (cortex only), 36 controls). We found changes associated with PD, cognitive status, levodopa levels, and disease progression. The affected pathways include neurotransmitters, bile acids, homocysteine metabolism, amino acids, TCA cycle, polyamines, β-alanine metabolism, fatty acids, acylcarnitines, ceramides, phosphatidylcholines, and several microbiome-derived metabolites. Previously reported levodopa-related homocysteine accumulation in cortex still best explains the dementia status in PD, which can be modified by dietary supplementation. Further investigation is needed to reveal the exact mechanisms behind this pathological change.

DOI: https://doi.org/10.1038/s41531-023-00531-y
J Neurooncol. 2023 Jun 06.

Tissue and plasma free amino acid detection by LC-MS/MS method in high grade glioma patients.

Sureyya Toklu, Rahsan Kemerdere, Tibet Kacira, Murat Serdar Gurses, Fehime Benli Aksungar, Taner Tanriverdi.

   PURPOSE: The changes in serum amino acid profiles are evaluated in different types of cancers and screening tests were developed for estimating the risk of cancer by rapid analysis of plasma free amino acid (PFAA) levels. There is scarce evidence about the metabolomics analysis of PFAA in malignant gliomas. The aim of the present study was to identify the most promising diagnostic amino acid biomarkers that could be objectively measured for high-grade glioma and to compare their level with the tissue counterpart.
METHODS: In this prospective study, we collected serum samples from 22 patients with the pathological diagnosis of high-grade diffuse glioma according to WHO 2016 classification and 22 healthy subjects, and brain tissue from 22 controls. Plasma and tissue amino acid concentrations were analyzed applying liquid chromatography-tandem mass spectrometry (LC-MS/MS) method.
RESULTS: Serum alanine, alpha-aminobutyric acid (AABA), lysine (Lys) and cysteine concentrations were significantly higher in high-grade glioma patients despite low levels of alanine and Lys in the tumor tissue. Aspartic acid, histidine and taurine were significantly decreased in both serum and tumors of glioma patients. A positive correlation was detected between tumor volumes and serum levels of latter three amino acids.
CONCLUSION: This study demonstrated potential amino acids which may have diagnostic value for high-grade glioma patients by utilizing LC-MS/MS method. Our results are preliminary to compare serum and tissue levels of amino acids in patients with malignant gliomas. The data presented here may provide feature ideas about the metabolic pathways in the pathogenesis of gliomas.

Keywords:  Amino acids; Biomarker; High grade glioma; LC-MS/MS; Serum

DOI:  https://doi.org/10.1007/s11060-023-04329-z
Biotechnol Adv. 2023 Jun 06. pii: S0734-9750(23)00091-5. [Epub ahead of print] 108184

Understanding glycosylation: Regulation through the metabolic flux of precursor pathways.

Aert F Scheper, Jack Schofield, Raghvendra Bohara, Thomas Ritter, Abhay Pandit.

  Glycosylation is how proteins and lipids are modified with complex carbohydrates known as glycans. The post-translational modification of proteins with glycans is not a template-driven process in the same way as genetic transcription or protein translation. Glycosylation is instead dynamically regulated by metabolic flux. This metabolic flux is determined by the concentrations and activities of the glycotransferase enzymes, which synthesise glycans, the metabolites that act as their precursors and transporter proteins. This review provides an overview of the metabolic pathways underlying glycan synthesis. Pathological dysregulation of glycosylation, particularly increased glycosylation occurring during inflammation, is also elucidated. The resulting inflammatory hyperglycosylation acts as a glycosignature of disease, and we report on the changes in the metabolic pathways which feed into glycan synthesis, revealing alterations to key enzymes. Finally, we examine studies in developing metabolic inhibitors targeting these critical enzymes. These results provide the tools for researchers investigating the role of glycan metabolism in inflammation and have helped to identify promising glycotherapeutic approaches to inflammation.

Keywords:  Glycan synthesis; Glycosylation; Inflammation; Metabolic flux

DOI:  https://doi.org/10.1016/j.biotechadv.2023.108184