bims-mascan 2021-07-04 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–07–04
25 papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

Tumor Microenvironment-Derived Metabolites: A Guide to Find New Metabolic Therapeutic Targets and Biomarkers.
Impact of acute lymphoblastic leukemia induction therapy: findings from metabolomics on non-fasted plasma samples from a biorepository.
Isomer Selective Comprehensive Lipidomics Analysis of Phosphoinositides in Biological Samples by Liquid Chromatography with Data Independent Acquisition Tandem Mass Spectrometry.
Metabolic Rewiring and the Characterization of Oncometabolites.
Accurate Lipid Quantification of Tissue Homogenates Requires Suitable Sample Concentration, Solvent Composition, and Homogenization Procedure-A Case Study in Murine Liver.
Susceptibility to false discovery in biomarker research using liquid chromatography-high resolution mass spectrometry based untargeted metabolomics profiling.
Transforming Growth Factor-β and Oxidative Stress in Cancer: A Crosstalk in Driving Tumor Transformation.
The Role of Fatty Acids in Non-Alcoholic Fatty Liver Disease Progression: An Update.
One-Carbon Metabolism Associated Vulnerabilities in Glioblastoma: A Review.
FATTY ACID SYNTHESIS IS REQUIRED FOR BREAST CANCER BRAIN METASTASIS.
Parallel, High-Quality Proteomic and Targeted Metabolomic Quantification Using Laser Capture Microdissected Tissues.
Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies.
Quantification and molecular imaging of fatty acid isomers from complex biological samples by mass spectrometry.
High-Throughput Proteomics and AI for Cancer Biomarker Discovery.
Cancer Metabolism as a New Real Target in Tumor Therapy.
Solving the enigma: Mass spectrometry and small molecule probes to study sphingolipid function.
Re-Examining the Impact of Minimal Scans in Liquid Chromatography-Mass Spectrometry Analysis.
Lipidomic Analysis to Assess Oxidative Stress in Acute Coronary Syndrome and Acute Stroke Patients.
Development of a Derivatization Reagent with a 2-Nitrophenylsulfonyl Moiety for UHPLC-HRMS/MS and Its Application to Detect Amino Acids Including Taurine.
Metabolic Anti-Cancer Effects of Melatonin: Clinically Relevant Prospects.
A delicate initiation: Lipolysis of lipid droplets fuels glioblastoma.
Plasma Metabolomics for Discovery of Early Metabolic Markers of Prostate Cancer Based on Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry.
Mass spectrometry-based clinical proteomics - a revival.
Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples.
Targeted Metabolomics: The LC-MS/MS Based Quantification of the Metabolites Involved in the Methylation Biochemical Pathways.

Cancers (Basel). 2021 Jun 28. pii: 3230. [Epub ahead of print]13(13):

Tumor Microenvironment-Derived Metabolites: A Guide to Find New Metabolic Therapeutic Targets and Biomarkers.

Juan C García-Cañaveras, Agustín Lahoz.

  Metabolic reprogramming is a hallmark of cancer that enables cancer cells to grow, proliferate and survive. This metabolic rewiring is intrinsically regulated by mutations in oncogenes and tumor suppressors, but also extrinsically by tumor microenvironment factors (nutrient and oxygen availability, cell-to-cell interactions, cytokines, hormones, etc.). Intriguingly, only a few cancers are driven by mutations in metabolic genes, which lead metabolites with oncogenic properties (i.e., oncometabolites) to accumulate. In the last decade, there has been rekindled interest in understanding how dysregulated metabolism and its crosstalk with various cell types in the tumor microenvironment not only sustains biosynthesis and energy production for cancer cells, but also contributes to immune escape. An assessment of dysregulated intratumor metabolism has long since been exploited for cancer diagnosis, monitoring and therapy, as exemplified by 18F-2-deoxyglucose positron emission tomography imaging. However, the efficient delivery of precision medicine demands less invasive, cheaper and faster technologies to precisely predict and monitor therapy response. The metabolomic analysis of tumor and/or microenvironment-derived metabolites in readily accessible biological samples is likely to play an important role in this sense. Here, we review altered cancer metabolism and its crosstalk with the tumor microenvironment to focus on energy and biomass sources, oncometabolites and the production of immunosuppressive metabolites. We provide an overview of current pharmacological approaches targeting such dysregulated metabolic landscapes and noninvasive approaches to characterize cancer metabolism for diagnosis, therapy and efficacy assessment.

Keywords:  LC-MS; MRI; MRS; biomarkers; cancer metabolism; cancer therapy; imaging; metabolic inhibitors; metabolomics; oncometabolites

DOI:  https://doi.org/10.3390/cancers13133230
Metabolomics. 2021 Jun 27. 17(7): 64

Impact of acute lymphoblastic leukemia induction therapy: findings from metabolomics on non-fasted plasma samples from a biorepository.

Toshie Saito, Yue Wei, Li Wen, Chaitanya Srinivasan, Benjamin O Wolthers, Cheng-Yu Tsai, Marian H Harris, Kristen Stevenson, Craig Byersdorfer, Judy-April Oparaji, Christian Fernandez, Amitava Mukherjee, Maisam Abu-El-Haija, Sameer Agnihotri, Kjeld Schmiegelow, Megan R Showalter, Paul W Fogle, Scott McCulloch, Kevin Contrepois, Lewis B Silverman, Ying Ding, Sohail Z Husain.

   INTRODUCTION: Acute lymphoblastic leukemia (ALL) is among the most common cancers in children. With improvements in combination chemotherapy regimens, the overall survival has increased to over 90%. However, the current challenge is to mitigate adverse events resulting from the complex therapy. Several chemotherapies intercept cancer metabolism, but little is known about their collective role in altering host metabolism.
OBJECTIVES: We profiled the metabolomic changes in plasma of ALL patients initial- and post- induction therapy.
METHODS: We exploited a biorepository of non-fasted plasma samples derived from the Dana Farber Cancer Institute ALL Consortium; these samples were obtained from 50 ALL patients initial- and post-induction therapy. Plasma metabolites and complex lipids were analyzed by high resolution tandem mass spectrometry and differential mobility tandem mass spectrometry. Data were analyzed using a covariate-adjusted regression model with multiplicity adjustment. Pathway enrichment analysis and co-expression network analysis were performed to identify unique clusters of molecules.
RESULTS: More than 1200 metabolites and complex lipids were identified in the total of global metabolomics and lipidomics platforms. Over 20% of those molecules were significantly altered. In the pathway enrichment analysis, lipids, particularly phosphatidylethanolamines (PEs), were identified. Network analysis indicated that the bioactive fatty acids, docosahexaenoic acid (DHA)-containing (22:6) triacylglycerols (TAGs), were decreased in the post-induction therapy.
CONCLUSION: Metabolomic profiling in ALL patients revealed a large number of alterations following induction chemotherapy. In particular, lipid metabolism was substantially altered. The changes in metabolites and complex lipids following induction therapy could provide insight into the adverse events experienced by ALL patients.

Keywords:  Acute lymphoblastic leukemia; Asparaginase phosphatidylethanolamine; Lipidomics; Metabolomics; Triacylglycerol

DOI:  https://doi.org/10.1007/s11306-021-01814-2
Anal Chem. 2021 Jun 30.

Isomer Selective Comprehensive Lipidomics Analysis of Phosphoinositides in Biological Samples by Liquid Chromatography with Data Independent Acquisition Tandem Mass Spectrometry.

Peng Li, Michael Lämmerhofer.

Phosphoinositides (PIPx) play central roles in membrane dynamics and signal transduction of key functions like cellular growth, proliferation, differentiation, migration, and adhesion. They are highly regulated through a network of distinct phosphatidylinositol phosphates consisting of seven groups and three regioisomers in two groups (PIP and PIP2), which arise from phosphorylation at 3', 4', and 5' positions of the inositol ring. Numerous studies have revealed the importance of both fatty acyl chains, degree of phosphorylation, and phosphorylation positions under physiological and pathological states. However, a comprehensive analytical method that allows differentiation of all regioisomeric forms with different acyl side chains and degrees of phosphorylation is still lacking. Here, we present an integrated comprehensive workflow of PIPx analysis utilizing a chiral polysaccharide stationary phase coupled with electrospray ionization high-resolution mass spectrometry with a data independent acquisition technique using the SWATH technology. Correspondingly, a targeted data mining strategy in the untargeted comprehensively acquired MS and MS/MS data was developed. This powerful highly selective method gives a full picture of PIPx profiles in biological samples. Herein, we present for the first time the full PIPx profiles of NIST SRM1950 plasma, Pichia pastoris lipid extract, and HeLa cell extract, including profile changes upon treatment with potential PI3K inhibitor wortmannin. We also illustrate using this inhibitor that measurements of the PIPx profile averaged over the distinct regioisomers by analytical procedures, which cannot differentiate between the individual PIPx isomers, can easily lead to biased conclusions.

DOI: https://doi.org/10.1021/acs.analchem.1c01751
Cancers (Basel). 2021 Jun 10. pii: 2900. [Epub ahead of print]13(12):

Metabolic Rewiring and the Characterization of Oncometabolites.

Diren Beyoğlu, Jeffrey R Idle.

  The study of low-molecular-weight metabolites that exist in cells and organisms is known as metabolomics and is often conducted using mass spectrometry laboratory platforms. Definition of oncometabolites in the context of the metabolic phenotype of cancer cells has been accomplished through metabolomics. Oncometabolites result from mutations in cancer cell genes or from hypoxia-driven enzyme promiscuity. As a result, normal metabolites accumulate in cancer cells to unusually high concentrations or, alternatively, unusual metabolites are produced. The typical oncometabolites fumarate, succinate, (2R)-hydroxyglutarate and (2S)-hydroxyglutarate inhibit 2-oxoglutarate-dependent dioxygenases, such as histone demethylases and HIF prolyl-4-hydroxylases, together with DNA cytosine demethylases. As a result of the cancer cell acquiring this new metabolic phenotype, major changes in gene transcription occur and the modification of the epigenetic landscape of the cell promotes proliferation and progression of cancers. Stabilization of HIF1α through inhibition of HIF prolyl-4-hydroxylases by oncometabolites such as fumarate and succinate leads to a pseudohypoxic state that promotes inflammation, angiogenesis and metastasis. Metabolomics has additionally been employed to define the metabolic phenotype of cancer cells and patient biofluids in the search for cancer biomarkers. These efforts have led to the uncovering of the putative oncometabolites sarcosine, glycine, lactate, kynurenine, methylglyoxal, hypotaurine and (2R,3S)-dihydroxybutanoate, for which further research is required.

Keywords:  (2R)-hydroxyglutarate; (2S)-hydroxyglutarate; DNA demethylation; fumarate; histone demethylation; hypoxia; metabolomics; oncometabolite; succinate

DOI:  https://doi.org/10.3390/cancers13122900
Metabolites. 2021 Jun 08. pii: 365. [Epub ahead of print]11(6):

Accurate Lipid Quantification of Tissue Homogenates Requires Suitable Sample Concentration, Solvent Composition, and Homogenization Procedure-A Case Study in Murine Liver.

Marcus Höring, Sabrina Krautbauer, Louisa Hiltl, Verena Babl, Alexander Sigruener, Ralph Burkhardt, Gerhard Liebisch.

  Lipidomics aim to quantify lipid species in all kinds of samples, including tissues. To subject a fixed amount of sample to various workflows, tissue homogenates were frequently prepared at defined concentrations in water or by addition of organic solvents. Here, we investigated this first step of tissue lipidomics by quantitative flow injection analysis coupled to Fourier-Transform mass spectrometry (FTMS). The influence of sample concentration, solvent composition, and homogenization procedure on the recovery of lipids was studied in murine liver. Liver homogenates were prepared either by grinding tissue in liquid nitrogen or by bead-based homogenization. Ground samples were dissolved at different concentrations in water, methanol, and water/methanol = 1/1 (v/v). Here, lipid recovery depends on solvent composition and sample concentration. The recovery of nonpolar lipid classes, including triglycerides and cholesteryl ester, was decreased in methanolic homogenates. In contrast, due to superior dispersion of precipitates, bead-based homogenization resulted in efficient lipid recovery independent of the solvent composition. However, lipid distribution within samples, i.e., lipid content of supernatant and pellet following centrifugation, was altered substantially by solvent composition. In conclusion, accurate lipid quantification of tissue homogenates requires evaluation of solvent composition, sample concentration, as well as the homogenization method to guarantee efficient lipid recovery. Due to a potential loss of lipids, removal of precipitates by centrifugation prior to lipid extraction should be avoided.

Keywords:  extraction; lipidomics; lipids; mass spectrometry; preanalytics; quantification; recovery; solvent; tissue homogenization

DOI:  https://doi.org/10.3390/metabo11060365
Clin Transl Med. 2021 Jun;11(6): e469

Susceptibility to false discovery in biomarker research using liquid chromatography-high resolution mass spectrometry based untargeted metabolomics profiling.

Pengwei Zhang, Irene L Ang, Melody M T Lam, Rui Wei, Kate M K Lei, Xingwang Zhou, Henry H N Lam, Qing-Yu He, Terence C W Poon.

DOI: https://doi.org/10.1002/ctm2.469
Cancers (Basel). 2021 Jun 21. pii: 3093. [Epub ahead of print]13(12):

Transforming Growth Factor-β and Oxidative Stress in Cancer: A Crosstalk in Driving Tumor Transformation.

Valeria Ramundo, Giuliana Giribaldi, Elisabetta Aldieri.

  Cancer metabolism involves different changes at a cellular level, and altered metabolic pathways have been demonstrated to be heavily involved in tumorigenesis and invasiveness. A crucial role for oxidative stress in cancer initiation and progression has been demonstrated; redox imbalance, due to aberrant reactive oxygen species (ROS) production or deregulated efficacy of antioxidant systems (superoxide dismutase, catalase, GSH), contributes to tumor initiation and progression of several types of cancer. ROS may modulate cancer cell metabolism by acting as secondary messengers in the signaling pathways (NF-kB, HIF-1α) involved in cellular proliferation and metastasis. It is known that ROS mediate many of the effects of transforming growth factor β (TGF-β), a key cytokine central in tumorigenesis and cancer progression, which in turn can modulate ROS production and the related antioxidant system activity. Thus, ROS synergize with TGF-β in cancer cell metabolism by increasing the redox imbalance in cancer cells and by inducing the epithelial mesenchymal transition (EMT), a crucial event associated with tumor invasiveness and metastases. Taken as a whole, this review is addressed to better understanding this crosstalk between TGF-β and oxidative stress in cancer cell metabolism, in the attempt to improve the pharmacological and therapeutic approach against cancer.

Keywords:  EMT; TGF-β; oxidative stress

DOI:  https://doi.org/10.3390/cancers13123093
Int J Mol Sci. 2021 Jun 27. pii: 6900. [Epub ahead of print]22(13):

The Role of Fatty Acids in Non-Alcoholic Fatty Liver Disease Progression: An Update.

Aleksandra Hliwa, Bruno Ramos-Molina, Dariusz Laski, Adriana Mika, Tomasz Sledzinski.

  Non-alcoholic fatty liver disease (NAFLD) is a major public health problem worldwide. NAFLD (both simple steatosis and steatohepatitis) is characterized by alterations in hepatic lipid metabolism, which may lead to the development of severe liver complications including cirrhosis and hepatocellular carcinoma. Thus, an exhaustive examination of lipid disorders in the liver of NAFLD patients is much needed. Mass spectrometry-based lipidomics platforms allow for in-depth analysis of lipid alterations in a number of human diseases, including NAFLD. This review summarizes the current research on lipid alterations associated with NAFLD and related complications, with special emphasis on the changes in long-chain and short-chain fatty acids levels in both serum and liver tissue, as well as in the hepatic expression of genes encoding the enzymes catalyzing lipid interconversions.

Keywords:  fatty acids; lipidomics; lipids; non-alcoholic fatty liver disease

DOI:  https://doi.org/10.3390/ijms22136900
Cancers (Basel). 2021 Jun 19. pii: 3067. [Epub ahead of print]13(12):

One-Carbon Metabolism Associated Vulnerabilities in Glioblastoma: A Review.

Kimia Ghannad-Zadeh, Sunit Das.

  Altered cell metabolism is a hallmark of cancer cell biology, and the adaptive metabolic strategies of cancer cells have been of recent interest to many groups. Metabolic reprogramming has been identified as a critical step in glial cell transformation, and the use of antimetabolites against glioblastoma has been investigated. One-carbon (1-C) metabolism and its associated biosynthetic pathways, particularly purine nucleotide synthesis, are critical for rapid proliferation and are altered in many cancers. Purine metabolism has also been identified as essential for glioma tumourigenesis. Additionally, alterations of 1-C-mediated purine synthesis have been identified as commonly present in brain tumour initiating cells (BTICs) and could serve as a phenotypic marker of cells responsible for tumour recurrence. Further research is required to elucidate mechanisms through which metabolic vulnerabilities may arise in BTICs and potential ways to therapeutically target these metabolic processes. This review aims to summarize the role of 1-C metabolism-associated vulnerabilities in glioblastoma tumourigenesis and progression and investigate the therapeutic potential of targeting this pathway in conjunction with other treatment strategies.

Keywords:  de novo purine synthesis; glioblastoma; glioma; metabolic reprogramming; metabolic treatment; one-carbon metabolism

DOI:  https://doi.org/10.3390/cancers13123067
Nat Cancer. 2021 Apr;2(4): 414-428

FATTY ACID SYNTHESIS IS REQUIRED FOR BREAST CANCER BRAIN METASTASIS.

Gino B Ferraro, Ahmed Ali, Alba Luengo, David P Kodack, Amy Deik, Keene L Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica M Possada, Jiang Chen, Christopher R Chin, Zohreh Amoozgar, Raphael Ferreira, Ivy Chen, Kamila Naxerova, Christopher Ng, Anna M Westermark, Mark Duquette, Sylvie Roberge, Neal I Lindeman, Costas A Lyssiotis, Jens Nielsen, David E Housman, Dan G Duda, Elena Brachtel, Todd R Golub, Lewis C Cantley, John M Asara, Shawn M Davidson, Dai Fukumura, Véronique A Dartois, Clary B Clish, Rakesh K Jain, Matthew G Vander Heiden.

Brain metastases are refractory to therapies that control systemic disease in patients with human epidermal growth factor receptor 2 (HER2+) breast cancer, and the brain microenvironment contributes to this therapy resistance. Nutrient availability can vary across tissues, therefore metabolic adaptations required for brain metastatic breast cancer growth may introduce liabilities that can be exploited for therapy. Here, we assessed how metabolism differs between breast tumors in brain versus extracranial sites and found that fatty acid synthesis is elevated in breast tumors growing in brain. We determine that this phenotype is an adaptation to decreased lipid availability in brain relative to other tissues, resulting in a site-specific dependency on fatty acid synthesis for breast tumors growing at this site. Genetic or pharmacological inhibition of fatty acid synthase (FASN) reduces HER2+ breast tumor growth in the brain, demonstrating that differences in nutrient availability across metastatic sites can result in targetable metabolic dependencies.

DOI: https://doi.org/10.1038/s43018-021-00183-y
Anal Chem. 2021 Jun 29. 93(25): 8711-8718

Parallel, High-Quality Proteomic and Targeted Metabolomic Quantification Using Laser Capture Microdissected Tissues.

Shichen Shen, Jun Li, Shihan Huo, Min Ma, Xiaoyu Zhu, Sailee Rasam, Xiaotao Duan, Miao Qu, Mark A Titus, Jun Qu.

Quantitative proteomics/metabolomics investigation of laser-capture-microdissection (LCM) cell populations from clinical cohorts affords precise insights into disease/therapeutic mechanisms, nonetheless high-quality quantification remains a prominent challenge. Here, we devised an LC/MS-based approach allowing parallel, robust global-proteomics and targeted-metabolomics quantification from the same LCM samples, using biopsies from prostate cancer (PCa) patients as the model system. The strategy features: (i) an optimized molecular weight cutoff (MWCO) filter-based separation of proteins and small-molecule fractions with high and consistent recoveries; (ii) microscale derivatization and charge-based enrichment for ultrasensitive quantification of key androgens (LOQ = 5 fg/1k cells) with excellent accuracy/precision; (iii) reproducible/precise proteomics quantification with low-missing-data using a detergent-cocktail-based sample preparation and an IonStar pipeline for reproducible and precise protein quantification with excellent data quality. Key parameters enabling robust/reproducible quantification have been meticulously evaluated and optimized, and the results underscored the importance of surveying quantitative performances against key parameters to facilitate fit-for-purpose method development. As a proof-of-concept, high-quality quantification of the proteome and androgens in LCM samples of PCa patient-matched cancerous and benign epithelial/stromal cells was achieved (N = 16), which suggested distinct androgen distribution patterns across cell types and regions, as well as the dysregulated pathways involved in tumor-stroma crosstalk in PCa pathology. This strategy markedly leverages the scope of quantitative-omics investigations using LCM samples, and combining with IonStar, can be readily adapted to larger-cohort clinical analysis. Moreover, the capacity of parallel proteomics/metabolomics quantification permits precise corroboration of regulatory processes on both protein and small-molecule levels, with decreased batch effect and enhanced utilization of samples.

DOI: https://doi.org/10.1021/acs.analchem.1c01026
Metabolites. 2021 Jun 07. pii: 364. [Epub ahead of print]11(6):

Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies.

Farideh Hosseinkhani, Anne-Charlotte Dubbelman, Naama Karu, Amy C Harms, Thomas Hankemeier.

  Gut microbiota and their metabolic products are increasingly being recognized as important modulators of human health. The fecal metabolome provides a functional readout of the interactions between human metabolism and the gut microbiota in health and disease. Due to the high complexity of the fecal matrix, sample preparation often introduces technical variation, which must be minimized to accurately detect and quantify gut bacterial metabolites. Here, we tested six different representative extraction methods (single-phase and liquid-liquid extractions) and compared differences due to fecal amount, extraction solvent type and solvent pH. Our results indicate that a minimum fecal (wet) amount of 0.50 g is needed to accurately represent the complex texture of feces. The MTBE method (MTBE/methanol/water, 3.6/2.8/3.5, v/v/v) outperformed the other extraction methods, reflected by the highest extraction efficiency for 11 different classes of compounds, the highest number of extracted features (97% of the total identified features in different extracts), repeatability (CV < 35%) and extraction recovery (≥70%). Importantly, optimization of the solvent volume of each step to the initial dried fecal material (µL/mg feces) offers a major step towards standardization, which enables confident assessment of the contributions of gut bacterial metabolites to human health.

Keywords:  LCMS (liquid chromatography mass spectrometry); fecal metabolites; gut microbiota; metabolomics; sample preparation

DOI:  https://doi.org/10.3390/metabo11060364
Chem Sci. 2021 May 04. 12(23): 8115-8122

Quantification and molecular imaging of fatty acid isomers from complex biological samples by mass spectrometry.

Hua Zhang, Meng Xu, Xudong Shi, Yuan Liu, Zihui Li, Justin C Jagodinsky, Min Ma, Nathan V Welham, Zachary S Morris, Lingjun Li.

Elucidating the isomeric structure of free fatty acids (FAs) in biological samples is essential to comprehend their biological functions in various physiological and pathological processes. Herein, we report a novel approach of using peracetic acid (PAA) induced epoxidation coupled with mass spectrometry (MS) for localization of the C[double bond, length as m-dash]C bond in unsaturated FAs, which enables both quantification and spatial visualization of FA isomers from biological samples. Abundant diagnostic fragment ions indicative of the C[double bond, length as m-dash]C positions were produced upon fragmentation of the FA epoxides derived from either in-solution or on-tissue PAA epoxidation of free FAs. The performance of the proposed approach was evaluated by analysis of FAs in human cell lines as well as mapping the FA isomers from cancer tissue samples with MALDI-TOF/TOF-MS. Merits of the newly developed method include high sensitivity, simplicity, high reaction efficiency, and capability of spatial characterization of FA isomers in tissue samples.

DOI: https://doi.org/10.1039/d1sc01614h
Adv Drug Deliv Rev. 2021 Jun 25. pii: S0169-409X(21)00236-2. [Epub ahead of print] 113844

High-Throughput Proteomics and AI for Cancer Biomarker Discovery.

Qi Xiao, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu, Tiannan Guo.

Biomarkers are assayed to assess biological and pathological status. Recent advances in high-throughput proteomic technology provide opportunities for developing next generation biomarkers for clinical practice aided by artificial intelligence (AI) based techniques. We summarize the advances and limitations of cancer biomarkers based on genomic and transcriptomic analysis, as well as classical antibody-based methodologies. Then we review recent progresses in mass spectrometry (MS)-based proteomics in terms of sample preparation, peptide fractionation by liquid chromatography (LC) and mass spectrometric data acquisition. We highlight applications of AI techniques in high-throughput clinical studies as compared with clinical decisions based on singular features. This review sets out our approach for discovering clinical biomarkers in studies using proteomic big data technology conjoined with computational and statistical methods.

DOI: https://doi.org/10.1016/j.addr.2021.113844
Cells. 2021 Jun 05. pii: 1393. [Epub ahead of print]10(6):

Cancer Metabolism as a New Real Target in Tumor Therapy.

Ferdinando Chiaradonna, Domenica Scumaci.

Cancer cells exhibit common hallmarks consisting of specific competencies acquired during the tumorigenesis process, including stimulation of cancer cell proliferation, insensitivity to growth signal inhibition, apoptosis evasion, enhancement of replicative potential, induction of angiogenesis, and tissue invasion and metastasis [...].

DOI: https://doi.org/10.3390/cells10061393
Curr Opin Chem Biol. 2021 Jun 24. pii: S1367-5931(21)00068-5. [Epub ahead of print]65 49-56

Solving the enigma: Mass spectrometry and small molecule probes to study sphingolipid function.

Alec Millner, G Ekin Atilla-Gokcumen.

  Sphingolipids are highly bioactive lipids. Sphingolipid metabolism produces key membrane components (e.g. sphingomyelin) and a variety of signaling lipids with different biological functions (e.g. ceramide, sphingosine-1-phosphate). The coordinated activity of tens of different enzymes maintains proper levels and localization of these lipids with key roles in cellular processes. In this review, we highlight the signaling roles of sphingolipids in cell death and survival. We discuss recent findings on the role of specific sphingolipids during these processes, enabled by the use of lipidomics to study compositional and spatial regulation of these lipids and synthetic sphingolipid probes to study subcellular localization and interaction partners of sphingolipids to understand the function of these lipids.

Keywords:  Apoptosis; Bifunctional; Ceramide; Ceramide-1-phosphate; Deoxyceramides; Inhibitor; Photoactivatable; Photoswitchable; Sphingomyelin; Sphingosine; Sphingosine-1-phosphate

DOI:  https://doi.org/10.1016/j.cbpa.2021.05.001
J Am Soc Mass Spectrom. 2021 Jun 30.

Re-Examining the Impact of Minimal Scans in Liquid Chromatography-Mass Spectrometry Analysis.

Jingwei Cai, Zhengyin Yan.

Liquid chromatography-mass spectrometry (LC-MS) is one of the most widely used analytical tools. High analysis volumes and sample complexity often demand more informative LC-MS acquisition schemes to improve efficiency and throughput without compromising data quality, and such a demand has been always hindered by the prerequisite that a minimum of 13-20 MS scans (data points) across an analyte peak are required for accurate quantitation. The current study systematically re-evaluated and compared the impact of different scan numbers on quantitation analysis using both triple quadrupoles mass spectrometry (TQMS) and high-resolution mass spectrometry (HRMS). Contrary to the 13-20 minimal scan prerequisite, the data obtained from a group of eight commercial drugs in the absence and presence of biological matrices suggest that 6 scans per analyte peak are sufficient to achieve highly comparable quantitation results compared to that obtained using 10 and 20 scans, respectively. The fewer minimal scan prerequisite is presumably attributed to an improved LC system and advanced column technology, better MS detector, and more intelligent peak detection and integration algorithms leading to a more symmetric peak shape and smaller peak standard deviation. As a result, more informative acquisition schemes can be broadly set up for higher throughput and more data-rich LC-MS/MS analysis as demonstrated in a hepatocyte clearance assay in which fewer MS scans executed on HRMS led to broader metabolite coverage without compromising data quality in hepatic clearance assessment. The demonstrated acquisition scheme would substantially increase the throughput, robustness, and richness of the nonregulatory analysis, which can be broadly applied in diverse fields including pharmaceutical, environmental, forensic, toxicological, and biotechnological.

DOI: https://doi.org/10.1021/jasms.1c00073
Metabolites. 2021 Jun 23. pii: 412. [Epub ahead of print]11(7):

Lipidomic Analysis to Assess Oxidative Stress in Acute Coronary Syndrome and Acute Stroke Patients.

Martin Malý, Martin Hajšl, Kamila Bechyňská, Ondřej Kučerka, Martin Šrámek, Jiří Suttnar, Alžběta Hlaváčková, Jana Hajšlová, Vít Kosek.

  Alterations in lipid metabolism mediated by oxidative stress play a key role in the process of atherosclerosis and superimposed thrombosis; these can lead to acute coronary syndrome (ACS) and acute ischemic stroke (AIS). Multiple studies have shown that the formation of atheromatous lesions is initiated by oxidation of low-density lipoproteins incorporated into the intima of the vessel wall. Here, we studied lipids in plasma samples from three cohorts: 61 patients with ACS (group A), 49 patients with AIS (group D), and 82 controls (group K). Untargeted lipidomics based on high-performance liquid chromatography coupled to mass spectrometry (UHPLC-HRMS) was employed to obtain comprehensive information on whether relationships exist between these patient categories based on lipid patterns. In addition, malondialdehyde (MDA) as a standard marker of oxidative stress was monitored. The most characteristic lipids in group K were fatty acyls of hydroxyfatty acids (FAHFAs). As expected, MDA concentrations were the lowest in group K. Our findings can better explain ongoing pathologies, both acute and chronic, with the potential for future diagnosis and treatment.

Keywords:  acute coronary syndrome; high-resolution mass spectrometry; lipidomics; plasma; stroke

DOI:  https://doi.org/10.3390/metabo11070412
Molecules. 2021 Jun 08. pii: 3498. [Epub ahead of print]26(12):

Development of a Derivatization Reagent with a 2-Nitrophenylsulfonyl Moiety for UHPLC-HRMS/MS and Its Application to Detect Amino Acids Including Taurine.

Shusuke Uekusa, Mayu Onozato, Tatsuya Sakamoto, Maho Umino, Hideaki Ichiba, Kenji Okoshi, Takeshi Fukushima.

  Taurine (Tau) has some important ameliorating effects on human health and is present in bivalve. For the selective analysis of Tau with other amino acids, we designed a derivatization reagent, 2,5-dioxopyrrolidin-1-yl(4-(((2-nitrophenyl)sulfonyl)oxy)-6-(3-oxomorpholino)quinoline-2-carbonyl)pyrrolidine-3-carboxylate (Ns-MOK-β-Pro-OSu). After derivatization with Ns-MOK-β-Pro-OSu, amino acids with Tau in Japanese littleneck clams were determined through ultra-high-performance-liquid chromatography with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) using an octadecyl silica column. We could detect 18 amino acids within 10 min. Tau, valine, glutamine, glutamic acid, and arginine in the clams were determined in the negative ion mode using the characteristic fragment ion, C6H4N1O5S, which corresponded to the 2-nitrobenzenesulfonylate moiety. The fragment ion, C6H4N1O5S, was recognized as a common feature regardless of the amino acid to be derivatized, and it was convenient for detecting amino acid derivatives with high selectivity and sensitivity. Therefore, highly selective quantification using UHPLC-HRMS/MS was possible using Ns-MOK-β-Pro-OSu.

Keywords:  clams; derivatization; glutamine; high-resolution mass spectrometry; taurine

DOI:  https://doi.org/10.3390/molecules26123498
Cancers (Basel). 2021 Jun 16. pii: 3018. [Epub ahead of print]13(12):

Metabolic Anti-Cancer Effects of Melatonin: Clinically Relevant Prospects.

Marek Samec, Alena Liskova, Lenka Koklesova, Kevin Zhai, Elizabeth Varghese, Samson Mathews Samuel, Miroslava Šudomová, Vincent Lucansky, Monika Kassayova, Martin Pec, Kamil Biringer, Aranka Brockmueller, Karol Kajo, Sherif T S Hassan, Mehdi Shakibaei, Olga Golubnitschaja, Dietrich Büsselberg, Peter Kubatka.

  Metabolic reprogramming characterized by alterations in nutrient uptake and critical molecular pathways associated with cancer cell metabolism represents a fundamental process of malignant transformation. Melatonin (N-acetyl-5-methoxytryptamine) is a hormone secreted by the pineal gland. Melatonin primarily regulates circadian rhythms but also exerts anti-inflammatory, anti-depressant, antioxidant and anti-tumor activities. Concerning cancer metabolism, melatonin displays significant anticancer effects via the regulation of key components of aerobic glycolysis, gluconeogenesis, the pentose phosphate pathway (PPP) and lipid metabolism. Melatonin treatment affects glucose transporter (GLUT) expression, glucose-6-phosphate dehydrogenase (G6PDH) activity, lactate production and other metabolic contributors. Moreover, melatonin modulates critical players in cancer development, such as HIF-1 and p53. Taken together, melatonin has notable anti-cancer effects at malignancy initiation, progression and metastasing. Further investigations of melatonin impacts relevant for cancer metabolism are expected to create innovative approaches supportive for the effective prevention and targeted therapy of cancers.

Keywords:  Warburg effect; anti-depressant; anti-inflammatory; anti-tumor; antioxidant; cancer; melatonin; metabolism; mitochondrial dysfunction; predictive preventive personalized medicine (PPPM/3PM)

DOI:  https://doi.org/10.3390/cancers13123018
Mol Cell. 2021 Jul 01. pii: S1097-2765(21)00492-5. [Epub ahead of print]81(13): 2686-2687

A delicate initiation: Lipolysis of lipid droplets fuels glioblastoma.

Kailin Yang, Jeremy N Rich.

Liu et al. (2021) demonstrate that CHKα2 is capable of promoting lipolysis of lipid droplets through mechanisms that require sequential steps of post-translational modifications after glucose deprivation. Intriguingly, the oxidation of fatty acids derived from lipid droplets is essential for the survival of tumor cells that informs clinical outcome among glioblastoma patients.

DOI: https://doi.org/10.1016/j.molcel.2021.06.013
Cancers (Basel). 2021 Jun 23. pii: 3140. [Epub ahead of print]13(13):

Plasma Metabolomics for Discovery of Early Metabolic Markers of Prostate Cancer Based on Ultra-High-Performance Liquid Chromatography-High Resolution Mass Spectrometry.

Xiangping Lin, Lucie Lécuyer, Xinyu Liu, Mohamed N Triba, Mélanie Deschasaux-Tanguy, Aïcha Demidem, Zhicheng Liu, Tony Palama, Adrien Rossary, Marie-Paule Vasson, Serge Hercberg, Pilar Galan, Philippe Savarin, Guowang Xu, Mathilde Touvier.

   BACKGROUND: The prevention and early screening of PCa is highly dependent on the identification of new biomarkers. In this study, we investigated whether plasma metabolic profiles from healthy males provide novel early biomarkers associated with future risk of PCa.
METHODS: Using the Supplémentation en Vitamines et Minéraux Antioxydants (SU.VI.MAX) cohort, we identified plasma samples collected from 146 PCa cases up to 13 years prior to diagnosis and 272 matched controls. Plasma metabolic profiles were characterized using ultra-high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS).
RESULTS: Orthogonal partial least squares discriminant analysis (OPLS-DA) discriminated PCa cases from controls, with a median area under the receiver operating characteristic curve (AU-ROC) of 0.92 using a 1000-time repeated random sub-sampling validation. Sparse Partial Least Squares Discriminant Analysis (sPLS-DA) identified the top 10 most important metabolites (p < 0.001) discriminating PCa cases from controls. Among them, phosphate, ethyl oleate, eicosadienoic acid were higher in individuals that developed PCa than in the controls during the follow-up. In contrast, 2-hydroxyadenine, sphinganine, L-glutamic acid, serotonin, 7-keto cholesterol, tiglyl carnitine, and sphingosine were lower.
CONCLUSION: Our results support the dysregulation of amino acids and sphingolipid metabolism during the development of PCa. After validation in an independent cohort, these signatures may promote the development of new prevention and screening strategies to identify males at future risk of PCa.

Keywords:  LC-MS; biomarkers; metabolomics; multivariate analysis; prostate cancer

DOI:  https://doi.org/10.3390/cancers13133140
Expert Rev Proteomics. 2021 Jul 01.

Mass spectrometry-based clinical proteomics - a revival.

Jarne Pauwels, Kris Gevaert.



Keywords:  biomarker discovery; clinical proteomics; mass spectrometry; proteoforms

DOI:  https://doi.org/10.1080/14789450.2021.1950536
Talanta. 2021 Oct 01. pii: S0039-9140(21)00489-6. [Epub ahead of print]233 122568

Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples.

Artur Pirog, Jakub Faktor, Zuzanna Urban-Wojciuk, Sachin Kote, Elżbieta Chruściel, Łukasz Arcimowicz, Natalia Marek-Trzonkowska, Borek Vojtesek, Ted R Hupp, Sofian Al Shboul, Paul M Brennan, Ryszard Tomasz Smoleński, David R Goodlett, Irena Dapic.

  Proteomics of human tissues and isolated cellular subpopulations create new opportunities for therapy and monitoring of a patients' treatment in the clinic. Important considerations in such analysis include recovery of adequate amounts of protein for analysis and reproducibility in sample collection. In this study we compared several protocols for proteomic sample preparation: i) filter-aided sample preparation (FASP), ii) in-solution digestion (ISD) and iii) a pressure-assisted digestion (PCT) method. PCT method is known for already a decade [1], however it is not widely used in proteomic research. We assessed protocols for proteome profiling of isolated immune cell subsets and formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that the ISD method has very good efficiency of protein and peptide identification from the whole proteome, while the FASP method is particularly effective in identification of membrane proteins. Pressure-assisted digestion methods generally provide lower numbers of protein/peptide identifications, but have gained in popularity due to their shorter digestion time making them considerably faster than for ISD or FASP. Furthermore, PCT does not result in substantial sample loss when applied to samples of 50 000 cells. Analysis of FFPE tissues shows comparable results. ISD method similarly yields the highest number of identifications. Furthermore, proteins isolated from FFPE samples show a significant reduction of cleavages at lysine sites due to chemical modifications with formaldehyde-such as methylation (+14 Da) being among the most common. The data we present will be helpful for making decisions about the robust preparation of clinical samples for biomarker discovery and studies on pathomechanisms of various diseases.

Keywords:  Cellular subpopulations; FASP; FFPE tissue Proteomics; In-solution digestion; Pressure-cycling digestion; Proteomics

DOI:  https://doi.org/10.1016/j.talanta.2021.122568
Metabolites. 2021 Jun 24. pii: 416. [Epub ahead of print]11(7):

Targeted Metabolomics: The LC-MS/MS Based Quantification of the Metabolites Involved in the Methylation Biochemical Pathways.

Georgia Ntasi, Anthony Tsarbopoulos, Emmanuel Mikros, Evagelos Gikas.

  Biochemical methylation reactions mediate the transfer of the methyl group regulating vital biochemical reactions implicated in various diseases as well as the methylation of DNA regulating the replication processes occurring in living organisms. As a finite number of methyl carriers are involved in the methyl transfer, their quantification could aid towards the assessment of an organism's methylation potential. An Hydrophilic Interaction Chromatography-Liquid Chromatography Multiple Reaction Monitoring (HILIC-LC-MRM) mass spectrometry (MS) methodology was developed and validated according to Food & Drug Administration (FDA), European Medicines Agency (EMA), and International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) for the simultaneous determination of nine metabolites i.e., B12, folic acid, 5-methyltetrahydrofolate, S-adenosylmethionine, S-adenosylhomocysteine, betaine, phosphocholine, N,N-dimethylglycine, and deoxythymidine monophosphate in human blood plasma. The sample pretreatment was based on a single step Solid-phase extraction (SPE) methodology using C18 cartridges. The methodology was found to accurately quantitate the analytes under investigation according to the corresponding dynamic range proposed in the literature for each analyte. The applicability of the method was assessed using blood donor samples and its applicability demonstrated by the assessment of their basal levels, which were shown to agree with the established basal levels. The methodology can be used for diagnostic purposes as well as for epigenetic screening.

Keywords:  Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS); methylation; solid phase extraction; validation

DOI:  https://doi.org/10.3390/metabo11070416