bims-mascan 2023-09-17 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2023–09–17
twenty-six papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.
Identification of pre-diagnostic lipid sets associated with liver cancer risk using untargeted lipidomics and chemical set analysis: A nested case-control study within the ATBC cohort.
Development of a targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry based lipidomics platform applied to a coronavirus disease severity study.
The Role of Stroma in Cancer Metabolism.
Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics.
Screening in serum-derived medium reveals differential response to compounds targeting metabolism.
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics.
Rapid probing of glucose influx into cancer cell metabolism: using adjuvant and a pH-dependent collection of central metabolites to improve in-cell D-DNP NMR.
RARRES2's impact on lipid metabolism in triple-negative breast cancer: a pathway to brain metastasis.
One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles.
Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species.
Automated sample preparation with 6-Aminoquinolyl-N-hydroxysuccinimidyl carbamate and iodoacetamide derivatization reagents for enantioselective liquid chromatography tandem mass spectrometry amino acid analysis.
4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-Linking Mass Spectrometry.
Tumor microenvironmental nutrients, cellular responses, and cancer.
Application and prospect of metabolomics in the early diagnosis of osteoporosis: a narrative review.
Metabolomics analysis of amino acid and fatty acids in colorectal cancer patients based on tandem mass spectrometry.
Nontargeted screening of aldehydes and ketones by chemical isotope labeling combined with ultra-high performance liquid chromatography-high resolution mass spectrometry followed by hybrid filtering of features.
Untargeted 4D-metabolomics using Trapped Ion Mobility combined with LC-HRMS in extra virgin olive oil adulteration study with lower-quality olive oils.
Development of a new online SPE-HPLC-MS/MS method for the profiling and quantification of sphingolipids and phospholipids in red blood cells - Application to the study of Gaucher's disease.
Serine starvation silences estrogen receptor signaling through histone hypoacetylation.
Cholesterol reprograms glucose and lipid metabolism to promote proliferation in colon cancer cells.
Metabolomics provides insights into acceleration of bone healing in fractured patients with traumatic brain injuries.
A protocol for isolating and imaging large extracellular vesicles or midbody remnants from mammalian cell culture.
Localization and Quantification of Post-Translational Modifications of Proteins Using Electron Activated Dissociation Fragmentation on a Fast-Acquisition Time-of-Flight Mass Spectrometer.
Dynamic lipidome alterations associated with human health, disease and ageing.
The lipoprotein-associated phospholipase A2 inhibitor Darapladib sensitises cancer cells to ferroptosis by remodelling lipid metabolism.

J Proteome Res. 2023 Sep 11.

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.

Georg Wallmann, Andrew Leduc, Nikolai Slavov.

  Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data-independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.

Keywords:  DO-MS; MS; acquisition; control; data; mass spectrometry; optimization; plexDIA; proteomics; quality; single-cell, visualization

DOI:  https://doi.org/10.1021/acs.jproteome.3c00177
Int J Cancer. 2023 Sep 11.

Identification of pre-diagnostic lipid sets associated with liver cancer risk using untargeted lipidomics and chemical set analysis: A nested case-control study within the ATBC cohort.

Dinesh K Barupal, Mark L Ramos, Andrea A Florio, William A Wheeler, Stephanie J Weinstein, Demetrius Albanes, Oliver Fiehn, Barry I Graubard, Jessica L Petrick, Katherine A McGlynn.

  In pre-disposed individuals, a reprogramming of the hepatic lipid metabolism may support liver cancer initiation. We conducted a high-resolution mass spectrometry based untargeted lipidomics analysis of pre-diagnostic serum samples from a nested case-control study (219 liver cancer cases and 219 controls) within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Out of 462 annotated lipids, 158 (34.2%) were associated with liver cancer risk in a conditional logistic regression analysis at a false discovery rate (FDR) <0.05. A chemical set enrichment analysis (ChemRICH) and co-regulatory set analysis suggested that 22/28 lipid classes and 47/83 correlation modules were significantly associated with liver cancer risk (FDR <0.05). Strong positive associations were observed for monounsaturated fatty acids (MUFA), triacylglycerols (TAGs) and phosphatidylcholines (PCs) having MUFA acyl chains. Negative associations were observed for sphingolipids (ceramides and sphingomyelins), lysophosphatidylcholines, cholesterol esters and polyunsaturated fatty acids (PUFA) containing TAGs and PCs. Stearoyl-CoA desaturase enzyme 1 (SCD1), a rate limiting enzyme in fatty acid metabolism and ceramidases seems to be critical in this reprogramming. In conclusion, our study reports pre-diagnostic lipid changes that provide novel insights into hepatic lipid metabolism reprogramming may contribute to a pro-cell growth and anti-apoptotic tissue environment and, in turn, support liver cancer initiation.

Keywords:  ATBC study; ChemRICH; ceramides; lipidomics; liver cancer; metabolic reprogramming

DOI:  https://doi.org/10.1002/ijc.34726
J Chromatogr A. 2023 Aug 31. pii: S0021-9673(23)00567-8. [Epub ahead of print]1708 464342

Development of a targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry based lipidomics platform applied to a coronavirus disease severity study.

Zhengzheng Zhang, Madhulika Singh, Alida Kindt, Agnieszka B Wegrzyn, Mackenzie J Pearson, Ahmed Ali, Amy C Harms, Paul Baker, Thomas Hankemeier.

  The importance of lipids seen in studies of metabolism, cancer, the recent COVID-19 pandemic and other diseases has brought the field of lipidomics to the forefront of clinical research. Quantitative and comprehensive analysis is required to understand biological interactions among lipid species. However, lipidomic analysis is often challenging due to the various compositional structures, diverse physicochemical properties, and wide dynamic range of concentrations of lipids in biological systems. To study the comprehensive lipidome, a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS)-based screening method with 1200 lipid features across 19 (sub)classes, including both nonpolar and polar lipids, has been developed. HILIC-MS/MS was selected due to its class separation property and fatty acyl chain level information. 3D models of class chromatographic retention behavior were established and evaluations of cross-class and within-class interferences were performed to avoid over-reporting these features. This targeted HILIC-MS/MS method was fully validated, with acceptable analytical parameters in terms of linearity, precision, reproducibility, and recovery. The accurate quantitation of 608 lipid species in the SRM 1950 NIST plasma was achieved using multi-internal standards per class and post-hoc correction, extending current databases by providing lipid concentrations resolved at fatty acyl chain level. The overall correlation coefficients (R2) of measured concentrations with values from literature range from 0.64 to 0.84. The applicability of the developed targeted lipidomics method was demonstrated by discovering 520 differential lipid features related to COVID-19 severity. This high coverage and targeted approach will aid in future investigations of the lipidome in various disease contexts.

Keywords:  COVID-19; Clinical lipidomics; HILIC-MS/MS; NIST SRM 1950 plasma; Over-reporting; Quantitation

DOI:  https://doi.org/10.1016/j.chroma.2023.464342
Cold Spring Harb Perspect Med. 2023 Sep 11. pii: a041540. [Epub ahead of print]

The Role of Stroma in Cancer Metabolism.

Alec C Kimmelman, Mara H Sherman.

The altered metabolism of tumor cells is a well-known hallmark of cancer and is driven by multiple factors such as mutations in oncogenes and tumor suppressor genes, the origin of the tissue where the tumor arises, and the microenvironment of the tumor. These metabolic changes support the growth of cancer cells by providing energy and the necessary building blocks to sustain proliferation. Targeting these metabolic alterations therapeutically is a potential strategy to treat cancer, but it is challenging due to the metabolic plasticity of tumors. Cancer cells have developed ways to scavenge nutrients through autophagy and macropinocytosis and can also form metabolic networks with stromal cells in the tumor microenvironment. Understanding the role of the tumor microenvironment in tumor metabolism is crucial for effective therapeutic targeting. This review will discuss tumor metabolism and the contribution of the stroma in supporting tumor growth through metabolic interactions.

DOI: https://doi.org/10.1101/cshperspect.a041540
bioRxiv. 2023 Aug 29. pii: 2023.08.28.555225. [Epub ahead of print]

Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics.

Ting Huang, Jian Wang, Alexey Stukalov, Margaret K R Donovan, Shadi Ferdosi, Lucy Williamson, Seth Just, Gabriel Castro, Lee S Cantrell, Eltaher Elgierari, Ryan W Benz, Yingxiang Huang, Khatereh Motamedchaboki, Amirmansoor Hakimi, Tabiwang Arrey, Eugen Damoc, Simion Kreimer, Omid C Farokhzad, Serafim Batzoglou, Asim Siddiqui, Jennifer E Van Eyk, Daniel Hornburg.

Background: The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic range of protein abundances into a mass spectrometry (MS)-accessible detection range. This enhances the depth and scalability of quantitative MS-based methods, which can elucidate the molecular mechanisms of biological processes, discover new protein biomarkers, and improve comprehensiveness of MS-based diagnostics.
Methods: Investigating multi-species spike-in experiments and a cohort, we investigated fold-change accuracy, linearity, precision, and statistical power for the using the Proteograph™ Product Suite, a deep plasma proteomics workflow, in conjunction with multiple MS instruments.
Results: We show that NP-based workflows enable accurate identification (false discovery rate of 1%) of more than 6,000 proteins from plasma (Orbitrap Astral) and, compared to a gold standard neat plasma workflow that is limited to the detection of hundreds of plasma proteins, facilitate quantification of more proteins with accurate fold-changes, high linearity, and precision. Furthermore, we demonstrate high statistical power for the discovery of biomarkers in small- and large-scale cohorts.
Conclusions: The automated NP workflow enables high-throughput, deep, and quantitative plasma proteomics investigation with sufficient power to discover new biomarker signatures with a peptide level resolution.

DOI: https://doi.org/10.1101/2023.08.28.555225
Cell Chem Biol. 2023 Aug 31. pii: S2451-9456(23)00279-9. [Epub ahead of print]

Screening in serum-derived medium reveals differential response to compounds targeting metabolism.

Keene L Abbott, Ahmed Ali, Dominick Casalena, Brian T Do, Raphael Ferreira, Jaime H Cheah, Christian K Soule, Amy Deik, Tenzin Kunchok, Daniel R Schmidt, Steffen Renner, Sophie E Honeder, Michelle Wu, Sze Ham Chan, Tenzin Tseyang, Andrew T Stoltzfus, Sarah L J Michel, Daniel Greaves, Peggy P Hsu, Christopher W Ng, Chelsea J Zhang, Ali Farsidjani, Johnathan R Kent, Maria Lucia L Madariaga, Iva Monique T Gramatikov, Nicholas J Matheson, Caroline A Lewis, Clary B Clish, Matthew G Rees, Jennifer A Roth, Lesley Mathews Griner, Alexander Muir, Douglas S Auld, Matthew G Vander Heiden.

  A challenge for screening new anticancer drugs is that efficacy in cell culture models is not always predictive of efficacy in patients. One limitation of standard cell culture is a reliance on non-physiological nutrient levels, which can influence cell metabolism and drug sensitivity. A general assessment of how physiological nutrients affect cancer cell response to small molecule therapies is lacking. To address this, we developed a serum-derived culture medium that supports the proliferation of diverse cancer cell lines and is amenable to high-throughput screening. We screened several small molecule libraries and found that compounds targeting metabolic enzymes were differentially effective in standard compared to serum-derived medium. We exploited the differences in nutrient levels between each medium to understand why medium conditions affected the response of cells to some compounds, illustrating how this approach can be used to screen potential therapeutics and understand how their efficacy is modified by available nutrients.

Keywords:  Cancer cell metabolism; Culture media; Drug sensitivity; High-throughput screening; Nutrient environment; Phenotypic drug screening; Physiologic media

DOI:  https://doi.org/10.1016/j.chembiol.2023.08.007
Proteomics. 2023 Sep 14. e2300236

Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics.

Nicolai B Palstrøm, Amanda J Campbell, Caroline A Lindegaard, Samir Cakar, Rune Matthiesen, Hans C Beck.

  Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching. Protein identifications made by the spectral library search engine demonstrated a high degree of complementarity with the sequence database search engine, indicating the feasibility of increasing the number of protein identifications without additional pre-analytical sample preparation. The TMTpro-specific spectral library provides a resource for future plasma proteomics research and optimization of search algorithms for greater accuracy and speed in protein identifications in human plasma proteomics, and is made publicly available to the research community via ProteomeXchange with identifier PXD042546.

Keywords:  TMTpro; peptide identification; plasma proteomics; spectral library search

DOI:  https://doi.org/10.1002/pmic.202300236
Anal Methods. 2023 Sep 13.

Rapid probing of glucose influx into cancer cell metabolism: using adjuvant and a pH-dependent collection of central metabolites to improve in-cell D-DNP NMR.

Francesca Sannelli, Ke-Chuan Wang, Pernille Rose Jensen, Sebastian Meier.

Changes to metabolism are a hallmark of many diseases. Disease metabolism under physiological conditions can be probed in real time with in-cell NMR assays. Here, we pursued a systematic approach towards improved in-cell NMR assays. Unambiguous identifications of metabolites and of intracellular pH are afforded by a comprehensive, downloadable collection of spectral data for central carbon metabolites in the physiological pH range (4.0-8.0). Chemical shifts of glycolytic intermediates provide unique pH dependent patterns akin to a barcode. Using hyperpolarized 13C1 enriched glucose as the probe molecule of central metabolism in cancer, we find that early glycolytic intermediates are detectable in PC-3 prostate cancer cell lines, concurrently yielding intracellular pH. Using non-enriched and non-enhanced pyruvate as an adjuvant, reactions of the pentose phosphate pathway become additionally detectable, without significant changes to the barriers in upper glycolysis and to intracellular pH. The scope of tracers for in-cell observations can thus be improved by the presence of adjuvants, showing that a recently proposed effect of pyruvate in the tumor environment is paralleled by a rerouting of cancer cell metabolism towards producing building blocks for proliferation. Overall, the combined use of reference data for compound identification, site specific labelling for reducing overlap, and use of adjuvant afford increasingly detailed insight into disease metabolism.

DOI: https://doi.org/10.1039/d3ay01120h
Mil Med Res. 2023 Sep 12. 10(1): 42

RARRES2's impact on lipid metabolism in triple-negative breast cancer: a pathway to brain metastasis.

Quazi T H Shubhra.



Keywords:  Brain metastasis; Cancer; Lipid metabolism; Metabolic reprogramming; PTEN-mTOR-SREBP1 signaling; Retinoic acid receptor responder 2 (RARRES2)

DOI:  https://doi.org/10.1186/s40779-023-00480-w
J Proteome Res. 2023 Sep 13.

One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles.

Yi-Kai Liu, Xiaofeng Wu, Marco Hadisurya, Li Li, Hristos Kaimakliotis, Anton Iliuk, W Andy Tao.

  Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.

Keywords:  EVtrap; bladder cancer; extracellular vesicles; proteomics; urine

DOI:  https://doi.org/10.1021/acs.jproteome.3c00361
J Am Soc Mass Spectrom. 2023 Sep 13.

Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species.

Komal Kedia, Rachel Harris, Kim Ekroos, Kelly W Moser, Daniel DeBord, Paolo Tiberi, Laura Goracci, Nanyan Rena Zhang, Weixun Wang, Daniel S Spellman, Kevin Bateman.

Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.

DOI: https://doi.org/10.1021/jasms.3c00157
J Chromatogr A. 2023 Sep 03. pii: S0021-9673(23)00574-5. [Epub ahead of print]1708 464349

Automated sample preparation with 6-Aminoquinolyl-N-hydroxysuccinimidyl carbamate and iodoacetamide derivatization reagents for enantioselective liquid chromatography tandem mass spectrometry amino acid analysis.

Feiyang Li, Ryan Karongo, Despoina Mavridou, Jeannie Horak, Adrian Sievers-Engler, Michael Lämmerhofer.

  Enantioselective amino acid analysis is gaining increasing importance in pharmaceutical, biomedical and food sciences. While there are many methods available for enantiomer separation of amino acids, the simultaneous analysis of all chiral proteinogenic amino acids by a single method with one column and a single condition is still challenging. Herein, we report an enantioselective high-performance liquid chromatography-tandem mass spectrometry (LC-MS) assay using Chiralpak QN-AX as chiral column. With 6-aminoquinolyl-N-hydrosysuccinimidyl carbamate (AQC) as derivatization reagent, efficient enantioselective separation of D- and L-amino acids using HPLC has become possible. Thiol-containing amino acids like Cys are alkylated prior to AQC-labelling. A protocol for automated sample preparation including both derivatization step and calibrator preparation is presented. For compensating matrix effects, u-13C15N-labelled internal standards (IS) were employed. The method was validated and applied to the enantioselective analysis of amino acids in a bacterial fermentation broth.

Keywords:  Amino acids analysis; Automation; Enantioselective separations; LC-MS/MS

DOI:  https://doi.org/10.1016/j.chroma.2023.464349
Anal Chem. 2023 Sep 10.

4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-Linking Mass Spectrometry.

Yanhong Hao, Moran Chen, Xiao Huang, Hui Xu, Pengfei Wu, Suming Chen.

Cross-linking mass spectrometry (XL-MS) is a powerful tool for examining protein structures and interactions. Nevertheless, analysis of low-abundance cross-linked peptides is often limited in the data-dependent acquisition (DDA) mode due to its semistochastic nature. To address this issue, we introduced a workflow called 4D-diaXLMS, representing the first-ever application of four-dimensional data-independent acquisition for proteome-wide cross-linking analysis. Cross-linking studies of the HeLa cell proteome were evaluated using the classical cross-linker disuccinimidyl suberate as an example. Compared with the DDA analysis, 4D-diaXLMS exhibited marked improvement in the identification coverage of cross-linked peptides, with a total increase of 36% in single-shot analysis across all 16 SCX fractions. This advantage was further amplified when reducing the fraction number to 8 and 4, resulting in 125 and 149% improvements, respectively. Using 4D-diaXLMS, up to 83% of the cross-linked peptides were repeatedly identified in three replicates, more than twice the 38% in the DDA mode. Furthermore, 4D-diaXLMS showed good performance in the quantitative analysis of yeast cross-linked peptides even in a 15-fold excess amount of HeLa cell matrix, with a low coefficient of variation and high quantitative accuracies in all concentrations. Overall, 4D-diaXLMS was proven to have high coverage, good reproducibility, and accurate quantification for in-depth XL-MS analysis in complex samples, demonstrating its immense potential for advances in the field.

DOI: https://doi.org/10.1021/acs.analchem.3c02824
Cell Chem Biol. 2023 Sep 01. pii: S2451-9456(23)00281-7. [Epub ahead of print]

Tumor microenvironmental nutrients, cellular responses, and cancer.

Graham P Lobel, Yanqing Jiang, M Celeste Simon.

  Over the last two decades, the rapidly expanding field of tumor metabolism has enhanced our knowledge of the impact of nutrient availability on metabolic reprogramming in cancer. Apart from established roles in cancer cells themselves, various nutrients, metabolic enzymes, and stress responses are key to the activities of tumor microenvironmental immune, fibroblastic, endothelial, and other cell types that support malignant transformation. In this article, we review our current understanding of how nutrient availability affects metabolic pathways and responses in both cancer and "stromal" cells, by dissecting major examples and their regulation of cellular activity. Understanding the relationship of nutrient availability to cellular behaviors in the tumor ecosystem will broaden the horizon of exploiting novel therapeutic vulnerabilities in cancer.

Keywords:  Cancer metabolism; cancer therapeutics; cancer-associated fibroblasts; immune cell metabolism; nutrient exchange; stress responses; tumor microenvironment

DOI:  https://doi.org/10.1016/j.chembiol.2023.08.011
Bioanalysis. 2023 Sep 11.

Application and prospect of metabolomics in the early diagnosis of osteoporosis: a narrative review.

Yan Li, Yuhao Si, Yong Ma, Heng Yin.

  This paper reviews the application of metabolomics in the early diagnosis of osteoporosis in recent years. The authors searched electronic databases for the keywords "metabolomics", "osteoporosis" and "biomarkers", then analyzed the relationship between functional markers and osteoporosis using categorical summarization. Lipid metabolism, amino acid metabolism and energy metabolism are closely related to osteoporosis development and can become early diagnostic markers of the condition. However, the existing studies in metabolomics suffer from varying application methods, difficulty in identifying isomers, small study cohorts and insufficient research on metabolic mechanisms. Consequently, it is important for future research to focus on broadening and standardizing the scope of the application of metabolomics. High-quality studies on a large scale should also be conducted while promoting the early diagnosis of osteoporosis in a more precise, comprehensive and sensitive manner.

Keywords:  amino acid metabolism; biomarkers; energy metabolism; lipid metabolism; metabolomics; osteoporosis

DOI:  https://doi.org/10.4155/bio-2023-0131
J Clin Biochem Nutr. 2023 Sep;73(2): 161-171

Metabolomics analysis of amino acid and fatty acids in colorectal cancer patients based on tandem mass spectrometry.

Zhuo Zhao, Jing Bai, Chang Liu, Yansong Wang, Shuang Wang, Furong Zhao, Qiufang Gu.

  Metabolic differences between colorectal cancer (CRC) and NI (NI) play an important role in early diagnoses and in-time treatments. We investigated the metabolic alterations between CRC patients and NI, and identified some potential biomarkers, and these biomarkers might be used as indicators for diagnosis of CRC. In this study, there were 79 NI, 50 CRC I patients, 52 CRC II patients, 56 CRC III patients, and 52 CRC IV patients. MS-MS was used to measure the metabolic alterations. Univariate and multivariate data analysis and metabolic pathway analysis were applied to analyze metabolic data and determine differential metabolites. These indicators revealed that amino acid and fatty acids could separate these groups. Several metabolites indicated an excellent variables capability in the separation of CRC patients and NI. Ornithine, arginine, octadecanoyl carnitine, palmitoyl carnitine, adipoyl carnitine, and butyryl carnitine/propanoyl carnitine were selected to distinguish the CRC patients and NI. And methionine and propanoyl carnitine, were directly linked to different stages of CRC. Receiver operating characteristics curves and variables importance in projection both represented an excellent performance of these metabolites. In conclusion, we assessed the difference between CRC patients and NI, which supports guidelines for an early diagnosis and effective treatment.

Keywords:  MS/MS; biomarkers; colorectal cancer; metabolomics; statistical analysis

DOI:  https://doi.org/10.3164/jcbn.22-110
J Chromatogr A. 2023 Aug 28. pii: S0021-9673(23)00557-5. [Epub ahead of print]1708 464332

Nontargeted screening of aldehydes and ketones by chemical isotope labeling combined with ultra-high performance liquid chromatography-high resolution mass spectrometry followed by hybrid filtering of features.

Ruizhi Zhu, Han Chen, Meiyan Liu, Yanqun Xu, Wei Jiang, Xiaoxi Si, Lunzhao Yi, Ying Gu, Dabing Ren, Juan Wang.

  Aldehydes and ketones are important carbonyl compounds that are widely present in foodstuffs, biological organisms and human living environment. However, it is still challenging to comprehensively detect and capture them using liquid chromatography - mass spectrometry. In this work, a chemical isotope labeling (CIL) coupled with ultra-high performance liquid chromatography - high resolution mass spectrometry (UHPLC-HRMS) strategy was developed for the capture and detection of this class of compounds. 2,4-Dinitrophenylhydrazine (DNPH) and isotope-labeled DNPH (DNPH-d3) were utilized to selectively label the target analytes. To address the difficulties in processing UHPLC-HRMS data, a post-acquisition data processing method called MSFilter was proposed to facilitate the screening and identification aldehydes and ketones in complex matrices. The MSFilter consists of four independent filters, namely statistical characteristic-based filtering, mass defect filtering, CIL paired peaks filtering, and diagnostic fragmentation ion filtering. These filters can be used individually or in combination to eliminate unrelated interfering MS features and efficiently detect DNPH-labeled aldehydes and ketones. The results of a mixture containing 48 model compounds showed that although all individual filtering methods could significantly reduce more than 95% of the raw MS features with acceptable recall rates above 85%, but they had relatively high false positive ratios of over 90%. In comparison, the hybrid filtering method combining four filters is able to eliminate massive interfering features (> 99.5%) with a high recall rate of 81.25% and a much lower false positive ratio of 15.22%. By implementing the hybrid filtering method in MSFilter, a total of 154 features were identified as potential signals of CCs from the original 45,961 features of real tobacco samples, of which 70 were annotated. We believe that the proposed strategy is promising to analyze the potential CCs in complex samples by UHPLC-HRMS.

Keywords:  Aldehydes and ketones; Chemical isotope labeling; Feature filtering; High resolution mass spectrometry; Targeted recognition

DOI:  https://doi.org/10.1016/j.chroma.2023.464332
Food Chem. 2023 Sep 12. pii: S0308-8146(23)02028-9. [Epub ahead of print]434 137410

Untargeted 4D-metabolomics using Trapped Ion Mobility combined with LC-HRMS in extra virgin olive oil adulteration study with lower-quality olive oils.

Sofia K Drakopoulou, Anastasia S Kritikou, Carsten Baessmann, Nikolaos S Thomaidis.

  Metabolomics is widely established in the field of food authenticity to address demanding issues, such as adulteration cases. Trapped ion mobility spectrometry (TIMS) coupled to liquid chromatography (LC) and high-resolution mass spectrometry (HRMS) provides an additional analytical dimension, introducing mobility-enhanced metabolomics in four dimensions (4D). In the present work, the potential of LC-TIMS-HRMS as a reliable analytical platform for authenticity studies is being explored, applied in extra virgin olive oil (EVOO) adulteration study. An integrated untargeted 4D-metabolomics approach is being implemented to investigate adulteration, with refined olive oils (ROOs) and olive pomace oils (OPOs) set as adulterants. Robust prediction models are built, successfully discriminating authentic EVOOs from adulterated ones and highlighting markers in each group. Noteworthy outcomes are retrieved regarding TIMS added value in LC-HRMS workflows, resulting in a significant increase of metabolic coverage, while, thanks to platform's enhanced sensitivity, detection of adulteration is being achieved down to 1%.

Keywords:  Adulteration; Extra virgin olive oil; LC-TIMS-HRMS; Metabolomics; Olive pomace oil; Refined olive oil

DOI:  https://doi.org/10.1016/j.foodchem.2023.137410
Anal Chim Acta. 2023 Oct 16. pii: S0003-2670(23)00940-6. [Epub ahead of print]1278 341719

Development of a new online SPE-HPLC-MS/MS method for the profiling and quantification of sphingolipids and phospholipids in red blood cells - Application to the study of Gaucher's disease.

Terkia Bettioui, Caroline Chipeaux, Kaouther Ben Arfa, Sylvie Héron, Nadia Belmatoug, Mélanie Franco, Marine de Person, Fathi Moussa.

  Red blood cells (RBCs) are the subject of clinical attention due to their biological importance. Recently, it has been shown that certain erythrocyte pathologies could be linked to an abnormal lipid composition. In this work, we have developed a simple and fast method using online sample preparation with liquid chromatography coupled to mass spectrometry (SPE-HPLC-MS/MS), to identify a large number of sphingolipids (SL) and phospholipids (PL). The use of online sample preparation considerably reduces analysis times (15 min including extraction and separation of lipids + 2 min for system re-equilibration) and facilitates experimentation while ensuring very good extraction yields. This method was then successfully applied to the quantification of 30 sphingolipids and phospholipids in plasma and erythrocyte extracts from a cohort of individuals with Gaucher disease, treated or not by enzymotherapy. Our results for the study of this disease, led us to establish the lipid profile of the healthy red blood cells, still not very well-known to date. For this, we adopted a semi-targeted approach, based on the use of a triple-quadrupole analyzer and identified more than two hundred different lipid species. These promising results will hopefully enable us to enrich our knowledge of the normal red blood cells lipidome.

Keywords:  Gaucher's disease; Online SPE-HPLC-MS/MS; Red blood cells lipidome; Sphingolipid and phospholipid profiling

DOI:  https://doi.org/10.1016/j.aca.2023.341719
Proc Natl Acad Sci U S A. 2023 Sep 19. 120(38): e2302489120

Serine starvation silences estrogen receptor signaling through histone hypoacetylation.

Albert M Li, Bo He, Dimitris Karagiannis, Yang Li, Haowen Jiang, Preethi Srinivasan, Yaniel Ramirez, Meng-Ning Zhou, Christina Curtis, Joshua J Gruber, Chao Lu, Erinn B Rankin, Jiangbin Ye.

  Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.

Keywords:  SLC25A1; breast cancer; estrogen receptor; histone acetylation; serine metabolism

DOI:  https://doi.org/10.1073/pnas.2302489120
Cancer Metab. 2023 Sep 13. 11(1): 15

Cholesterol reprograms glucose and lipid metabolism to promote proliferation in colon cancer cells.

Shyamananda Singh Mayengbam, Abhijeet Singh, Himanshi Yaduvanshi, Firoz Khan Bhati, Bhavana Deshmukh, Dipti Athavale, Pranay L Ramteke, Manoj Kumar Bhat.

  Hypercholesterolemia is often correlated with obesity which is considered a risk factor for various cancers. With the growing population of hypercholesterolemic individuals, there is a need to understand the role of increased circulatory cholesterol or dietary cholesterol intake towards cancer etiology and pathology. Recently, abnormality in the blood cholesterol level of colon cancer patients has been reported. In the present study, we demonstrate that alteration in cholesterol levels (through a high-cholesterol or high-fat diet) increases the incidence of chemical carcinogen-induced colon polyp occurrence and tumor progression in mice. At the cellular level, low-density lipoprotein cholesterol (LDLc) and high-density lipoprotein cholesterol (HDLc) promote colon cancer cell proliferation by tuning the cellular glucose and lipid metabolism. Mechanistically, supplementation of LDLc or HDLc promotes cellular glucose uptake, and utilization, thereby, causing an increase in lactate production by colon cancer cells. Moreover, LDLc or HDLc upregulates aerobic glycolysis, causing an increase in total ATP production through glycolysis, and a decrease in ATP generation by OXPHOS. Interestingly, the shift in the metabolic status towards a more glycolytic phenotype upon the availability of cholesterol supports rapid cell proliferation. Additionally, an alteration in the expression of the molecules involved in cholesterol uptake along with the increase in lipid and cholesterol accumulation was observed in cells supplemented with LDLc or HDLc. These results indicate that colon cancer cells directly utilize the cholesterol associated with LDLc or HDLc. Moreover, targeting glucose metabolism through LDH inhibitor (oxamate) drastically abrogates the cellular proliferation induced by LDLc or HDLc. Collectively, we illustrate the vital role of cholesterol in regulating the cellular glucose and lipid metabolism of cancer cells and its direct effect on the colon tumorigenesis.

Keywords:  Cholesterol; Colon cancer; Glucose metabolism; HDLc; LDLc; Lipid metabolism

DOI:  https://doi.org/10.1186/s40170-023-00315-1
Biomed Chromatogr. 2023 Sep 13. e5733

Metabolomics provides insights into acceleration of bone healing in fractured patients with traumatic brain injuries.

Demeng Xia, Rui Wu, Qian Xue, Gehan Jiang, Shuogui Xu.

  While clinical surveys have frequently reported that patients with traumatic brain injuries (TBIs) and comorbidities experience faster healing, the underlying mechanisms have been investigated but remain unclear. As a comprehensive comparison and analysis of the metabolic characteristics of these two pathologies have not been undertaken, we developed a rat model of fracture and TBI and collected serum samples for metabolomic analysis using ultra-high performance liquid chromatography-quadrupole time-of-flight MS (UHPLC-Q-TOF/MS). In total, we identified 40 differential metabolites and uncovered related pathways and potential mechanisms, including aminoacyl-transfer RNA biosynthesis; differential amino acids such as leucine, cholylhistidine, aspartyl-lysine; and related lipid metabolism, and discussed their impacts on bone formation in detail. This study highlights that the UHPLC-Q-TOF/MS-based metabolomics approach offers a better understanding of the metabolic links between TBI and accelerated bone recovery.

Keywords:  TBI; bone recovery; fracture; metabolomics; serum

DOI:  https://doi.org/10.1002/bmc.5733
STAR Protoc. 2023 Sep 09. pii: S2666-1667(23)00529-4. [Epub ahead of print]4(4): 102562

A protocol for isolating and imaging large extracellular vesicles or midbody remnants from mammalian cell culture.

Sungjin Park, Smit A Patel, Elizabeth E Torr, Ashley-Grace N Dureke, Alina M McIntyre, Ahna R Skop.

  Traditionally, midbody remnants (MBRs) are isolated from cell culture medium using ultracentrifugation, which is expensive and time consuming. Here, we present a protocol for isolating MBRs or large extracellular vesicles (EVs) from mammalian cell culture using either 1.5% polyethylene glycol 6000 (PEG6000) or PEG5000-coated gold nanoparticles. We describe steps for growing cells, collecting media, and precipitating MBRs and EVs from cell culture medium. We then detail characterization of MBRs through immunofluorescent antibody staining and immunofluorescent imaging.

Keywords:  Cancer; Cell Biology; Cell Culture; Cell Isolation; Cell Separation/Fractionation; Microscopy; Molecular/Chemical Probes

DOI:  https://doi.org/10.1016/j.xpro.2023.102562
J Am Soc Mass Spectrom. 2023 Sep 11.

Localization and Quantification of Post-Translational Modifications of Proteins Using Electron Activated Dissociation Fragmentation on a Fast-Acquisition Time-of-Flight Mass Spectrometer.

Joanna Bons, Christie L Hunter, Rita Chupalov, Jason Causon, Alexandra Antonoplis, Jacob Rose, Brendan MacLean, Birgit Schilling.

Protein post-translational modifications (PTMs) are crucial and dynamic players in a large variety of cellular processes and signaling. Proteomic technologies have emerged as the method of choice to profile PTMs. However, these analyses remain challenging due to potential low PTM stoichiometry, the presence of multiple PTMs per proteolytic peptide, PTM site localization of isobaric peptides, and neutral losses. Collision-induced dissociation (CID) is commonly used to characterize PTMs, but the application of collision energy can lead to neutral losses and incomplete peptide sequencing for labile PTM groups. In this study, we assessed the performance of an alternative fragmentation, electron activated dissociation (EAD), to characterize, site localize, and quantify peptides with labile modifications in comparison to CID, both operated on a recently introduced fast-scanning quadrupole-time-of-flight (QqTOF) mass spectrometer. We analyzed biologically relevant phosphorylated, succinylated, malonylated, and acetylated synthetic peptides using targeted parallel reaction monitoring (PRM or MRMHR) assays. We report that electron-based fragmentation preserves the malonyl group from neutral losses. The novel tunable EAD kinetic energy maintained labile modification integrity and provided better peptide sequence coverage with strong PTM-site localization fragment ions. Activation of a novel trap-and-release technology significantly improves the duty cycle and provided significant MS/MS sensitivity gains by an average of 6-11-fold for EAD analyses. Evaluation of the quantitative EAD PRM workflows revealed high reproducibility with coefficients of variation of ∼2-7%, as well as very good linearity and quantification accuracy. This novel workflow combining EAD and trap-and-release technology provides high sensitivity, alternative fragmentation information to achieve confident PTM characterization and quantification.

DOI: https://doi.org/10.1021/jasms.3c00144
Nat Metab. 2023 Sep 11.

Dynamic lipidome alterations associated with human health, disease and ageing.

Daniel Hornburg, Si Wu, Mahdi Moqri, Xin Zhou, Kevin Contrepois, Nasim Bararpour, Gavin M Traber, Baolong Su, Ahmed A Metwally, Monica Avina, Wenyu Zhou, Jessalyn M Ubellacker, Tejaswini Mishra, Sophia Miryam Schüssler-Fiorenza Rose, Paula B Kavathas, Kevin J Williams, Michael P Snyder.

Lipids can be of endogenous or exogenous origin and affect diverse biological functions, including cell membrane maintenance, energy management and cellular signalling. Here, we report >800 lipid species, many of which are associated with health-to-disease transitions in diabetes, ageing and inflammation, as well as cytokine-lipidome networks. We performed comprehensive longitudinal lipidomic profiling and analysed >1,500 plasma samples from 112 participants followed for up to 9 years (average 3.2 years) to define the distinct physiological roles of complex lipid subclasses, including large and small triacylglycerols, ester- and ether-linked phosphatidylethanolamines, lysophosphatidylcholines, lysophosphatidylethanolamines, cholesterol esters and ceramides. Our findings reveal dynamic changes in the plasma lipidome during respiratory viral infection, insulin resistance and ageing, suggesting that lipids may have roles in immune homoeostasis and inflammation regulation. Individuals with insulin resistance exhibit disturbed immune homoeostasis, altered associations between lipids and clinical markers, and accelerated changes in specific lipid subclasses during ageing. Our dataset based on longitudinal deep lipidome profiling offers insights into personalized ageing, metabolic health and inflammation, potentially guiding future monitoring and intervention strategies.

DOI: https://doi.org/10.1038/s42255-023-00880-1
Nat Commun. 2023 Sep 15. 14(1): 5728

The lipoprotein-associated phospholipase A2 inhibitor Darapladib sensitises cancer cells to ferroptosis by remodelling lipid metabolism.

Mihee Oh, Seo Young Jang, Ji-Yoon Lee, Jong Woo Kim, Youngae Jung, Jiwoo Kim, Jinho Seo, Tae-Su Han, Eunji Jang, Hye Young Son, Dain Kim, Min Wook Kim, Jin-Sung Park, Kwon-Ho Song, Kyoung-Jin Oh, Won Kon Kim, Kwang-Hee Bae, Yong-Min Huh, Soon Ha Kim, Doyoun Kim, Baek-Soo Han, Sang Chul Lee, Geum-Sook Hwang, Eun-Woo Lee.

Arachidonic and adrenic acids in the membrane play key roles in ferroptosis. Here, we reveal that lipoprotein-associated phospholipase A2 (Lp-PLA2) controls intracellular phospholipid metabolism and contributes to ferroptosis resistance. A metabolic drug screen reveals that darapladib, an inhibitor of Lp-PLA2, synergistically induces ferroptosis in the presence of GPX4 inhibitors. We show that darapladib is able to enhance ferroptosis under lipoprotein-deficient or serum-free conditions. Furthermore, we find that Lp-PLA2 is located in the membrane and cytoplasm and suppresses ferroptosis, suggesting a critical role for intracellular Lp-PLA2. Lipidomic analyses show that darapladib treatment or deletion of PLA2G7, which encodes Lp-PLA2, generally enriches phosphatidylethanolamine species and reduces lysophosphatidylethanolamine species. Moreover, combination treatment of darapladib with the GPX4 inhibitor PACMA31 efficiently inhibits tumour growth in a xenograft model. Our study suggests that inhibition of Lp-PLA2 is a potential therapeutic strategy to enhance ferroptosis in cancer treatment.

DOI: https://doi.org/10.1038/s41467-023-41462-9