bims-mascan 2023-01-01 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2023–01–01
thirteen papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition.
Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier.
Improving SWATH-MS analysis by Deep-learning.
Tandem Mass Spectrometry Imaging Enables High Definition for Mapping Lipids in Tissues.
Guidelines and considerations for building multidimensional libraries for untargeted MS-based metabolomics.
Multi-substrate metabolic tracing reveals marked heterogeneity and dependency on fatty acid metabolism in human prostate cancer.
A review on the role of fatty acids in colorectal cancer progression.
The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics.
Kidney tubular epithelial cell ferroptosis links glomerular injury to tubulointerstitial pathology in lupus nephritis.
Recent progress in the analysis of unsaturated fatty acids in biological samples by chemical derivatization-based chromatography-mass spectrometry methods.
Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data.
The lipid flippase SLC47A1 blocks metabolic vulnerability to ferroptosis.

Mol Cell Proteomics. 2022 Dec 21. pii: S1535-9476(22)00297-3. [Epub ahead of print] 100489

Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition.

Patricia Skowronek, Florian Krohs, Markus Lubeck, Georg Wallmann, Ericka C M Itang, Polina Koval, Maria Wahle, Marvin Thielert, Florian Meier, Sander Willems, Oliver Raether, Matthias Mann.

  Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation - serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor - fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock and key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.

Keywords:  PASEF; TIMS; TOF; data-independent acquisition; scan mode

DOI:  https://doi.org/10.1016/j.mcpro.2022.100489
J Vis Exp. 2022 Dec 09.

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier.

Aleksandra A Petelski, Nikolai Slavov, Harrison Specht.

Single-cell proteomics analysis requires sensitive, quantitatively accurate, widely accessible, and robust methods. To meet these requirements, the Single-Cell ProtEomics (SCoPE2) protocol was developed as a second-generation method for quantifying hundreds to thousands of proteins from limited samples, down to the level of a single cell. Experiments using this method have achieved quantifying over 3,000 proteins across 1,500 single mammalian cells (500-1,000 proteins per cell) in 10 days of mass spectrometer instrument time. SCoPE2 leverages a freeze-heat cycle for cell lysis, obviating the need for clean-up of single cells and consequently reducing sample losses, while expediting sample preparation and simplifying its automation. Additionally, the method uses an isobaric carrier, which aids protein identification and reduces sample losses. This video protocol provides detailed guidance to enable the adoption of automated single-cell protein analysis using only equipment and reagents that are widely accessible. We demonstrate critical steps in the procedure of preparing single cells for proteomic analysis, from harvesting up to injection to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Additionally, viewers are guided through the principles of experimental design with the isobaric carrier, quality control for both isobaric carrier and single-cell preparations, and representative results with a discussion of limitations of the approach.

DOI: https://doi.org/10.3791/63802
Proteomics. 2022 Dec 26. e2200179

Improving SWATH-MS analysis by Deep-learning.

Bo Sun, Pawel Smialowski, Wasim Aftab, Andreas Schmidt, Ignasi Forne, Tobias Straub, Axel Imhof.

Data-independent acquisition (DIA) of tandem mass spectrometry spectra has emerged as a promising technology to improve coverage and quantification of proteins in complex mixtures. The success of DIA experiments is dependent on the quality of spectral libraries used for data base searching. Frequently, these libraries need to be generated by labor and time intensive data dependent acquisition (DDA) experiments. Recently, several algorithms have been published that allow the generation of theoretical libraries by an efficient prediction of retention time and intensity of the fragment ions. Sequential windowed acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) is a DIA method that can be applied at an unprecedented speed, but the fragmentation spectra suffer from a lower quality than data acquired on Orbitrap instruments. To reliably generate theoretical libraries that can be used in SWATH experiments, we developed deep-learning for SWATH analysis (dpSWATH), to improve the sensitivity and specificity of data generated by Q-TOF mass spectrometers. The theoretical library built by dpSWATH allowed us to increase the identification rate of proteins compared to traditional or library-free methods. Based on our analysis we conclude that dpSWATH is a superior prediction framework for SWATH-MS measurements than other algorithms based on Orbitrap data. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/pmic.202200179
Angew Chem Int Ed Engl. 2022 Dec 27.

Tandem Mass Spectrometry Imaging Enables High Definition for Mapping Lipids in Tissues.

Xiangyu Guo, Wenbo Cao, Xiaomin Fan, Zhiying Guo, Donghui Zhang, Haoyue Zhang, Xiaoxiao Ma, Jiahong Dong, Yunfang Wang, Wenpeng Zhang, Zheng Ouyang.

  Mass spectrometry imaging (MSI) of lipids in biological tissues is useful for correlating molecular distribution with pathological results, which could provide useful information for both biological research and disease diagnosis. It is well understood that the lipidome could not be clearly deciphered without tandem mass spectrometry analysis, but this is challenging to achieve in MSI due to the limitation in sample amount at each image spot. Here we develop a multiplexed MS2 imaging (MS2I) method that can provide MS2 images for 10 lipid species or more for each sampling spot, providing spatial structural lipidomic information. Coupling with on-tissue photochemical derivatization, imaging of 20 phospholipid C=C location isomers is also realized, showing enhanced molecular images with high definition in structure for mouse brain and human liver cancer tissue sections. Spatially mapped t-distributed stochastic neighbor embedding has also been adopted to visualize the tumor margin with enhancement by structural lipidomic information.

Keywords:  Lipidomics; MS/MS imaging; lipid biomarker; lipid isomer; mass spectrometry imaging

DOI:  https://doi.org/10.1002/anie.202214804
Metabolomics. 2022 Dec 28. 19(1): 4

Guidelines and considerations for building multidimensional libraries for untargeted MS-based metabolomics.

Katyeny Manuela da Silva, Maria van de Lavoir, Rani Robeyns, Elias Iturrospe, Lisa Verheggen, Adrian Covaci, Alexander L N van Nuijs.

   INTRODUCTION: Feature annotation is crucial in untargeted metabolomics but remains a major challenge. The large pool of metabolites collected under various instrumental conditions is underrepresented in publicly available databases. Retention time (RT) and collision cross section (CCS) measurements from liquid chromatography ion mobility high-resolution mass spectrometers can be employed in addition to MS/MS spectra to improve the confidence of metabolite annotation. Recent advancements in machine learning focus on improving the accuracy of predictions for CCS and RT values. Therefore, high-quality experimental data are crucial to be used either as training datasets or as a reference for high-confidence matching.
METHODS: This manuscript provides an easy-to-use workflow for the creation of an in-house metabolite library, offers an overview of alternative solutions, and discusses the challenges and advantages of using open-source software. A total of 100 metabolite standards from various classes were analyzed and subjected to the described workflow for library generation.
RESULTS AND DISCUSSION: The outcome was an open-access available NIST format metabolite library (.msp) with multidimensional information. The library was used to evaluate CCS prediction tools, MS/MS spectra heterogeneities (e.g., multiple adducts, in-source fragmentation, radical fragment ions using collision-induced dissociation), and the reporting of RT.

Keywords:  Collision cross section; Ion mobility; Open-source; RMassBank; Retention time; Tandem mass spectrometry

DOI:  https://doi.org/10.1007/s11306-022-01965-w
Mol Cancer Res. 2022 Dec 27. pii: MCR-22-0796. [Epub ahead of print]

Multi-substrate metabolic tracing reveals marked heterogeneity and dependency on fatty acid metabolism in human prostate cancer.

Gio Fidelito, David P De Souza, Birunthi Niranjan, William de Nardo, Shivakumar Keerthikumar, Kristin Brown, Renea A Taylor, Matthew J Watt.

Cancer cells undergo metabolic reprogramming to meet increased bioenergetic demands. Studies in cells and mice have highlighted the importance of oxidative metabolism and lipogenesis in prostate cancer, however, the metabolic landscape of human prostate cancer remains unclear. To address this knowledge gap, we performed radiometric (14C) and stable (13C) isotope tracing assays in precision-cut slices of patient-derived xenografts (PDXs). Glucose, glutamine, and fatty acid oxidation was variably upregulated in malignant PDXs compared to benign PDXs. De novo lipogenesis (DNL) and storage of free fatty acids into phospholipids and triacylglycerols were increased in malignant PDXs. There was no difference in substrate utilization between localized and metastatic PDXs and hierarchical clustering revealed marked metabolic heterogeneity across all PDXs. Mechanistically, glucose utilization was mediated by acetyl-CoA production rather than carboxylation of pyruvate, while glutamine entered the TCA cycle through transaminase reactions before being utilized via oxidative or reductive pathways. Blocking fatty acid uptake or fatty acid oxidation with pharmacological inhibitors was sufficient to reduce cell viability in PDX-derived organoids (PDXOs), whereas blockade of DNL, or glucose or glutamine oxidation induced variable and limited therapeutic efficacy. These findings demonstrate that human prostate cancer, irrespective of disease stage, can effectively utilize all metabolic substrates, albeit with marked heterogeneity across tumors. We also confirm that fatty acid uptake and oxidation are targetable metabolic dependencies in human prostate cancer. Implications: Prostate cancer utilizes multiple substrates to fuel energy requirements, yet pharmacological targeting of fatty acid uptake and oxidation reveals metabolic dependencies in localised and metastatic tumors.

DOI: https://doi.org/10.1158/1541-7786.MCR-22-0796
Front Pharmacol. 2022 ;13 1032806

A review on the role of fatty acids in colorectal cancer progression.

Malvina Hoxha, Bruno Zappacosta.

  Colorectal cancer (CRC) is the third leading cause of mortality in cancer patients. The role of fatty acids (FA) and their metabolism in cancer, particularly in CRC raises a growing interest. In particular, dysregulation of synthesis, desaturation, elongation, and mitochondrial oxidation of fatty acids are involved. Here we review the current evidence on the link between cancer, in particular CRC, and fatty acids metabolism, not only to provide insight on its pathogenesis, but also on the development of novel biomarkers and innovative pharmacological therapies that are based on FAs dependency of cancer cells.

Keywords:  PUFA; cancer; colorectal cancer; eicosanoid; fatty acid

DOI:  https://doi.org/10.3389/fphar.2022.1032806
Elife. 2022 Dec 30. pii: e83658. [Epub ahead of print]11

The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics.

Andrea Bonicelli, Hayley L Mickleburgh, Alberto Chighine, Emanuela Locci, Daniel J Wescott, Noemi Procopio.

  The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.

Keywords:  biochemistry; chemical biology; decomposition; human; human bone; lipidomics; metabolomics; multi-omics; postmortem interval; proteomics

DOI:  https://doi.org/10.7554/eLife.83658
Clin Immunol. 2022 Dec 22. pii: S1521-6616(22)00294-7. [Epub ahead of print] 109213

Kidney tubular epithelial cell ferroptosis links glomerular injury to tubulointerstitial pathology in lupus nephritis.

Abdel A Alli, Dhruv Desai, Ahmed Elshika, Marcus Conrad, Bettina Proneth, William Clapp, Carl Atkinson, Mark Segal, Louis A Searcy, Nancy D Denslow, Subhashini Bolisetty, Borna Mehrad, Laurence Morel, Yogesh Scindia.

  Ferroptosis is a druggable, iron-dependent form of cell death that is characterized by lipid peroxidation but has received little attention in lupus nephritis. Kidneys of lupus nephritis patients and mice showed increased lipid peroxidation mainly in the tubular segments and an increase in Acyl-CoA synthetase long-chain family member 4, a pro-ferroptosis enzyme. Nephritic mice had an attenuated expression of SLC7A11, a cystine importer, an impaired glutathione synthesis pathway, and low expression of glutathione peroxidase 4, a ferroptosis inhibitor. Lipidomics of nephritic kidneys confirmed ferroptosis. Using nephrotoxic serum, we induced immune complex glomerulonephritis in congenic mice and demonstrate that impaired iron sequestration within the proximal tubules exacerbates ferroptosis. Lupus nephritis patient serum rendered human proximal tubular cells susceptibility to ferroptosis which was inhibited by Liproxstatin-2, a novel ferroptosis inhibitor. Collectively, our findings identify intra-renal ferroptosis as a pathological feature and contributor to tubular injury in human and murine lupus nephritis.

Keywords:  ACSL4; Ferroptosis; GPX4; Iron; Liproxstatin; Lupus nephritis; SLE

DOI:  https://doi.org/10.1016/j.clim.2022.109213
J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Dec 15. pii: S1570-0232(22)00477-9. [Epub ahead of print]1215 123572

Recent progress in the analysis of unsaturated fatty acids in biological samples by chemical derivatization-based chromatography-mass spectrometry methods.

Chang Chen, Ruijuan Li, Huan Wu.

  Unsaturated fatty acids (UFAs) are essential fatty acids that execute various biological functions in the human body. Therefore, the qualitative and quantitative analysis of UFAs in biological samples can help to clarify their roles in the occurrence and development of diseases, so to reveal the mechanisms of pathogenesis and potential drug intervention strategies. Chromatography-mass spectrometry is one of the most commonly used techniques for the analysis of UFAs in biological samples. However, due to factors such as the complex structural information of UFAs (the number and specific location of CC double bonds) and the low concentration of UFAs in biological samples, it is still difficult to conduct accurate qualitative and/or quantitative studies of UFAs in complex biological samples. In recent years, the integration and application of chemical derivatization and chromatography-mass spectrometry has been widely used in the detection of UFAs. Based on this overview, we reviewed recent developments and application progress for chemical derivatization-based chromatography-mass spectrometry methods for the qualitative and/or quantitative analysis of UFAs in biological samples over the past ten years. Potential trends for the design and improvement of novel derivatization reagents were proposed.

Keywords:  Biological samples; Chemical derivatization; Chromatography-mass spectrometry; Quantitative analysis; Unsaturated fatty acids (UFAs)

DOI:  https://doi.org/10.1016/j.jchromb.2022.123572
Cell Rep Med. 2022 Dec 23. pii: S2666-3791(22)00441-4. [Epub ahead of print] 100877

Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.

Jakob Maximilian Bader, Nikolaus Deigendesch, Martin Misch, Matthias Mann, Arend Koch, Felix Meissner.

  High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.

Keywords:  1p/19q codeletion; IDH; glioblastoma; glioma; isocitrate dehydrogenase; proteomics

DOI:  https://doi.org/10.1016/j.xcrm.2022.100877
Brief Bioinform. 2022 Dec 26. pii: bbac553. [Epub ahead of print]

Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data.

Yao Lu, Zhiqiang Pang, Jianguo Xia.

   BACKGROUND: Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics data remains a daunting task. Recent years have seen growing applications of pathway enrichment analysis based on putative annotations of liquid chromatography coupled with mass spectrometry (LC-MS) peaks for functional interpretation of LC-MS-based global metabolomics data. However, due to intricate peak-metabolite and metabolite-pathway relationships, considerable variations are observed among results obtained using different approaches. There is an urgent need to benchmark these approaches to inform the best practices.
RESULTS: We have conducted a benchmark study of common peak annotation approaches and pathway enrichment methods in current metabolomics studies. Representative approaches, including three peak annotation methods and four enrichment methods, were selected and benchmarked under different scenarios. Based on the results, we have provided a set of recommendations regarding peak annotation, ranking metrics and feature selection. The overall better performance was obtained for the mummichog approach. We have observed that a ~30% annotation rate is sufficient to achieve high recall (~90% based on mummichog), and using semi-annotated data improves functional interpretation. Based on the current platforms and enrichment methods, we further propose an identifiability index to indicate the possibility of a pathway being reliably identified. Finally, we evaluated all methods using 11 COVID-19 and 8 inflammatory bowel diseases (IBD) global metabolomics datasets.

Keywords:  LC-MS; global metabolomics; identifiability index; pathway enrichment analysis; peak annotation

DOI:  https://doi.org/10.1093/bib/bbac553
Nat Commun. 2022 Dec 27. 13(1): 7965

The lipid flippase SLC47A1 blocks metabolic vulnerability to ferroptosis.

Zhi Lin, Jiao Liu, Fei Long, Rui Kang, Guido Kroemer, Daolin Tang, Minghua Yang.

Ferroptosis is a type of regulated necrosis caused by unrestricted lipid peroxidation and subsequent plasma membrane rupture. However, the lipid remodeling mechanism that determines sensitivity to ferroptosis remains poorly understood. Here, we report a previously unrecognized role for the lipid flippase solute carrier family 47 member 1 (SLC47A1) as a regulator of lipid remodeling and survival during ferroptosis. Among 49 phospholipid scramblases, flippases, and floppases we analyzed, only SLC47A1 had mRNA that was selectively upregulated in multiple cancer cells exposed to ferroptotic inducers. Large-scale lipidomics and functional analyses revealed that the silencing of SLC47A1 increased RSL3- or erastin-induced ferroptosis by favoring ACSL4-SOAT1-mediated production of polyunsaturated fatty acid cholesterol esters. We identified peroxisome proliferator activated receptor alpha (PPARA) as a transcription factor that transactivates SLC47A1. The depletion of PPARA and SLC47A1 similarly sensitized cells to ferroptosis induction, whereas transfection-enforced re-expression of SLC47A1 restored resistance to ferroptosis in PPARA-deficient cells. Pharmacological or genetic blockade of the PPARA-SLC47A1 pathway increased the anticancer activity of a ferroptosis inducer in mice. These findings establish a direct molecular link between ferroptosis and lipid transporters, which may provide metabolic targets for overcoming drug resistance.

DOI: https://doi.org/10.1038/s41467-022-35707-2