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Pointner T, Rauh K, Auñon-Lopez A, Kostadinović Veličkovska S, Mitrev S, Arsov E, Pignitter M. Comprehensive analysis of oxidative stability and nutritional values of germinated linseed and sunflower seed oil. Food Chem 2024; 454:139790. [PMID: 38805931 DOI: 10.1016/j.foodchem.2024.139790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Germination of seeds is known to affect the nutritional composition of cold-pressed oils. This study focused on the effects of germination on the antioxidants and oxidative stability of linseed and sunflower seed oil. As hypothesized, germination led to increased antioxidant activities and tocopherol, chlorophyll and carotenoid content. Analysis revealed a 37.2 ± 3.5-fold and 11.6 ± 1.5-fold increase in polyphenol content in linseed and sunflower seed oil from germinated seeds, respectively. Using LC-HRMS/MS, profiles with up to 69 polyphenolic substances were identified in germinated seed oils for the first time. Germination promoted lipid hydrolysis, as evidenced by NMR, with overall significant decreases in triacylglycerol content leading to increased diacylglycerol and free fatty acid values. Rancimat measurements predicted a 4.10 ± 0.52-fold longer shelf-life for germinated linseed oil. This study successfully demonstrated the potential of germination to develop PUFA-rich oils with enhanced antioxidant capacity and oxidative stability.
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Affiliation(s)
- Tobias Pointner
- Institute of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria.
| | - Katharina Rauh
- Institute of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria.
| | - Arturo Auñon-Lopez
- Institute of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria.
| | | | - Saša Mitrev
- Faculty of Agriculture, University Goce Delčev, Štip, Republic of North Macedonia.
| | - Emilija Arsov
- Faculty of Agriculture, University Goce Delčev, Štip, Republic of North Macedonia.
| | - Marc Pignitter
- Institute of Physiological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria.
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2
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Thesbjerg MN, Sundekilde UK, Poulsen NA, Larsen LB, Nielsen SDH. A novel proteomic approach for the identification and relative quantification of disulfide-bridges in the human milk proteome. J Proteomics 2024; 301:105194. [PMID: 38723850 DOI: 10.1016/j.jprot.2024.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/26/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
This study explores the disulfide bridges present in the human milk proteome by a novel approach permitting both positional identification and relative quantification of the disulfide bridges. Human milk from six donors was subjected to trypsin digestion without reduction. The digested human milk proteins were analyzed by nanoLC-timsTOF Pro combined with data analysis using xiSEARCH. A total of 85 unique disulfide bridges were identified in 25 different human milk proteins. The total relative abundance of disulfide bridge-containing peptides constituted approximately 5% of the total amount of tryptic-peptides. Seven inter-molecular disulfide bridges were identified between either α-lactalbumin and lactotransferrin (5) or αS1-casein and κ-casein (2). All cysteines involved in the observed disulfide bridges of α-lactalbumin and lactotransferrin were mapped onto protein models using AlphaFold2 Multimer to estimate the length of the observed disulfide bridges. The lengths of the disulfide bridges of lactotransferrin indicate a potential for multi- or poly-merization of lactotransferrin. The high number of intramolecular lactotransferrin disulfide bridges identified, suggests that these are more heterogeneous than previously presumed. SIGNIFICANCE: Disulfide-bridges in the human milk proteome are an often overseen post-transaltional modification. Thus, mapping the disulfide-bridges, their positions and relative abundance, are valuable new knowledge needed for an improved understanding of human milk protein behaviour. Although glycosylation and phosphorylation have been described, even less information is available on the disulfide bridges and the disulfide-bridge derived protein complexes. This is important for future work in precision fermentation for recombinant production of human milk proteins, as this will highlight which disulfide-bridges are naturally occouring in human milk proteins. Further, this knowledge would be of value for the infant formula industry as it provides more information on how to humanize bovine-milk based infant formula. The novel method developed here can be broadly applied in other biological systems as the disulfid-brigdes are important for the structure and functionality of proteins.
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Affiliation(s)
- Martin Nørmark Thesbjerg
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark; Sino-Danish College (SDC), University of Chinese Academy of Science, Huairou District, Beijing 101408, China.
| | | | - Nina Aagaard Poulsen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark
| | - Lotte Bach Larsen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark
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3
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Zheng Y, Peng W, Wen X, Wan Q. Protein interactome analysis of ATP1B1 in alveolar epithelial cells using Co-Immunoprecipitation mass spectrometry and parallel reaction monitoring assay. Heliyon 2024; 10:e32579. [PMID: 38912441 PMCID: PMC11193012 DOI: 10.1016/j.heliyon.2024.e32579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Aims Alveolar epithelial barrier integrity is essential for lung homeostasis. Na, K-ATPase β1 subunit (ATP1B1) involves alveolar edema fluid clearance and alveolar epithelial barrier stability. However, the underlying molecular mechanism of ATP1B1 in alveolar epithelial cells still needs to be understood. Main methods We utilized Co-Immunoprecipitation mass spectrometry proteomic analysis, protein-protein interaction (PPI) analysis, enrichment analysis, and parallel reaction monitoring (PRM) analysis to investigate proteins interacting with ATP1B1 in A549 cells. Key findings A total of 159 proteins were identified as significant proteins interacting with ATP1B1 in A549 cells. Ribosomal and heat shock proteins were major constituents of the two main functional modules based on the PPI network. Enrichment analysis showed that significant proteins were involved in protein translation, posttranslational processing, and function regulation. Moreover, 10 proteins of interest were verified by PRM, and fold changes in 6 proteins were consistent with proteomics results. Finally, HSP90AB1, EIF4A1, TUBB4B, HSPA8, STAT1, and PLEC were considered candidates for binding to ATP1B1 to function in alveolar epithelial cells. Significance Our study provides new insights into the role of ATP1B1 in alveolar epithelial cells and indicates that six proteins, in particular HSP90AB1, may be key proteins interacting with and regulating ATP1B1, which might be potential targets for the treatment of acute respiratory distress syndrome.
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Affiliation(s)
- Yu Zheng
- Department of Transplant Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Weiting Peng
- 8-Year Clinical Medicine Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xupeng Wen
- Department of Transplant Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiquan Wan
- Department of Transplant Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
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4
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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics. Mol Cell Proteomics 2024:100800. [PMID: 38880244 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given mass-to-charge range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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5
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Hu Y, Schnaubelt M, Chen L, Zhang B, Hoang T, Lih TM, Zhang Z, Zhang H. MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses. Anal Chem 2024. [PMID: 38869158 DOI: 10.1021/acs.analchem.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Rapid development and wide adoption of mass spectrometry-based glycoproteomic technologies have empowered scientists to study proteins and protein glycosylation in complex samples on a large scale. This progress has also created unprecedented challenges for individual laboratories to store, manage, and analyze proteomic and glycoproteomic data, both in the cost for proprietary software and high-performance computing and in the long processing time that discourages on-the-fly changes of data processing settings required in explorative and discovery analysis. We developed an open-source, cloud computing-based pipeline, MS-PyCloud, with graphical user interface (GUI), for proteomic and glycoproteomic data analysis. The major components of this pipeline include data file integrity validation, MS/MS database search for spectral assignments to peptide sequences, false discovery rate estimation, protein inference, quantitation of global protein levels, and specific glycan-modified glycopeptides as well as other modification-specific peptides such as phosphorylation, acetylation, and ubiquitination. To ensure the transparency and reproducibility of data analysis, MS-PyCloud includes open-source software tools with comprehensive testing and versioning for spectrum assignments. Leveraging public cloud computing infrastructure via Amazon Web Services (AWS), MS-PyCloud scales seamlessly based on analysis demand to achieve fast and efficient performance. Application of the pipeline to the analysis of large-scale LC-MS/MS data sets demonstrated the effectiveness and high performance of MS-PyCloud. The software can be downloaded at https://github.com/huizhanglab-jhu/ms-pycloud.
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Affiliation(s)
- Yingwei Hu
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Michael Schnaubelt
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Li Chen
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Bai Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Trung Hoang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - T Mamie Lih
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Zhen Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21231, United States
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6
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Yannone SM, Tuteja V, Goleva O, Leung DYM, Stotland A, Keoseyan AJ, Hendricks NG, Van Eyk JE, Kreimer S. Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596979. [PMID: 38853916 PMCID: PMC11160709 DOI: 10.1101/2024.06.01.596979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Multi-step multi-hour tryptic proteolysis has limited the utility of bottom-up proteomics for cases that require immediate quantitative information. The recently available hyperthermoacidic (HTA) protease "Krakatoa" digests samples in a single 5 to 30-minute step at pH 3 and >80 °C; conditions that disrupt most cells and tissues, denature proteins, and block disulfide reformation. The combination of quick single-step sample preparation with high throughput dual trapping column single analytical column (DTSC) liquid chromatography-mass spectrometry (LC-MS) achieves "Rapid Proteomics" in which the time from sample collection to actionable data is less than 1 hour. The presented development and systematic evaluation of this methodology found reproducible quantitation of over 160 proteins from just 1 microliter of whole blood. Furthermore, the preference of the HTA-protease for intact proteins over peptides allows for sensitive targeted quantitation of the Angiotensin I and II bioactive peptides in under half an hour. With these methods we analyzed serum and plasma from 53 individuals and quantified Angiotensin and proteins that were not detected with trypsin. This assessment of Rapid Proteomics suggests that concentration of circulating protein and peptide biomarkers could be measured in almost real-time by LC-MS. TOC Figure Rapid proteomics enables near real-time monitoring of circulating blood biomarkers. One microliter of blood is collected every 8 minutes, digested for 20 minutes, and then analyzed by targeted mass spectrometry for 8 minutes. This results in a 30-minute delay with datapoints every 8 minutes.
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7
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Shafaei Pishabad Z, Ledgerwood EC. The Y49H cytochrome c variant enhances megakaryocytic maturation of K-562 cells. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167134. [PMID: 38531481 DOI: 10.1016/j.bbadis.2024.167134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Five pathogenic variants in the gene encoding cytochrome c (CYCS) associated with mild autosomal dominant thrombocytopenia have been reported. Previous studies of peripheral blood CD34+ or CD45+ cells from subjects with the G42S CYCS variant showed an acceleration in megakaryopoiesis compared to wild-type (WT) cells. To determine whether this result reflects a common feature of the CYCS variants, the c.145T>C mutation (Y49H variant) was introduced into the endogenous CYCS locus in K-562 cells, which undergo megakaryocytic maturation in response to treatment with a phorbol ester. The c.145T>C (Y49H) variant enhanced the megakaryocyte maturation of the K-562 cells, and this effect was seen when the cells were cultured at both 18 % and 5 % oxygen. Thus, alteration of megakaryopoiesis is common to both the G42S and Y49H CYCS variants and may contribute to the low platelet phenotype. The Y49H CYCS variant has previously been reported to impair mitochondrial respiratory chain function in vitro, however using extracellular flux analysis the c.145T>C (Y49H) variant does not alter mitochondrial bioenergetics of the K-562 cells, consistent with the lack of a phenotype characteristic of mitochondrial diseases in CYCS variant families. The Y49H variant has also been reported to enhance the ability of cytochrome c to trigger caspase activation in the intrinsic apoptosis pathway. However, as seen in peripheral blood cells from G42S CYCS variant carriers, the presence of Y49H cytochrome c in K-562 cells did not significantly change their response to an apoptotic stimulus.
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Affiliation(s)
- Zahra Shafaei Pishabad
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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8
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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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9
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Separovich RJ, Karakatsanis NM, Gao K, Fuh D, Hamey JJ, Wilkins MR. Proline-directed yeast and human MAP kinases phosphorylate the Dot1p/DOT1L histone H3K79 methyltransferase. FEBS J 2024; 291:2590-2614. [PMID: 38270553 DOI: 10.1111/febs.17062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/24/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Disruptor of telomeric silencing 1 (Dot1p) is an exquisitely conserved histone methyltransferase and is the sole enzyme responsible for H3K79 methylation in the budding yeast Saccharomyces cerevisiae. It has been shown to be highly phosphorylated in vivo; however, the upstream kinases that act on Dot1p are almost entirely unknown in yeast and all other eukaryotes. Here, we used in vitro and in vivo kinase discovery approaches to show that mitogen-activated protein kinase HOG1 (Hog1p) is a bona fide kinase of the Dot1p methyltransferase. In vitro kinase assays showed that Hog1p phosphorylates Dot1p at multiple sites, including at several proline-adjacent sites that are consistent with known Hog1p substrate preferences. The activity of Hog1p was specifically enhanced at these proline-adjacent sites on Dot1p upon Hog1p activation by the osmostress-responsive MAP kinase kinase PBS2 (Pbs2p). Genomic deletion of HOG1 reduced phosphorylation at specific sites on Dot1p in vivo, providing further evidence for Hog1p kinase activity on Dot1p in budding yeast cells. Phenotypic analysis of knockout and phosphosite mutant yeast strains revealed the importance of Hog1p-catalysed phosphorylation of Dot1p for cellular responses to ultraviolet-induced DNA damage. In mammalian systems, this kinase-substrate relationship was found to be conserved: human DOT1L (the ortholog of yeast Dot1p) can be phosphorylated by the proline-directed kinase p38β (also known as MAPK11; the ortholog of yeast Hog1p) at multiple sites in vitro. Taken together, our findings establish Hog1p and p38β as newly identified upstream kinases of the Dot1p/DOT1L H3K79 methyltransferase enzymes in eukaryotes.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Nicola M Karakatsanis
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Kelley Gao
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David Fuh
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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10
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Li K, Teo GC, Yang KL, Yu F, Nesvizhskii AI. diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595875. [PMID: 38854051 PMCID: PMC11160675 DOI: 10.1101/2024.05.25.595875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches.
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Affiliation(s)
- Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin L. Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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11
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Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ. Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596554. [PMID: 38853953 PMCID: PMC11160738 DOI: 10.1101/2024.05.29.596554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same dataset.
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Affiliation(s)
- Deanna L Plubell
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Eric Huang
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Sandra E Spencer
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kathleen Poston
- Stanford University, Department of Neurology & Neurological Sciences, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Stanford University, Department of Pathology, Stanford, CA, 94305, USA
| | - Michael J MacCoss
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
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12
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Chang Q, Chen Y, Yin J, Wang T, Dai Y, Wu Z, Guo Y, Wang L, Zhao Y, Yuan H, Song D, Zhang L. Comprehensive Urinary Proteome Profiling Analysis Identifies Diagnosis and Relapse Surveillance Biomarkers for Bladder Cancer. J Proteome Res 2024. [PMID: 38787199 DOI: 10.1021/acs.jproteome.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Bladder cancer (BCa) is the predominant malignancy of the urinary system. Herein, a comprehensive urine proteomic feature was initially established for the noninvasive diagnosis and recurrence monitoring of bladder cancer. 279 cases (63 primary BCa, 87 nontumor controls (NT), 73 relapsed BCa (BCR), and 56 nonrelapsed BCa (BCNR)) were collected to screen urinary protein biomarkers. 4761 and 3668 proteins were qualified and quantified by DDA and sequential window acquisition of all theoretical mass spectra (SWATH-MS) analysis in two discovery sets, respectively. Upregulated proteins were validated by multiple reaction monitoring (MRM) in two independent combined sets. Using the multi-support vector machine-recursive feature elimination (mSVM-RFE) algorithm, a model comprising 13 proteins exhibited good performance between BCa and NT with an AUC of 0.821 (95% CI: 0.675-0.967), 90.9% sensitivity (95% CI: 72.7-100%), and 73.3% specificity (95% CI: 53.3-93.3%) in the diagnosis test set. Meanwhile, an 11-marker classifier significantly distinguished BCR from BCNR with 75.0% sensitivity (95% CI: 50.0-100%), 81.8% specificity (95% CI: 54.5-100%), and an AUC of 0.784 (95% CI: 0.609-0.959) in the test cohort for relapse surveillance. Notably, six proteins (SPR, AK1, CD2AP, ADGRF1, GMPS, and C8A) of 24 markers were newly reported. This paper reveals novel urinary protein biomarkers for BCa and offers new theoretical insights into the pathogenesis of bladder cancer (data identifier PXD044896).
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Affiliation(s)
- Qi Chang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongqiang Chen
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jianjian Yin
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yuanheng Dai
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zixin Wu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufeng Guo
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lingang Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufen Zhao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hang Yuan
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Dongkui Song
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450001, China
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13
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Do K, Mehta S, Wagner R, Bhuming D, Rajczewski AT, Skubitz APN, Johnson JE, Griffin TJ, Jagtap PD. A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. mSphere 2024:e0079323. [PMID: 38780289 DOI: 10.1128/msphere.00793-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification, and prioritization of microbial proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant [to generate peptide-spectral matches (PSMs) and quantification], PepQuery2 (to verify the quality of PSMs), Unipept (for taxonomic and functional annotation), and MSstatsTMT (for statistical analysis). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies. IMPORTANCE Clinical metaproteomics has immense potential to offer functional insights into the microbiome and its contributions to human disease. However, there are numerous challenges in the metaproteomic analysis of clinical samples, including handling of very large protein sequence databases for sensitive and accurate peptide and protein identification from mass spectrometry data, as well as taxonomic and functional annotation of quantified peptides and proteins to enable interpretation of results. To address these challenges, we have developed a novel clinical metaproteomics workflow that provides customized bioinformatic identification, verification, quantification, and taxonomic and functional annotation. This bioinformatic workflow is implemented in the Galaxy ecosystem and has been used to characterize diverse clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness and availability for use by the research community via analysis of residual fluid from cervical swabs.
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Affiliation(s)
- Katherine Do
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dechen Bhuming
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew T Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amy P N Skubitz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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14
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Wang N, Mcneer NA, Eton E, Fass J, Kentsis A. Proteomic Barcoding Platform for Macromolecular Screening and Delivery. J Proteome Res 2024. [PMID: 38776430 DOI: 10.1021/acs.jproteome.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.
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Affiliation(s)
- Ning Wang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nicole A Mcneer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Elliot Eton
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Josh Fass
- Tri-I PhD Program in Computational Biology and Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
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15
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Kiss AE, Venkatasubramani AV, Pathirana D, Krause S, Sparr A, Hasenauer J, Imhof A, Müller M, Becker P. Processivity and specificity of histone acetylation by the male-specific lethal complex. Nucleic Acids Res 2024; 52:4889-4905. [PMID: 38407474 PMCID: PMC11109948 DOI: 10.1093/nar/gkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
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Affiliation(s)
- Anna E Kiss
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Anuroop V Venkatasubramani
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Dilan Pathirana
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Silke Krause
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Axel Imhof
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Marisa Müller
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
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16
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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17
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Peinado-Izaguerri J, Corbishley A, Zarzuela E, Pina-Beltrán B, Riva F, McKeegan DEF, Bain M, Muñoz J, Bhide M, McLaughlin M, Preston T. Effect of an immune challenge and two feed supplements on broiler chicken individual breast muscle protein synthesis rate. J Proteomics 2024; 299:105158. [PMID: 38484873 DOI: 10.1016/j.jprot.2024.105158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken's growth. Despite its importance, research on broiler chicken muscle protein dynamics has mostly been limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of citrus and cucumber extracts on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. Twenty-one day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analysed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein synthesis which could be essential for improving the efficiency of broiler chicken meat production. SIGNIFICANCE: The present study constitutes the first dynamic proteomics study conducted in a farm animal species which has characterized FSR in a large number of proteins, establishing a precedent for biomarker discovery and assessment of health and growth status. Moreover, it has been evidenced that the decrease in broiler chicken breast muscle protein following an immune challenge is a coordinated event which seems to be the main cause of the decreased growth observed in these animals.
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Affiliation(s)
- Jorge Peinado-Izaguerri
- University of Glasgow, School of Biodiversity, One Health and Veterinary Medicine, Ilay Road, Glasgow G61 1QH, United Kingdom; University of Veterinary Medicine and Pharmacy in Košice, Laboratory of biomedical microbiology and immunology, Komenskeho 73, Košice 04001, Slovakia.
| | - Alexander Corbishley
- University of Edinburgh, Roslin Institute, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
| | - Eduardo Zarzuela
- Spanish National Cancer Research Center, Proteomics Unit, Calle de Melchor Fernández Almagro 3, Madrid 28029, Spain.
| | - Blanca Pina-Beltrán
- Aix-Marseille Université, Marseille, Centre de Recherche en Cardiovasculaire et Nutrition, Bd Jean Moulin 27, Marseille 13385, France.
| | - Francesca Riva
- University of Glasgow, School of Biodiversity, One Health and Veterinary Medicine, Ilay Road, Glasgow G61 1QH, United Kingdom; University of Zagreb, Clinic for Internal Diseases faculty of Veterinary Medicine, Heinzelova 55, Zagreb 10000, Croatia.
| | - Dorothy E F McKeegan
- University of Glasgow, School of Biodiversity, One Health and Veterinary Medicine, Ilay Road, Glasgow G61 1QH, United Kingdom.
| | - Maureen Bain
- University of Glasgow, School of Biodiversity, One Health and Veterinary Medicine, Ilay Road, Glasgow G61 1QH, United Kingdom.
| | - Javier Muñoz
- Spanish National Cancer Research Center, Proteomics Unit, Calle de Melchor Fernández Almagro 3, Madrid 28029, Spain.
| | - Mangesh Bhide
- University of Veterinary Medicine and Pharmacy in Košice, Laboratory of biomedical microbiology and immunology, Komenskeho 73, Košice 04001, Slovakia.
| | - Mark McLaughlin
- University of Glasgow, School of Biodiversity, One Health and Veterinary Medicine, Ilay Road, Glasgow G61 1QH, United Kingdom.
| | - Tom Preston
- University of Glasgow, SUERC, Stable Isotope Biochemistry Laboratory, East Kilbride, Glasgow G75 0QF, United Kingdom.
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18
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Kurmasheva N, Said A, Wong B, Kinderman P, Han X, Rahimic AHF, Kress A, Carter-Timofte ME, Holm E, van der Horst D, Kollmann CF, Liu Z, Wang C, Hoang HD, Kovalenko E, Chrysopoulou M, Twayana KS, Ottosen RN, Svenningsen EB, Begnini F, Kiib AE, Kromm FEH, Weiss HJ, Di Carlo D, Muscolini M, Higgins M, van der Heijden M, Bardoul A, Tong T, Ozsvar A, Hou WH, Schack VR, Holm CK, Zheng Y, Ruzek M, Kalucka J, de la Vega L, Elgaher WAM, Korshoej AR, Lin R, Hiscott J, Poulsen TB, O'Neill LA, Roy DG, Rinschen MM, van Montfoort N, Diallo JS, Farin HF, Alain T, Olagnier D. Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways. Nat Commun 2024; 15:4096. [PMID: 38750019 PMCID: PMC11096414 DOI: 10.1038/s41467-024-48422-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
The presence of heterogeneity in responses to oncolytic virotherapy poses a barrier to clinical effectiveness, as resistance to this treatment can occur through the inhibition of viral spread within the tumor, potentially leading to treatment failures. Here we show that 4-octyl itaconate (4-OI), a chemical derivative of the Krebs cycle-derived metabolite itaconate, enhances oncolytic virotherapy with VSVΔ51 in various models including human and murine resistant cancer cell lines, three-dimensional (3D) patient-derived colon tumoroids and organotypic brain tumor slices. Furthermore, 4-OI in combination with VSVΔ51 improves therapeutic outcomes in a resistant murine colon tumor model. Mechanistically, we find that 4-OI suppresses antiviral immunity in cancer cells through the modification of cysteine residues in MAVS and IKKβ independently of the NRF2/KEAP1 axis. We propose that the combination of a metabolite-derived drug with an oncolytic virus agent can greatly improve anticancer therapeutic outcomes by direct interference with the type I IFN and NF-κB-mediated antiviral responses.
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Affiliation(s)
- Naziia Kurmasheva
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Aida Said
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Boaz Wong
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Ottawa Hospital Research Insitute, Ottawa, ON, K1H 8L6, Canada
| | - Priscilla Kinderman
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Xiaoying Han
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Anna H F Rahimic
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Alena Kress
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University, 60438, Frankfurt am Main, Germany
| | | | - Emilia Holm
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | | | | | - Zhenlong Liu
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Chen Wang
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Huy-Dung Hoang
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Elina Kovalenko
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | | | | | - Rasmus N Ottosen
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | | | - Fabio Begnini
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders E Kiib
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | | | - Hauke J Weiss
- School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Ireland
| | - Daniele Di Carlo
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Michela Muscolini
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Maureen Higgins
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Mirte van der Heijden
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angelina Bardoul
- Cancer Axis, CHUM Research Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada
- Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Tong Tong
- Department of Neurosurgery, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
- DCCC Brain Tumor Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Attila Ozsvar
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Wen-Hsien Hou
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Vivien R Schack
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Christian K Holm
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Yunan Zheng
- Small Molecule Therapeutics & Platform Technologies, AbbVie Inc., 1 North Waukegon Road, North Chicago, IL, 60064, USA
| | - Melanie Ruzek
- AbbVie, Bioresearch Center, 100 Research Drive, Worcester, MA, 01608, USA
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Laureano de la Vega
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Walid A M Elgaher
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, E8.1, 66123, Saarbrücken, Germany
| | - Anders R Korshoej
- Department of Neurosurgery, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
- DCCC Brain Tumor Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rongtuan Lin
- Lady Davis Institute, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, H3T 1E2, Canada
| | - John Hiscott
- Pasteur Laboratories, Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, 00161, Italy
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Luke A O'Neill
- School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Ireland
| | - Dominic G Roy
- Cancer Axis, CHUM Research Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada
- Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Markus M Rinschen
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
- III. Department of Medicine and Hamburg Center for Kidney Health, Hamburg, Germany
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Nadine van Montfoort
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jean-Simon Diallo
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Ottawa Hospital Research Insitute, Ottawa, ON, K1H 8L6, Canada
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt/Mainz partner site and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Tommy Alain
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - David Olagnier
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark.
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19
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Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem 2024; 96:7373-7379. [PMID: 38696819 PMCID: PMC11099889 DOI: 10.1021/acs.analchem.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.
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Affiliation(s)
- Juan Camilo Rojas Echeverri
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Frank Hause
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Institute
for Molecular Medicine, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Claudio Iacobucci
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Department
of Physical and Chemical Sciences, University
of L’Aquila, 67100 L’Aquila, Italy
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Dirk Tänzler
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
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20
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Garapati K, Jain A, Madden BJ, Mun DG, Sharma J, Budhraja R, Pandey A. Defining albumin as a glycoprotein with multiple N-linked glycosylation sites. J Transl Med 2024; 22:454. [PMID: 38741158 DOI: 10.1186/s12967-024-05000-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Glycosylation is an enzyme-catalyzed post-translational modification that is distinct from glycation and is present on a majority of plasma proteins. N-glycosylation occurs on asparagine residues predominantly within canonical N-glycosylation motifs (Asn-X-Ser/Thr) although non-canonical N-glycosylation motifs Asn-X-Cys/Val have also been reported. Albumin is the most abundant protein in plasma whose glycation is well-studied in diabetes mellitus. However, albumin has long been considered a non-glycosylated protein due to absence of canonical motifs. Albumin contains two non-canonical N-glycosylation motifs, of which one was recently reported to be glycosylated. METHODS We enriched abundant serum proteins to investigate their N-linked glycosylation followed by trypsin digestion and glycopeptide enrichment by size-exclusion or mixed-mode anion-exchange chromatography. Glycosylation at canonical as well as non-canonical sites was evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) of enriched glycopeptides. Deglycosylation analysis was performed to confirm N-linked glycosylation at non-canonical sites. Albumin-derived glycopeptides were fragmented by MS3 to confirm attached glycans. Parallel reaction monitoring was carried out on twenty additional samples to validate these findings. Bovine and rabbit albumin-derived glycopeptides were similarly analyzed by LC-MS/MS. RESULTS Human albumin is N-glycosylated at two non-canonical sites, Asn68 and Asn123. N-glycopeptides were detected at both sites bearing four complex sialylated glycans and validated by MS3-based fragmentation and deglycosylation studies. Targeted mass spectrometry confirmed glycosylation in twenty additional donor samples. Finally, the highly conserved Asn123 in bovine and rabbit serum albumin was also found to be glycosylated. CONCLUSIONS Albumin is a glycoprotein with conserved N-linked glycosylation sites that could have potential clinical applications.
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Affiliation(s)
- Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jyoti Sharma
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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21
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Choudhury R, Venkateswaran Venkatasubramani A, Hua J, Borsò M, Franconi C, Kinkley S, Forné I, Imhof A. The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry. eLife 2024; 13:e95718. [PMID: 38717135 PMCID: PMC11147508 DOI: 10.7554/elife.95718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.
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Affiliation(s)
- Rupam Choudhury
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Anuroop Venkateswaran Venkatasubramani
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jie Hua
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Marco Borsò
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Celeste Franconi
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Sarah Kinkley
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
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22
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Vymola P, Garcia-Borja E, Cervenka J, Balaziova E, Vymolova B, Veprkova J, Vodicka P, Skalnikova H, Tomas R, Netuka D, Busek P, Sedo A. Fibrillar extracellular matrix produced by pericyte-like cells facilitates glioma cell dissemination. Brain Pathol 2024:e13265. [PMID: 38705944 DOI: 10.1111/bpa.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Gliomagenesis induces profound changes in the composition of the extracellular matrix (ECM) of the brain. In this study, we identified a cellular population responsible for the increased deposition of collagen I and fibronectin in glioblastoma. Elevated levels of the fibrillar proteins collagen I and fibronectin were associated with the expression of fibroblast activation protein (FAP), which is predominantly found in pericyte-like cells in glioblastoma. FAP+ pericyte-like cells were present in regions rich in collagen I and fibronectin in biopsy material and produced substantially more collagen I and fibronectin in vitro compared to other cell types found in the GBM microenvironment. Using mass spectrometry, we demonstrated that 3D matrices produced by FAP+ pericyte-like cells are rich in collagen I and fibronectin and contain several basement membrane proteins. This expression pattern differed markedly from glioma cells. Finally, we have shown that ECM produced by FAP+ pericyte-like cells enhances the migration of glioma cells including glioma stem-like cells, promotes their adhesion, and activates focal adhesion kinase (FAK) signaling. Taken together, our findings establish FAP+ pericyte-like cells as crucial producers of a complex ECM rich in collagen I and fibronectin, facilitating the dissemination of glioma cells through FAK activation.
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Affiliation(s)
- Petr Vymola
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elena Garcia-Borja
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jakub Cervenka
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Laboratory of proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eva Balaziova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Vymolova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Veprkova
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vodicka
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Helena Skalnikova
- Laboratory of Applied Proteome Analyses, Research Center PIGMOD, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Laboratory of proteomics, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Robert Tomas
- Department of Neurosurgery, Na Homolce Hospital, Prague, Czech Republic
| | - David Netuka
- Department of Neurosurgery and Neurooncology, First Faculty of Medicine, Charles University and Military University Hospital, Prague, Czech Republic
| | - Petr Busek
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Aleksi Sedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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23
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Chen S, Downs ML. Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting Oil. J AOAC Int 2024; 107:443-452. [PMID: 38430003 DOI: 10.1093/jaoacint/qsae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Food allergen cross-contact during food preparation and production is one of the causes of unintentional allergen presence in packaged foods. However, little is known about allergen cross-contact in shared frying or roasting oil, which prevents the establishment of effective allergen controls and may put allergic individuals at risk. To better understand the quantity of allergen transferred to frying oil and subsequent products, an analytical method is needed for quantifying protein in oil that has been exposed to frying/roasting conditions. OBJECTIVE The goal of this study was to develop a parallel reaction monitoring LC-MS/MS method to quantify the amount of cashew protein in shared roasting oil. METHODS The sample preparation method was evaluated to improve protein extractability and peptide performance. Four quantitative peptides representing cashew 2S and 11S proteins were selected as targets based on their sensitivity, heat stability, and specificity. A calibration strategy was developed to quantify the amount of total cashew protein in oil. Method performance was evaluated using a heated cashew-in-oil model system. RESULTS The method showed high recovery in oil samples spiked with 100 or 10 parts per million (ppm) total cashew protein heated at 138 or 166°C for 2-30 min. Samples (100 ppm total cashew protein) heated for 30 min had more than 90% recovery when treated at 138°C and more than 50% when heated at 166°C. CONCLUSION The method is fit-for-purpose for the analysis of cashew allergen cross-contact in oil. HIGHLIGHTS A novel MS-based method was developed that can accurately quantify the amount of cashew protein present in heated oil.
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Affiliation(s)
- Shimin Chen
- University of Nebraska-Lincoln, Food Allergy Research and Resource Program, Department of Food Science and Technology, 283 Food Innovation Center, 1901 North 21st St, Lincoln, NE 68588, United States
- George L. Wright Jr. Center for Biomedical Proteomics, Eastern Virginia Medical School, 429 Lester Hall, 651 Colley Ave, Norfolk, VA 23507, United States
| | - Melanie L Downs
- University of Nebraska-Lincoln, Food Allergy Research and Resource Program, Department of Food Science and Technology, 283 Food Innovation Center, 1901 North 21st St, Lincoln, NE 68588, United States
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24
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Serrano LR, Peters-Clarke TM, Arrey TN, Damoc E, Robinson ML, Lancaster NM, Shishkova E, Moss C, Pashkova A, Sinitcyn P, Brademan DR, Quarmby ST, Peterson AC, Zeller M, Hermanson D, Stewart H, Hock C, Makarov A, Zabrouskov V, Coon JJ. The One Hour Human Proteome. Mol Cell Proteomics 2024; 23:100760. [PMID: 38579929 PMCID: PMC11103439 DOI: 10.1016/j.mcpro.2024.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
We describe deep analysis of the human proteome in less than 1 h. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, and data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high tandem mass spectrometry acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data-independent acquisition or data-dependent acquisition modes of operation. The fast-switching capabilities of the new quadrupole complement the sensitivity and fast ion scanning of the Astral analyzer to enable narrow-bin data-independent analysis methods. Over a 30-min active chromatographic method consuming a total analysis time of 56 min, the Q-Orbitrap-Astral hybrid MS collects an average of 4319 MS1 scans and 438,062 tandem mass spectrometry scans per run, producing 235,916 peptide sequences (1% false discovery rate). On average, each 30-min analysis achieved detection of 10,411 protein groups (1% false discovery rate). We conclude, with these results and alongside other recent reports, that the 1-h human proteome is within reach.
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Affiliation(s)
- Lia R Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Eugen Damoc
- Thermo Fisher Scientific GmbH, Bremen, Germany
| | - Margaret Lea Robinson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah M Lancaster
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Corinne Moss
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Pavel Sinitcyn
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | | | | | | | | | | | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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25
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O’Lone C, Juhász A, Nye-Wood M, Moody D, Dunn H, Ral JP, Colgrave ML. Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley ( Hordeum vulgare L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10149-10161. [PMID: 38635353 PMCID: PMC11066872 DOI: 10.1021/acs.jafc.4c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
The conversion of raw barley (Hordeum vulgare L.) to malt requires a process of controlled germination, where the grain is submerged in water to raise the moisture content to >40%. The transmembrane proteins, aquaporins, influence water uptake during the initial stage of controlled germination, yet little is known of their involvement in malting. With the current focus on sustainability, understanding the mechanisms of water uptake and usage during the initial stages of malting has become vital in improving efficient malting practices. In this study, we used quantitative proteomics analysis of two malting barley genotypes demonstrating differing water-uptake phenotypes in the initial stages of malting. Our study quantified 19 transmembrane proteins from nine families, including seven distinct aquaporin isoforms, including the plasma intrinsic proteins (PIPs) PIP1;1, PIP2;1, and PIP2;4 and the tonoplast intrinsic proteins (TIPs) TIP1;1, TIP2;3, TIP3;1, and TIP3;2. Our findings suggest that the presence of TIP1;1, TIP3;1, and TIP3;2 in the mature barley grain proteome is essential for facilitating water uptake, influencing cell turgor and the formation of large central lytic vacuoles aiding storage reserve hydrolysis and endosperm modification efficiency. This study proposes that TIP3s mediate water uptake in malting barley grain, offering potential breeding targets for improving sustainable malting practices.
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Affiliation(s)
- Clare
E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - David Moody
- InterGrain
Pty Ltd, Bibra
Lake 6163, Western Australia, Australia
| | - Hugh Dunn
- Pilot
Malting Australia, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
| | - Jean-Philippe Ral
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, Black
Mountain, Australian Capital Territory 2601, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, School of Science, Edith
Cowan University, Joondalup 6027, Western Australia, Australia
- Agriculture
and Food, Commonwealth Scientific and Industrial
Research Organization, St Lucia 4067, Queensland, Australia
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26
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Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wierenga KA, Westendorp B, Altelaar MAFM, Berkers C, van Kuppeveld FJM, Heck AJR. Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection. Mol Cell Proteomics 2024; 23:100757. [PMID: 38556169 PMCID: PMC11067349 DOI: 10.1016/j.mcpro.2024.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/16/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lonneke V Nouwen
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Heyrhyoung Lyoo
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Kathryn A Wierenga
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bart Westendorp
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Celia Berkers
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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27
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Bérouti M, Lammens K, Heiss M, Hansbauer L, Bauernfried S, Stöckl J, Pinci F, Piseddu I, Greulich W, Wang M, Jung C, Fröhlich T, Carell T, Hopfner KP, Hornung V. Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation. Immunity 2024:S1074-7613(24)00215-2. [PMID: 38697119 DOI: 10.1016/j.immuni.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation products: pocket 1 recognizes guanosine, while pocket 2 coordinates pyrimidine-rich RNA fragments. We found that the endonuclease RNase T2, along with 5' exonucleases PLD3 and PLD4, collaboratively generate the ligands for TLR7. Specifically, RNase T2 generated guanosine 2',3'-cyclic monophosphate-terminated RNA fragments. PLD exonuclease activity further released the terminal 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) to engage pocket 1 and was also needed to generate RNA fragments for pocket 2. Loss-of-function studies in cell lines and primary cells confirmed the critical requirement for PLD activity. Biochemical and structural studies showed that PLD enzymes form homodimers with two ligand-binding sites important for activity. Previously identified disease-associated PLD mutants failed to form stable dimers. Together, our data provide a mechanistic basis for the detection of RNA fragments by TLR7.
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Affiliation(s)
- Marleen Bérouti
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Larissa Hansbauer
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Stefan Bauernfried
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jan Stöckl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Francesca Pinci
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ignazio Piseddu
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany; Department of Medicine II, University Hospital Munich, Munich, Germany
| | - Wilhelm Greulich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Meiyue Wang
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christophe Jung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Fröhlich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.
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28
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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A framework for quality control in quantitative proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589318. [PMID: 38645098 PMCID: PMC11030400 DOI: 10.1101/2024.04.12.589318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.
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Affiliation(s)
- Kristine A. Tsantilas
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Julia E. Robbins
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael S. Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607
| | - Sandra E. Spencer
- Canada’s Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Washington 98195, United States
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29
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Mudbhari S, Lofgren L, Appidi MR, Vilgalys R, Hettich RL, Abraham PE. Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity. mSystems 2024; 9:e0122523. [PMID: 38470040 PMCID: PMC11019867 DOI: 10.1128/msystems.01225-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Ectomycorrhizal fungi establish mutually beneficial relationships with trees, trading nutrients for carbon. Suillus are ectomycorrhizal fungi that are critical to the health of boreal and temperate forest ecosystems. Comparative genomics has identified a high number of non-ribosomal peptide synthetase and terpene biosynthetic gene clusters (BGC) potentially involved in fungal competition and communication. However, the functionality of these BGCs is not known. This study employed co-culture techniques to activate BGC expression and then used metabolomics to investigate the diversity of metabolic products produced by three Suillus species (Suillus hirtellus EM16, Suillus decipiens EM49, and Suillus cothurnatus VC1858), core members of the pine microbiome. After 28 days of growth on solid media, liquid chromatography-tandem mass spectrometry identified a diverse range of extracellular metabolites (exometabolites) along the interaction zone between Suillus co-cultures. Prenol lipids were among the most abundant chemical classes. Out of the 62 unique terpene BGCs predicted by genome mining, 41 putative prenol lipids (includes 37 putative terpenes) were identified across the three Suillus species using metabolomics. Notably, some terpenes were significantly more abundant in co-culture conditions. For example, we identified a metabolite matching to isomers isopimaric acid, sandaracopimaric acid, and abietic acid, which can be found in pine resin and play important roles in host defense mechanisms and Suillus spore germination. This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication.IMPORTANCEUsing a combination of genomics and metabolomics, this study's findings offer new insights into the chemical diversity of Suillus fungi, which serve a critical role in forest ecosystems.
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Affiliation(s)
- Sameer Mudbhari
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lotus Lofgren
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Manasa R. Appidi
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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30
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Wen Q, Wang C, Chen D, Luo N, Fan J, Zhou Y, Yu X, Chen W. Proteomics-Based Identification of Potential Therapeutic Targets of Artesunate in a Lupus Nephritis MRL/lpr Mouse Model. J Proteome Res 2024; 23:1150-1162. [PMID: 38394376 DOI: 10.1021/acs.jproteome.3c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
This study aimed to identify potential therapeutic targets of artesunate in an MRL/lpr lupus nephritis mouse model by quantitative proteomics. We detected serum autoimmune markers and proteinuria in 40 female mice that were divided into 4 groups (n = 10): normal C57BL/6 control group; untreated MRL/lpr lupus; 9 mg/kg/day prednisone positive control MRL/lpr lupus; and 15 mg/kg/day artesunate-treated MRL/lpr lupus groups. Renal pathology in the untreated MRL/lpr lupus and artesunate groups was examined by Periodic acid-Schiff (PAS) staining. Artesunate treatment in lupus mice decreased serum autoantibody levels and proteinuria while alleviating lupus nephritis pathology. Through tandem mass tag-tandem mass spectrometry (TMT-MS/MS) analyses, differentially expressed proteins were identified in the artesunate group, and subsequent functional prediction suggested associations with antigen presentation, apoptosis, and immune regulation. Data are available via ProteomeXchange with the identifier PXD046815. Parallel reaction monitoring (PRM) analysis of the top 19 selected proteins confirmed the TMT-MS/MS results. Immunohistochemistry, immunofluorescence, and Western blotting of an enriched protein from PRM analysis, cathepsin S, linked to antigen presentation, highlighted its upregulation in the untreated MRL/lpr lupus group and downregulation following artesunate treatment. This study suggests that artesunate holds potential as a therapeutic agent for lupus nephritis, with cathepsin S identified as a potential target.
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Affiliation(s)
- Qiong Wen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Cong Wang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Dongni Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518000, China
| | - Ning Luo
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Jinjin Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Yi Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Xueqing Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou 510080, China
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31
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Torkamannejad S, Chang G, Aroge FA, Sun B. Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS. J Proteome Res 2024; 23:1351-1359. [PMID: 38445850 DOI: 10.1021/acs.jproteome.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Targeted mass spectrometry (MS)-based absolute quantitative analysis has been increasingly used in biomarker discovery. The ability to accurately measure the masses by MS enabled the use of isotope-incorporated surrogates having virtually identical physiochemical properties with the target analytes as calibrators. Such a unique capacity allowed for accurate in-sample calibration. Current in-sample calibration uses multiple isotopologues or structural analogues for both the surrogate and the internal standard. Here, we simplified this common practice by using endogenous light peptides as the internal standards and used a mathematical deduction of "heavy matching light, HML" to directly quantify an endogenous analyte. This method provides all necessary assay performance parameters in the authentic matrix, including the lower limit of quantitation (LLOQ) and intercept of the calibration curve, by using only a single isotopologue of the analyte. This method can be applied to the quantitation of proteins, peptides, and small molecules. Using this method, we quantified the efficiency of heart tissue digestion and recovery using sodium deoxycholate as a detergent and two spiked exogenous proteins as mimics of heart proteins. The results demonstrated the robustness of the assay.
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Affiliation(s)
- Soroush Torkamannejad
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Ge Chang
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Fabusuyi A Aroge
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia V3T0A3, Canada
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
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32
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Lum KK, Reed TJ, Yang J, Cristea IM. Differential Contributions of Interferon Classes to Host Inflammatory Responses and Restricting Virus Progeny Production. J Proteome Res 2024. [PMID: 38564653 DOI: 10.1021/acs.jproteome.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Fundamental to mammalian intrinsic and innate immune defenses against pathogens is the production of Type I and Type II interferons, such as IFN-β and IFN-γ, respectively. The comparative effects of IFN classes on the cellular proteome, protein interactions, and virus restriction within cell types that differentially contribute to immune defenses are needed for understanding immune signaling. Here, a multilayered proteomic analysis, paired with biochemical and molecular virology assays, allows distinguishing host responses to IFN-β and IFN-γ and associated antiviral impacts during infection with several ubiquitous human viruses. In differentiated macrophage-like monocytic cells, we classified proteins upregulated by IFN-β, IFN-γ, or pro-inflammatory LPS. Using parallel reaction monitoring, we developed a proteotypic peptide library for shared and unique ISG signatures of each IFN class, enabling orthogonal confirmation of protein alterations. Thermal proximity coaggregation analysis identified the assembly and maintenance of IFN-induced protein interactions. Comparative proteomics and cytokine responses in macrophage-like monocytic cells and primary keratinocytes provided contextualization of their relative capacities to restrict virus production during infection with herpes simplex virus type-1, adenovirus, and human cytomegalovirus. Our findings demonstrate how IFN classes induce distinct ISG abundance and interaction profiles that drive antiviral defenses within cell types that differentially coordinate mammalian immune responses.
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Affiliation(s)
- Krystal K Lum
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Tavis J Reed
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Jinhang Yang
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
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Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.10.544439. [PMID: 38617345 PMCID: PMC11014469 DOI: 10.1101/2023.06.10.544439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
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Affiliation(s)
- Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Justin A. Sanders
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Gennifer Merrihew
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Edward D. Parker
- Vision Core Lab, Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Kathleen L. Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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34
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Hua QQH, Kültz D, Wiltshire K, Doubleday ZA, Gillanders BM. Projected ocean temperatures impair key proteins used in vision of octopus hatchlings. GLOBAL CHANGE BIOLOGY 2024; 30:e17255. [PMID: 38572638 DOI: 10.1111/gcb.17255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/02/2024] [Indexed: 04/05/2024]
Abstract
Global warming is one of the most significant and widespread effects of climate change. While early life stages are particularly vulnerable to increasing temperatures, little is known about the molecular processes that underpin their capacity to adapt to temperature change during early development. Using a quantitative proteomics approach, we investigated the effects of thermal stress on octopus embryos. We exposed Octopus berrima embryos to different temperature treatments (control 19°C, current summer temperature 22°C, or future projected summer temperature 25°C) until hatching. By comparing their protein expression levels, we found that future projected temperatures significantly reduced levels of key eye proteins such as S-crystallin and retinol dehydrogenase 12, suggesting the embryonic octopuses had impaired vision at elevated temperature. We also found that this was coupled with a cellular stress response that included a significant elevation of proteins involved in molecular chaperoning and redox regulation. Energy resources were also redirected away from non-essential processes such as growth and digestion. These findings, taken together with the high embryonic mortality observed under the highest temperature, identify critical physiological functions of embryonic octopuses that may be impaired under future warming conditions. Our findings demonstrate the severity of the thermal impacts on the early life stages of octopuses as demonstrated by quantitative proteome changes that affect vision, protein chaperoning, redox regulation and energy metabolism as critical physiological functions that underlie the responses to thermal stress.
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Affiliation(s)
- Qiaz Q H Hua
- Environment Institute, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Dietmar Kültz
- Department of Animal Sciences and Genome Centre, University of California, Davis, USA
| | - Kathryn Wiltshire
- Environment Institute, School of Biological Sciences, The University of Adelaide, South Australia, Australia
- South Australian Research and Development Institute, West Beach, South Australia
| | - Zoe A Doubleday
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Bronwyn M Gillanders
- Environment Institute, School of Biological Sciences, The University of Adelaide, South Australia, Australia
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35
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Lapcik P, Stacey RG, Potesil D, Kulhanek P, Foster LJ, Bouchal P. Global Interactome Mapping Reveals Pro-tumorigenic Interactions of NF-κB in Breast Cancer. Mol Cell Proteomics 2024; 23:100744. [PMID: 38417630 PMCID: PMC10988130 DOI: 10.1016/j.mcpro.2024.100744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
NF-κB pathway is involved in inflammation; however, recent data shows its role also in cancer development and progression, including metastasis. To understand the role of NF-κB interactome dynamics in cancer, we study the complexity of breast cancer interactome in luminal A breast cancer model and its rearrangement associated with NF-κB modulation. Liquid chromatography-mass spectrometry measurement of 160 size-exclusion chromatography fractions identifies 5460 protein groups. Seven thousand five hundred sixty eight interactions among these proteins have been reconstructed by PrInCE algorithm, of which 2564 have been validated in independent datasets. NF-κB modulation leads to rearrangement of protein complexes involved in NF-κB signaling and immune response, cell cycle regulation, and DNA replication. Central NF-κB transcription regulator RELA co-elutes with interactors of NF-κB activator PRMT5, and these complexes are confirmed by AlphaPulldown prediction. A complementary immunoprecipitation experiment recapitulates RELA interactions with other NF-κB factors, associating NF-κB inhibition with lower binding of NF-κB activators to RELA. This study describes a network of pro-tumorigenic protein interactions and their rearrangement upon NF-κB inhibition with potential therapeutic implications in tumors with high NF-κB activity.
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Affiliation(s)
- Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - David Potesil
- Proteomics Core Facility, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhanek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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36
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Gomez-Zepeda D, Michna T, Ziesmann T, Distler U, Tenzer S. HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments. Proteomics 2024; 24:e2300134. [PMID: 37679057 DOI: 10.1002/pmic.202300134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
Contaminants derived from consumables, reagents, and sample handling often negatively affect LC-MS data acquisition. In proteomics experiments, they can markedly reduce identification performance, reproducibility, and quantitative robustness. Here, we introduce a data analysis workflow combining MS1 feature extraction in Skyline with HowDirty, an R-markdown-based tool, that automatically generates an interactive report on the molecular contaminant level in LC-MS data sets. To facilitate the interpretation of the results, the HTML report is self-contained and self-explanatory, including plots that can be easily interpreted. The R package HowDirty is available from https://github.com/DavidGZ1/HowDirty. To demonstrate a showcase scenario for the application of HowDirty, we assessed the impact of ultrafiltration units from different providers on sample purity after filter-assisted sample preparation (FASP) digestion. This allowed us to select the filter units with the lowest contamination risk. Notably, the filter units with the lowest contaminant levels showed higher reproducibility regarding the number of peptides and proteins identified. Overall, HowDirty enables the efficient evaluation of sample quality covering a wide range of common contaminant groups that typically impair LC-MS analyses, facilitating corrective or preventive actions to minimize instrument downtime.
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Affiliation(s)
- David Gomez-Zepeda
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), Mainz, Rheinland-Pfalz, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Tanja Ziesmann
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
| | - Stefan Tenzer
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), Mainz, Rheinland-Pfalz, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Rheinland-Pfalz, Germany
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37
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Picciani M, Gabriel W, Giurcoiu VG, Shouman O, Hamood F, Lautenbacher L, Jensen CB, Müller J, Kalhor M, Soleymaniniya A, Kuster B, The M, Wilhelm M. Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit. Proteomics 2024; 24:e2300112. [PMID: 37672792 DOI: 10.1002/pmic.202300112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Machine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting the adoption of state-of-the-art ML/DL models in proteomics analysis pipelines. We demonstrate its ability to reproduce and even improve our results from previously published rescoring analyses on two distinct use cases. Oktoberfest is freely available on GitHub (https://github.com/wilhelm-lab/oktoberfest) and can easily be installed locally through the cross-platform PyPI Python package.
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Affiliation(s)
- Mario Picciani
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wassim Gabriel
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Victor-George Giurcoiu
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Omar Shouman
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Firas Hamood
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Cecilia Bang Jensen
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mostafa Kalhor
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Armin Soleymaniniya
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Shrestha R, Karunadasa S, Grismer TS, Reyes AV, Xu SL. SECRET AGENT O-GlcNAcylates Hundreds of Proteins Involved in Diverse Cellular Processes in Arabidopsis. Mol Cell Proteomics 2024; 23:100732. [PMID: 38336175 PMCID: PMC10979276 DOI: 10.1016/j.mcpro.2024.100732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
O-GlcNAcylation is a critical post-translational modification of proteins observed in both plants and animals and plays a key role in growth and development. While considerable knowledge exists about over 3000 substrates in animals, our understanding of this modification in plants remains limited. Unlike animals, plants possess two putative homologs: SECRET AGENT (SEC) and SPINDLY, with SPINDLY also exhibiting O-fucosylation activity. To investigate the role of SEC as a major O-GlcNAc transferase in plants, we utilized lectin-weak affinity chromatography enrichment and stable isotope labeling in Arabidopsis labeling, quantifying at both MS1 and MS2 levels. Our findings reveal a significant reduction in O-GlcNAc levels in the sec mutant, indicating the critical role of SEC in mediating O-GlcNAcylation. Through a comprehensive approach, combining higher-energy collision dissociation and electron-transfer high-energy collision dissociation fragmentation with substantial fractionations, we expanded our GlcNAc profiling, identifying 436 O-GlcNAc targets, including 227 new targets. The targets span diverse cellular processes, suggesting broad regulatory functions of O-GlcNAcylation. The expanded targets also enabled exploration of crosstalk between O-GlcNAcylation and O-fucosylation. We also examined electron-transfer high-energy collision dissociation fragmentation for site assignment. This report advances our understanding of O-GlcNAcylation in plants, facilitating further research in this field.
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Affiliation(s)
- Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - Sumudu Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA
| | - TaraBryn S Grismer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Andres V Reyes
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA.
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Williams G, Couchman L, Taylor DR, Sandhu JK, Slingsby OC, Ng LL, Moniz CF, Jones DJL, Maxwell CB. Use of Nonhuman Sera as a Highly Cost-Effective Internal Standard for Quantitation of Multiple Human Proteins Using Species-Specific Tryptic Peptides: Applicability in Clinical LC-MS Analyses. J Proteome Res 2024. [PMID: 38533909 DOI: 10.1021/acs.jproteome.3c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Quantitation of proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is complex, with a multiplicity of options ranging from label-free techniques to chemically and metabolically labeling proteins. Increasingly, for clinically relevant analyses, stable isotope-labeled (SIL) internal standards (ISs) represent the "gold standard" for quantitation due to their similar physiochemical properties to the analyte, wide availability, and ability to multiplex to several peptides. However, the purchase of SIL-ISs is a resource-intensive step in terms of cost and time, particularly for screening putative biomarker panels of hundreds of proteins. We demonstrate an alternative strategy utilizing nonhuman sera as the IS for quantitation of multiple human proteins. We demonstrate the effectiveness of this strategy using two high abundance clinically relevant analytes, vitamin D binding protein [Gc globulin] (DBP) and albumin (ALB). We extend this to three putative risk markers for cardiovascular disease: plasma protease C1 inhibitor (SERPING1), annexin A1 (ANXA1), and protein kinase, DNA-activated catalytic subunit (PRKDC). The results show highly specific, reproducible, and linear measurement of the proteins of interest with comparable precision and accuracy to the gold standard SIL-IS technique. This approach may not be applicable to every protein, but for many proteins it can offer a cost-effective solution to LC-MS/MS protein quantitation.
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Affiliation(s)
- Geraldine Williams
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Lewis Couchman
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE2 7LX, United Kingdom
- Viapath Analytics, King's College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
- Department of Clinical Biochemistry, King's College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
| | - David R Taylor
- Viapath Analytics, King's College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
| | - Jatinderpal K Sandhu
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Oliver C Slingsby
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Leong L Ng
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Cajetan F Moniz
- Department of Clinical Biochemistry, King's College Hospital, Denmark Hill, London SE5 9RS, United Kingdom
| | - Donald J L Jones
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE2 7LX, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
| | - Colleen B Maxwell
- Leicester van Geest MS-OMICS Facility, Hodgkin Building, University of Leicester, Leicester LE1 9HN, United Kingdom
- Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, United Kingdom
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40
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Lereim RR, Nytrova P, Guldbrandsen A, Havrdova EK, Myhr KM, Barsnes H, Berven FS. Natalizumab promotes anti-inflammatory and repair effects in multiple sclerosis. PLoS One 2024; 19:e0300914. [PMID: 38527011 PMCID: PMC10962820 DOI: 10.1371/journal.pone.0300914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system leading to demyelination and axonal loss. Relapsing-remitting multiple sclerosis (RRMS) is commonly treated by anti-inflammatory drugs, where one of the most effective drugs to date is the monoclonal antibody natalizumab. METHODS The cerebrospinal fluid (CSF) proteome was analyzed in 56 patients with RRMS before and after natalizumab treatment, using label-free mass spectrometry and a subset of the changed proteins were verified by parallel reaction monitoring in a new cohort of 20 patients, confirming the majority of observed changes. RESULTS A total of 287 differentially abundant proteins were detected including (i) the decrease of proteins with roles in immunity, such as immunoglobulin heavy constant mu, chitinase-3-like protein 1 and chitotriosidase, (ii) an increase of proteins involved in metabolism, such as lactate dehydrogenase A and B and malate-dehydrogenase cytoplasmic, and (iii) an increase of proteins associated with the central nervous system, including lactadherin and amyloid precursor protein. Comparison with the CSF-PR database provided evidence that natalizumab counters protein changes commonly observed in RRMS. Furthermore, vitamin-D binding protein and apolipoprotein 1 and 2 were unchanged during treatment with natalizumab, implying that these may be involved in disease activity unaffected by natalizumab. CONCLUSIONS Our study revealed that some of the previously suggested biomarkers for MS were affected by the natalizumab treatment while others were not. Proteins not previously suggested as biomarkers were also found affected by the treatment. In sum, the results provide new information on how the natalizumab treatment impacts the CSF proteome of MS patients, and points towards processes affected by the treatment. These findings ought to be explored further to disclose potential novel disease mechanisms and predict treatment responses.
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Affiliation(s)
- Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Petra Nytrova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Eva Kubala Havrdova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kjell-Morten Myhr
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
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Kac PR, González-Ortiz F, Emeršič A, Dulewicz M, Koutarapu S, Turton M, An Y, Smirnov D, Kulczyńska-Przybik A, Varma VR, Ashton NJ, Montoliu-Gaya L, Camporesi E, Winkel I, Paradowski B, Moghekar A, Troncoso JC, Lashley T, Brinkmalm G, Resnick SM, Mroczko B, Kvartsberg H, Gregorič Kramberger M, Hanrieder J, Čučnik S, Harrison P, Zetterberg H, Lewczuk P, Thambisetty M, Rot U, Galasko D, Blennow K, Karikari TK. Plasma p-tau212 antemortem diagnostic performance and prediction of autopsy verification of Alzheimer's disease neuropathology. Nat Commun 2024; 15:2615. [PMID: 38521766 PMCID: PMC10960791 DOI: 10.1038/s41467-024-46876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
Blood phosphorylated tau (p-tau) biomarkers, including p-tau217, show high associations with Alzheimer's disease (AD) neuropathologic change and clinical stage. Certain plasma p-tau217 assays recognize tau forms phosphorylated additionally at threonine-212, but the contribution of p-tau212 alone to AD is unknown. We developed a blood-based immunoassay that is specific to p-tau212 without cross-reactivity to p-tau217. Here, we examined the diagnostic utility of plasma p-tau212. In five cohorts (n = 388 participants), plasma p-tau212 showed high performances for AD diagnosis and for the detection of both amyloid and tau pathology, including at autopsy as well as in memory clinic populations. The diagnostic accuracy and fold changes of plasma p-tau212 were similar to those for p-tau217 but higher than p-tau181 and p-tau231. Immunofluorescent staining of brain tissue slices showed prominent p-tau212 reactivity in neurofibrillary tangles that co-localized with p-tau217 and p-tau202/205. These findings support plasma p-tau212 as a peripherally accessible biomarker of AD pathophysiology.
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Grants
- R01 AG075336 NIA NIH HHS
- R01 AG078796 NIA NIH HHS
- R01 AG083874 NIA NIH HHS
- R01 AG072641 NIA NIH HHS
- R01 AG068398 NIA NIH HHS
- R21 AG078538 NIA NIH HHS
- R01 MH108509 NIMH NIH HHS
- RF1 AG025516 NIA NIH HHS
- P30 AG066468 NIA NIH HHS
- R01 AG073267 NIA NIH HHS
- P01 AG025204 NIA NIH HHS
- #AARF-21-850325 Alzheimer's Association
- R01 MH121619 NIMH NIH HHS
- R37 AG023651 NIA NIH HHS
- R21 AG080705 NIA NIH HHS
- U24 AG082930 NIA NIH HHS
- RF1 AG052525 NIA NIH HHS
- R01 AG053952 NIA NIH HHS
- Demensförbundet (Dementia Association)
- Anna Lisa and Brother Björnsson’s Foundation
- BrightFocus Foundation (BrightFocus)
- Alzheimerfonden
- the Swedish Dementia Foundation, Gun and Bertil Stohnes Foundation, Åhlén-stifelsen, and Gamla Tjänarinnor Foundation.
- Vetenskapsrådet (Swedish Research Council)
- Alzheimer’s Drug Discovery Foundation (ADDF)
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- EU Joint Programme – Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)
- Swedish State Support for Clinical Research (#ALFGBG-71320), the AD Strategic Fund and the Alzheimer’s Association (#ADSF-21-831376-C, #ADSF-21-831381-C, and #ADSF-21-831377-C) the Bluefield Project, the Olav Thon Foundation, the Erling-Persson Family Foundation, Hjärnfonden, Sweden (#FO2022-0270), the National Institute for Health and Care Research University College London Hospitals Biomedical Research Centre, and the UK Dementia Research Institute at UCL (UKDRI-1003)
- the Swedish Alzheimer Foundation (#AF-930351, #AF-939721 and #AF-968270), Hjärnfonden, Sweden (#FO2017-0243 and #ALZ2022-0006), the Swedish state under the agreement between the Swedish government and the County Councils, the ALF-agreement (#ALFGBG-715986 and #ALFGBG-965240), the National Institute of Health (NIH), USA, (grant #1R01AG068398-01) the Alzheimer’s Association 2021 Zenith Award (ZEN-21-848495).
- Alzheimer’s Association
- National Institute of Health (NIH) - (R01 AG083874-01, U24 AG082930-01 1 RF1 AG052525-01A1, 5 P30 AG066468-04, 5 R01 AG053952-05, 3 R01 MH121619-04S1, 5 R37 AG023651-18, 2 RF1 AG025516-12A1, 5 R01 AG073267-02, 2 R01 MH108509-06, 5 R01 AG075336-02, 5 R01 AG072641-02, 2 P01 AG025204-16) the Swedish Alzheimer Foundation (Alzheimerfonden), the Aina (Ann) Wallströms and Mary-Ann Sjöbloms stiftelsen, and the Emil och Wera Cornells stiftelsen.
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Affiliation(s)
- Przemysław R Kac
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden.
| | - Fernando González-Ortiz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Andreja Emeršič
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Maciej Dulewicz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Srinivas Koutarapu
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | | | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Denis Smirnov
- Department of Neurosciences, University of California, San Diego, CA, 92161, USA
| | | | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Old Age Psychiatry, King's College London, London, SE5 8AF, UK
- Centre for Age-Related Medicine, Stavanger University Hospital, 4011, Stavanger, Norway
- South London & Maudsley NHS Foundation, NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia, SE5 8AF, London, UK
| | - Laia Montoliu-Gaya
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Elena Camporesi
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Izabela Winkel
- Dementia Disorders Center, Medical University of Wrocław, 59-330, Ścinawa, Poland
| | - Bogusław Paradowski
- Department of Neurology, Medical University of Wrocław, 50-556, Wrocław, Poland
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, WC1N 1PJ, London, UK
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok, 15-269, Poland
| | - Hlin Kvartsberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Milica Gregorič Kramberger
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, 141 52, Huddinge, Sweden
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, UK
| | - Saša Čučnik
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Department of Rheumatology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
- Department of Neurodegenerative Disease, Dementia Research Centre, UCL Institute of Neurology, Queen Square, London, WC1E 6BT, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
- Hong Kong Center for Neurodegenerative Diseases, HKCeND, Hong Kong, 1512-1518, China
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Piotr Lewczuk
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok, 15-269, Poland
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Uroš Rot
- Department of Neurology, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, CA, 92161, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 431 80, Sweden
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, 431 80, Sweden
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
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St Paul M, Saibil SD, Kates M, Han S, Lien SC, Laister RC, Hezaveh K, Kloetgen A, Penny S, Guo T, Garcia-Batres C, Smith LK, Chung DC, Elford AR, Sayad A, Pinto D, Mak TW, Hirano N, McGaha T, Ohashi PS. Ex vivo activation of the GCN2 pathway metabolically reprograms T cells, leading to enhanced adoptive cell therapy. Cell Rep Med 2024; 5:101465. [PMID: 38460518 PMCID: PMC10983112 DOI: 10.1016/j.xcrm.2024.101465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/14/2023] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
The manipulation of T cell metabolism to enhance anti-tumor activity is an area of active investigation. Here, we report that activating the amino acid starvation response in effector CD8+ T cells ex vivo using the general control non-depressible 2 (GCN2) agonist halofuginone (halo) enhances oxidative metabolism and effector function. Mechanistically, we identified autophagy coupled with the CD98-mTOR axis as key downstream mediators of the phenotype induced by halo treatment. The adoptive transfer of halo-treated CD8+ T cells into tumor-bearing mice led to robust tumor control and curative responses. Halo-treated T cells synergized in vivo with a 4-1BB agonistic antibody to control tumor growth in a mouse model resistant to immunotherapy. Importantly, treatment of human CD8+ T cells with halo resulted in similar metabolic and functional reprogramming. These findings demonstrate that activating the amino acid starvation response with the GCN2 agonist halo can enhance T cell metabolism and anti-tumor activity.
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Affiliation(s)
- Michael St Paul
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Samuel D Saibil
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
| | - Meghan Kates
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - SeongJun Han
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Scott C Lien
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Rob C Laister
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Kebria Hezaveh
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Penny
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tingxi Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Carlos Garcia-Batres
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Logan K Smith
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Douglas C Chung
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Alisha R Elford
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Azin Sayad
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Devanand Pinto
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tak W Mak
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Tracy McGaha
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Pamela S Ohashi
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
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43
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Krawic JR, Ladd NA, Cansler M, McMurtrey C, Devereaux J, Worley A, Ahmed T, Froyd C, Kulicke CA, Swarbrick G, Nilsen A, Lewinsohn DM, Adams EJ, Hildebrand W. Multiple Isomers of Photolumazine V Bind MR1 and Differentially Activate MAIT Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:933-940. [PMID: 38275935 PMCID: PMC10909690 DOI: 10.4049/jimmunol.2300609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024]
Abstract
In response to microbial infection, the nonclassical Ag-presenting molecule MHC class I-related protein 1 (MR1) presents secondary microbial metabolites to mucosal-associated invariant T (MAIT) cells. In this study, we further characterize the repertoire of ligands captured by MR1 produced in Hi5 (Trichoplusia ni) cells from Mycobacterium smegmatis via mass spectrometry. We describe the (to our knowledge) novel MR1 ligand photolumazine (PL)V, a hydroxyindolyl-ribityllumazine with four isomers differing in the positioning of a hydroxyl group. We show that all four isomers are produced by M. smegmatis in culture and that at least three can induce MR1 surface translocation. Furthermore, human MAIT cell clones expressing distinct TCR β-chains differentially responded to the PLV isomers, demonstrating that the subtle positioning of a single hydroxyl group modulates TCR recognition. This study emphasizes structural microheterogeneity within the MR1 Ag repertoire and the remarkable selectivity of MAIT cell TCRs.
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Affiliation(s)
- Jason R. Krawic
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Nicole A. Ladd
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Meghan Cansler
- Department of Pediatrics, Oregon Health and Sciences University, Portland, OR
| | | | - Jordan Devereaux
- Oregon Health and Sciences University Medicinal Chemistry Core, Portland, OR
| | - Aneta Worley
- Research and Development, VA Portland Health Care System, Portland, OR
| | - Tania Ahmed
- Department of Pediatrics, Oregon Health and Sciences University, Portland, OR
| | - Cara Froyd
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - Corinna A. Kulicke
- Division of Pulmonary, Allergy, and Critical Care Medicine, Oregon Health & Science University, Por
| | - Gwendolyn Swarbrick
- Department of Pediatrics, Oregon Health and Sciences University, Portland, OR
| | - Aaron Nilsen
- Oregon Health and Sciences University Medicinal Chemistry Core, Portland, OR
| | - David M. Lewinsohn
- Research and Development, VA Portland Health Care System, Portland, OR
- Division of Pulmonary, Allergy, and Critical Care Medicine, Oregon Health & Science University, Por
| | - Erin J. Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - William Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
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Ser Z, Gascoigne NRJ, MacAry PA, Sobota RM. Protocol for structural modeling of antibody to human leukocyte antigen interaction using discovery and targeted cross-linking mass spectrometry. STAR Protoc 2024; 5:102927. [PMID: 38431839 PMCID: PMC10914520 DOI: 10.1016/j.xpro.2024.102927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/20/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Cross-linking mass spectrometry (XL-MS) provides low-resolution structural information to model protein structures. Here, we present a protocol to identify cross-links of purified antibody binding to purified human leukocyte antigen (HLA). We describe steps for using a discovery-based XL-MS approach followed by a targeted XL-MS approach. We then detail procedures for using the identified cross-links with other structural data for molecular docking of the antibody to HLA. This protocol has applications for modeling the interacting structure of purified antibody to antigen. For complete details on the use and execution of this protocol, please refer to Ser et al.1.
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Affiliation(s)
- Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore.
| | - Nicholas R J Gascoigne
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore.
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Troitzsch D, Knop R, Dittmann S, Bartel J, Zühlke D, Möller TA, Trän L, Echelmeyer T, Sievers S. Characterizing the flavodoxin landscape in Clostridioides difficile. Microbiol Spectr 2024; 12:e0189523. [PMID: 38319052 PMCID: PMC10913485 DOI: 10.1128/spectrum.01895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/23/2023] [Indexed: 02/07/2024] Open
Abstract
Clostridioides difficile infections have become a major challenge in medical facilities. The bacterium is capable of spore formation allowing the survival of antibiotic treatment. Therefore, research on the physiology of C. difficile is important for the development of alternative treatment strategies. In this study, we investigated eight putative flavodoxins of C. difficile 630. Flavodoxins are small electron transfer proteins of specifically low potential. The unusually high number of flavodoxins in C. difficile suggests that they are expressed under different conditions. We determined high transcription levels for several flavodoxins during the exponential growth phase, especially for floX. Since flavodoxins are capable of replacing ferredoxins under iron deficiency conditions in other bacteria, we also examined their expression in C. difficile under low iron and no iron levels. In particular, the amount of fldX increased with decreasing iron concentration and thus could possibly replace ferredoxins. Moreover, we demonstrated that fldX is increasingly expressed under different oxidative stress conditions and thus may play an important role in the oxidative stress response. While increased fldX expression was detectable at both RNA and protein level, CD2825 showed increased expression only at mRNA level under H2O2 stress with sufficient iron availability and may indicate hydroxyl radical-dependent transcription. Although the exact function of the individual flavodoxins in C. difficile needs to be further investigated, the present study shows that flavodoxins could play an important role in several physiological processes and under infection-relevant conditions. IMPORTANCE The gram-positive, anaerobic, and spore-forming bacterium Clostridioides difficile has become a vast problem in human health care facilities. The antibiotic-associated infection with this intestinal pathogen causes serious and recurrent inflammation of the intestinal epithelium, in many cases with a severe course. To come up with novel targeted therapies against C. difficile infections, a more detailed knowledge on the pathogen's physiology is mandatory. Eight putative flavodoxins, an extraordinarily high copy number of this type of small electron transfer proteins, are annotated for C. difficile. Flavodoxins are known to be essential electron carriers in other bacteria, for instance, during infection-relevant conditions such as iron limitation and oxidative stress. This work is a first and comprehensive overview on characteristics and expression profiles of the putative flavodoxins in the pathogen C. difficile.
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Affiliation(s)
- Daniel Troitzsch
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Robert Knop
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Silvia Dittmann
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Timon Alexander Möller
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Linda Trän
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thaddäus Echelmeyer
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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46
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Castaldi V, Langella E, Buonanno M, Di Lelio I, Aprile AM, Molisso D, Criscuolo MC, D'Andrea LD, Romanelli A, Amoresano A, Pinto G, Illiano A, Chiaiese P, Becchimanzi A, Pennacchio F, Rao R, Monti SM. Intrinsically disordered Prosystemin discloses biologically active repeat motifs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111969. [PMID: 38159610 DOI: 10.1016/j.plantsci.2023.111969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The in-depth studies over the years on the defence barriers by tomato plants have shown that the Systemin peptide controls the response to a wealth of environmental stress agents. This multifaceted stress reaction seems to be related to the intrinsic disorder of its precursor protein, Prosystemin (ProSys). Since latest findings show that ProSys has biological functions besides Systemin sequence, here we wanted to assess if this precursor includes peptide motifs able to trigger stress-related pathways. Candidate peptides were identified in silico and synthesized to test their capacity to trigger defence responses in tomato plants against different biotic stressors. Our results demonstrated that ProSys harbours several repeat motifs which triggered plant immune reactions against pathogens and pest insects. Three of these peptides were detected by mass spectrometry in plants expressing ProSys, demonstrating their effective presence in vivo. These experimental data shed light on unrecognized functions of ProSys, mediated by multiple biologically active sequences which may partly account for the capacity of ProSys to induce defense responses to different stress agents.
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Affiliation(s)
- Valeria Castaldi
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy
| | - Emma Langella
- Institute of Biostructures and Bioimaging, National Research Council (IBB, CNR), via Pietro Castellino 111, Naples 80131, Italy.
| | - Martina Buonanno
- Institute of Biostructures and Bioimaging, National Research Council (IBB, CNR), via Pietro Castellino 111, Naples 80131, Italy
| | - Ilaria Di Lelio
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, via Università 100, Portici, 80055 Naples, Italy
| | - Anna Maria Aprile
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy
| | - Donata Molisso
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy
| | - Martina Chiara Criscuolo
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy
| | - Luca Domenico D'Andrea
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), via Alfonso Corti 12, 20131 Milano, Italy
| | | | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, via Cynthia 8, Napoli and Interuniversitary Consortium "Istituto Nazionale Biostrutture e Biosistemi, 80126 Roma, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, via Cynthia 8, Napoli and Interuniversitary Consortium "Istituto Nazionale Biostrutture e Biosistemi, 80126 Roma, Italy
| | - Anna Illiano
- Department of Chemical Sciences, University of Naples Federico II, via Cynthia 8, Napoli and Interuniversitary Consortium "Istituto Nazionale Biostrutture e Biosistemi, 80126 Roma, Italy
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy
| | - Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, via Università 100, Portici, 80055 Naples, Italy
| | - Francesco Pennacchio
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, via Università 100, Portici, 80055 Naples, Italy
| | - Rosa Rao
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, Naples 80055, Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, via Università 100, Portici, 80055 Naples, Italy.
| | - Simona Maria Monti
- Institute of Biostructures and Bioimaging, National Research Council (IBB, CNR), via Pietro Castellino 111, Naples 80131, Italy.
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47
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Fashe MM, Le TV, Gower MN, Mulrenin IR, Dorman KF, Smith S, Fallon JK, Dumond JB, Boggess KA, Lee CR. Impact of Pregnancy on the Pharmacokinetics and Metabolism of Nicotinamide in Humans. Clin Pharmacol Ther 2024; 115:556-564. [PMID: 38093631 DOI: 10.1002/cpt.3146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
In pre-eclampsia models, nicotinamide (NAM) has protective effects in pre-eclampsia and is being evaluated as a therapeutic nutraceutical in clinical studies. NAM undergoes extensive hepatic metabolism by NAM N-methyltransferase to methylnicotinamide (MNA), which is subsequently metabolized to methyl-2-pyridone-5-carboxamide (M2PY) by aldehyde oxidase. However, the pharmacokinetics of NAM and its major metabolites has never been studied in pregnant individuals. Blood samples were collected before and 1, 2, 4, 8, and 24 hours after single 1 g oral NAM dose in healthy pregnant (gestational age 24-33 weeks) and nonpregnant female volunteers (n = 6/group). Pooled urine was collected from 0 to 8 hours. NAM, MNA, and M2PY area under the concentration-time curve (AUC) data were analyzed by noncompartmental analysis. No difference in the plasma AUC0→24 of NAM (median (25%-75%): 463 (436-576) vs. 510 (423, 725) μM*hour, P = 0.430) and its intermediate metabolite MNA (89.1 (60.4, 124.4) vs. 83.8 (62.7, 93.7) μM*hour, P = 0.515) was observed in pregnant and nonpregnant volunteers, respectively; however, the terminal metabolite M2PY AUC0 → 24 was significantly lower in pregnant individuals (218 (188, 254) vs. 597 (460, 653) μM*hour, P < 0.001). NAM renal clearance (CLR ; P = 0.184), MNA CLR (P = 0.180), and total metabolite formation clearance (P = 0.405) did not differ across groups; however, M2PY CLR was significantly higher in pregnant individuals (10.5 (9.3-11.3) vs. 7.5 (6.4-8.5) L/h, P = 0.002). These findings demonstrate that the PK of NAM and systemic exposure to its intermediate metabolite MNA are not significantly altered during pregnancy, and systemic exposure to NAM's major metabolite M2PY was reduced during pregnancy due to increased renal elimination.
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Affiliation(s)
- Muluneh M Fashe
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tien V Le
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Megan N Gower
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ian R Mulrenin
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karen F Dorman
- Department of Obstetrics & Gynecology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Spenser Smith
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John K Fallon
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julie B Dumond
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kim A Boggess
- Department of Obstetrics & Gynecology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Craig R Lee
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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48
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Hu E, Yang T, Cai L, Ouyang J, Wang F, Li Z, Wang Y, Xing X, Liu X. Proteomic Analysis Identifies GSN as a Noninvasive Circulating Serum Biomarker for Predicting Early Recurrence of Hepatocellular Carcinoma. J Proteome Res 2024; 23:1062-1074. [PMID: 38373391 DOI: 10.1021/acs.jproteome.3c00813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Hepatocellular carcinoma (HCC) is susceptible to early recurrence, but it lacks effective predictive biomarkers. In this study, we retrospectively selected 179 individuals as a discovery cohort (126 HCC patients and 53 liver cirrhosis (LC) patients) for screening candidate serum biomarkers of early recurrence based on data independent acquisition-mass spectrometry strategy. And then, the candidate biomarkers were validated in an additional independent cohort with 192 individuals (142 HCC patients and 50 LC patients) using parallel reaction monitoring targeted quantitative techniques (PXD047852). Eventually, we validated that gelsolin (GSN) concentrations were significantly lower in HCC than in LC (p < 0.0001), patients with low GSN concentrations had a poor prognosis (p < 0.0001), and GSN concentrations were significantly lower in early recurrence HCC than in late recurrence HCC (p < 0.0001). These trends were also observed in alpha-fetoprotein (AFP)-negative HCC patients. The area under the curve of machine-learning-based predictive model (GSN and microvascular invasion) for predicting early recurrence risk reached 0.803 (95% confidence interval (CI): 0.786-0.820) and maintained the same efficacy in AFP-negative patients. In conclusion, GSN is a novel serum biomarker for early recurrence of HCC. The model could provide timely warning to HCC patients at high risk of recurrence.
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Affiliation(s)
- En Hu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Tao Yang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Linsheng Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Zongman Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
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49
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Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P. Pan-cancer proteogenomics characterization of tumor immunity. Cell 2024; 187:1255-1277.e27. [PMID: 38359819 PMCID: PMC10988632 DOI: 10.1016/j.cell.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024]
Abstract
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Francesca Pia Caruso
- BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua M Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Erol Evangelista
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoyu Song
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Berk Turhan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David A Lewis
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rossana Lazcano Segura
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Maciej Wiznerowicz
- Department of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland
| | - Tania J González-Robles
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Antonio Iavarone
- Department of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Alexey I Nesvizhskii
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcin Cieslik
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Pukale DD, Adkins-Travis K, Aryal SR, Shriver LP, Patti GJ, Leipzig ND. Investigating post-traumatic syringomyelia and local fluid osmoregulation via a rat model. Fluids Barriers CNS 2024; 21:19. [PMID: 38409031 PMCID: PMC10895764 DOI: 10.1186/s12987-024-00514-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Syringomyelia (SM) is characterized by the development of fluid-filled cavities, referred to as syrinxes, within the spinal cord tissue. The molecular etiology of SM post-spinal cord injury (SCI) is not well understood and only invasive surgical based treatments are available to treat SM clinically. This study builds upon our previous omics studies and in vitro cellular investigations to further understand local fluid osmoregulation in post-traumatic SM (PTSM) to highlight important pathways for future molecular interventions. METHODS A rat PTSM model consisting of a laminectomy at the C7 to T1 level followed by a parenchymal injection of 2 μL quisqualic acid (QA) and an injection of 5 μL kaolin in the subarachnoid space was utilized 6 weeks after initial surgery, parenchymal fluid and cerebrospinal fluid (CSF) were collected, and the osmolality of fluids were analyzed. Immunohistochemistry (IHC), metabolomics analysis using LC-MS, and mass spectrometry-based imaging (MSI) were performed on injured and laminectomy-only control spinal cords. RESULTS We demonstrated that the osmolality of the local parenchymal fluid encompassing syrinxes was higher compared to control spinal cords after laminectomy, indicating a local osmotic imbalance due to SM injury. Moreover, we also found that parenchymal fluid is more hypertonic than CSF, indicating establishment of a local osmotic gradient in the PTSM injured spinal cord (syrinx site) forcing fluid into the spinal cord parenchyma to form and/or expand syrinxes. IHC results demonstrated upregulation of betaine, ions, water channels/transporters, and enzymes (BGT1, AQP1, AQP4, CHDH) at the syrinx site as compared to caudal and rostral sites to the injury, implying extensive local osmoregulation activities at the syrinx site. Further, metabolomics analysis corroborated alterations in osmolality at the syrinx site by upregulation of small molecule osmolytes including betaine, carnitine, glycerophosphocholine, arginine, creatine, guanidinoacetate, and spermidine. CONCLUSIONS In summary, PTSM results in local osmotic disturbance that propagates at 6 weeks following initial injury. This coincides with and may contribute to syrinx formation/expansion.
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Affiliation(s)
- Dipak D Pukale
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Kayla Adkins-Travis
- Departments of Chemistry and Medicine, Center for Proteomics, Metabolomics, and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Siddhartha R Aryal
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Leah P Shriver
- Departments of Chemistry and Medicine, Center for Proteomics, Metabolomics, and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Gary J Patti
- Departments of Chemistry and Medicine, Center for Proteomics, Metabolomics, and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nic D Leipzig
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA.
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA.
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