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Hibi Y. Reference-free quantitative mass spectrometry in the presence of nonlinear distortion caused by in situ chemical reactions among constituents. Analyst 2024. [PMID: 39318224 DOI: 10.1039/d4an00961d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Materials performance is primarily influenced by chemical composition, making compositional analysis (CA) essential in materials science. Traditional quantitative mass spectrometry, which deconvolutes analyte spectra into reference spectra, struggles with reactive systems where spectral variations occur, such as peak shifts and new peak emergences. Additionally, obtaining reference spectra for all pure constituents is often impractical. To address these challenges, I propose nonlinear reference-free quantitative mass spectrometry (NL-RQMS). This method simultaneously determines composition, reference spectra, and nonlinear interaction effects directly from a spectral dataset of mixtures, eliminating the need for prior reference spectra. In a benchmark test on ternary reactive polymers of epoxy and amines, NL-RQMS inferred compositions with an error margin of just 3 wt%, significantly outperforming the 6 wt% error margin of linear RQMS. The inferred interaction terms clearly indicate in situ reactions between epoxy and amine moieties. This framework enables accurate compositional analysis without prior knowledge of the constituents, even in systems with interactive components, and holds significant potential for applications such as grading recycled plastics, where pristine materials, degradation compounds, and stabilizers interact complexly, causing nonlinear spectral distortions.
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Affiliation(s)
- Yusuke Hibi
- Data-driven Polymer Design Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
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Hibi Y, Uesaka S, Naito M. Thermogravimetry-synchronized, reference-free quantitative mass spectrometry for accurate compositional analysis of polymer systems without prior knowledge of constituents. Analyst 2024; 149:4388-4394. [PMID: 39007205 DOI: 10.1039/d4an00624k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Compositional analysis (CA)-identification and quantification of the system constituents-is the most fundamental and decisive approach for investigating the system of interest. Pyrolysis mass spectrometry (MS) with a high resolution of over 10 000 is very effective for chemical identification and is directly applicable to polymer materials regardless of their solubilities. However, it is less helpful for quantification, especially when the references, i.e., pure constituents, are unknown, non-isolable and thus cannot be prepared. To compensate for this weakness, herein we propose reference-free quantitative mass spectrometry (RQMS) with enhanced quantification accuracy assisted by synchronized thermogravimetry (TG). The key to success lies in correlating the instantaneous weight loss from TG with the MS signal, enabling the quantitative evaluation of the distinct ionization efficiency for each fragment individually. The determined ionization efficiencies allow the conversion of MS signal intensities of pyrolyzed fragments into weight abundances. In a benchmark test using ternary polymer systems, this new framework named TG-RQMS demonstrates accurate CA within ±1.3 wt% errors without using any prior knowledge or spectra of the references. This simple yet accurate and versatile CA method would be an invaluable tool to investigate polymer materials whose composition is hardly accessible via other analytical methods.
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Affiliation(s)
- Yusuke Hibi
- Data-driven Polymer Design Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
| | - Shiho Uesaka
- Data-driven Polymer Design Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
| | - Masanobu Naito
- Data-driven Polymer Design Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
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Popova L, Carr RA, Carabetta VJ. Recent Contributions of Proteomics to Our Understanding of Reversible N ε-Lysine Acylation in Bacteria. J Proteome Res 2024; 23:2733-2749. [PMID: 38442041 PMCID: PMC11296938 DOI: 10.1021/acs.jproteome.3c00912] [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] [Indexed: 03/07/2024]
Abstract
Post-translational modifications (PTMs) have been extensively studied in both eukaryotes and prokaryotes. Lysine acetylation, originally thought to be a rare occurrence in bacteria, is now recognized as a prevalent and important PTM in more than 50 species. This expansion in interest in bacterial PTMs became possible with the advancement of mass spectrometry technology and improved reagents such as acyl-modification specific antibodies. In this Review, we discuss how mass spectrometry-based proteomic studies of lysine acetylation and other acyl modifications have contributed to our understanding of bacterial physiology, focusing on recently published studies from 2018 to 2023. We begin with a discussion of approaches used to study bacterial PTMs. Next, we discuss newly characterized acylomes, including acetylomes, succinylomes, and malonylomes, in different bacterial species. In addition, we examine proteomic contributions to our understanding of bacterial virulence and biofilm formation. Finally, we discuss the contributions of mass spectrometry to our understanding of the mechanisms of acetylation, both enzymatic and nonenzymatic. We end with a discussion of the current state of the field and possible future research avenues to explore.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Rachel A Carr
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
| | - Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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Aluksanasuwan S, Somsuan K, Wanna-Udom S, Roytrakul S, Morchang A, Rongjumnong A, Sakulsak N. Proteomic insights into the regulatory function of ARID1A in colon cancer cells. Oncol Lett 2024; 28:392. [PMID: 38966585 PMCID: PMC11223007 DOI: 10.3892/ol.2024.14525] [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: 03/26/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
The AT-rich interacting domain-containing protein 1A (ARID1A) is a tumor suppressor gene that has been implicated in several cancers, including colorectal cancer (CRC). The present study used a proteomic approach to elucidate the molecular mechanisms of ARID1A in CRC carcinogenesis. Stable ARID1A-overexpressing SW48 colon cancer cells were established using lentivirus transduction and the successful overexpression of ARID1A was confirmed by western blotting. Label-free quantitative proteomic analysis using liquid chromatography-tandem mass spectrometry identified 705 differentially altered proteins in the ARID1A-overexpressing cells, with 310 proteins significantly increased and 395 significantly decreased compared with empty vector control cells. Gene Ontology enrichment analysis highlighted the involvement of the altered proteins mainly in the Wnt signaling pathway. Western blotting supported these findings, as a decreased protein expression of Wnt target genes, including c-Myc, transcription factor T cell factor-1/7 and cyclin D1, were observed in ARID1A-overexpressing cells. Among the altered proteins involved in the Wnt signaling pathway, the interaction network analysis revealed that ARID1A exhibited a direct interaction with E3 ubiquitin-protein ligase zinc and ring finger 3 (ZNRF3), a negative regulator of the Wnt signaling pathway. Further analyses using the The Cancer Genome Atlas colon adenocarcinoma public dataset revealed that ZNRF3 expression significantly impacted the overall survival of patients with CRC and was positively correlated with ARID1A expression. Finally, an increased level of ZNRF3 in ARID1A-overexpressing cells was confirmed by western blotting. In conclusion, the findings of the present study suggest that ARID1A negatively regulates the Wnt signaling pathway through ZNRF3, which may contribute to CRC carcinogenesis.
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Affiliation(s)
- Siripat Aluksanasuwan
- School of Medicine, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Keerakarn Somsuan
- School of Medicine, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Sasithorn Wanna-Udom
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klongluang, Pathum Thani 12120, Thailand
| | - Atthapan Morchang
- School of Medicine, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Artitaya Rongjumnong
- School of Medicine, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
- Cancer and Immunology Research Unit, Mae Fah Luang University, Muang, Chiang Rai 57100, Thailand
| | - Natthiya Sakulsak
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
- Faculty of Medicine, Praboromarajchanok Institute, Ministry of Public Health, Mueang, Nonthaburi 11000, Thailand
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Subedi K, Roy PC, Saiz B, Basile F, Wall D. Cell-cell transfer of adaptation traits benefits kin and actor in a cooperative microbe. Proc Natl Acad Sci U S A 2024; 121:e2402559121. [PMID: 39012831 PMCID: PMC11287280 DOI: 10.1073/pnas.2402559121] [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: 02/09/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Microbes face many physical, chemical, and biological insults from their environments. In response, cells adapt, but whether they do so cooperatively is poorly understood. Here, we use a model social bacterium, Myxococcus xanthus, to ask whether adapted traits are transferable to naïve kin. To do so we isolated cells adapted to detergent stresses and tested for trait transfer. In some cases, strain-mixing experiments increased sibling fitness by transferring adaptation traits. This cooperative behavior depended on a kin recognition system called outer membrane exchange (OME) because mutants defective in OME could not transfer adaptation traits. Strikingly, in mixed stressed populations, the transferred trait also benefited the adapted (actor) cells. This apparently occurred by alleviating a detergent-induced stress response in kin that otherwise killed actor cells. Additionally, this adaptation trait when transferred also conferred resistance against a lipoprotein toxin delivered to targeted kin. Based on these and other findings, we propose a model for stress adaptation and how OME in myxobacteria promotes cellular cooperation in response to environmental stresses.
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Affiliation(s)
- Kalpana Subedi
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Pravas C. Roy
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
| | - Brandon Saiz
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Franco Basile
- Department of Chemistry, University of Wyoming, Laramie, WY82071
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY82071
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Beregoi M, Oprea D, Bunea MC, Enculescu M, Enache TA. Electrospun fibrillary scaffold for electrochemical cell biomarkers detection. Mikrochim Acta 2024; 191:435. [PMID: 38949689 PMCID: PMC11217050 DOI: 10.1007/s00604-024-06523-w] [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: 03/27/2024] [Accepted: 06/21/2024] [Indexed: 07/02/2024]
Abstract
A novel scaffold for in situ electrochemical detection of cell biomarkers was developed using electrospun nanofibers and commercial adhesive polymeric membranes. The electrochemical sensing of cell biomarkers requires the cultivation of the cells on/near the (bio)sensor surface in a manner to preserve an appropriate electroactive available surface and to avoid the surface passivation and sensor damage. This can be achieved by employing biocompatible nanofiber meshes that allow the cells to have a normal behavior and do not alter the electrochemical detection. For a better mechanical stability and ease of handling, nylon 6/6 nanofibers were collected on commercial polymeric membranes, at an optimal fiber density, obtaining a double-layered platform. To demonstrate the functionality of the fabricated scaffold, the screening of cellular stress has been achieved integrating melanoma B16-F10 cells and the (bio)sensor components on the transducer whereas the melanin exocytosis was successfully quantified using a commercial electrode. Either directly on the surface of the (bio)sensor or spatially detached from it, the integration of cell cultures in biosensing platforms based on electrospun nanofibers represents a powerful bioanalytical tool able to provide real-time information about the biomarker release, enzyme activity or inhibition, and monitoring of various cellular events.
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Affiliation(s)
- Mihaela Beregoi
- Functional Nanostructures Laboratory, National Institute of Materials Physics, Atomistilor Str. 405A, 077125, Magurele, Romania
| | - Daniela Oprea
- Functional Nanostructures Laboratory, National Institute of Materials Physics, Atomistilor Str. 405A, 077125, Magurele, Romania
- Faculty of Physics, University of Bucharest, Atomistilor Str. 405, 077125, Magurele, Romania
| | - Mihaela Cristina Bunea
- Functional Nanostructures Laboratory, National Institute of Materials Physics, Atomistilor Str. 405A, 077125, Magurele, Romania
| | - Monica Enculescu
- Functional Nanostructures Laboratory, National Institute of Materials Physics, Atomistilor Str. 405A, 077125, Magurele, Romania
| | - Teodor Adrian Enache
- Functional Nanostructures Laboratory, National Institute of Materials Physics, Atomistilor Str. 405A, 077125, Magurele, Romania.
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Ma X, Wang X, Chen F, Zou W, Ren J, Xin L, He P, Liang J, Xu Z, Dong C, Lan K, Wu S, Zhou HB. Novel Acyl Thiourea-Based Hydrophobic Tagging Degraders Exert Potent Anti-Influenza Activity through Two Distinct Endonuclease Polymerase Acidic-Targeted Degradation Pathways. J Med Chem 2024; 67:8791-8816. [PMID: 38775356 DOI: 10.1021/acs.jmedchem.4c00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The spread of the influenza virus has caused devastating pandemics and huge economic losses worldwide. Antiviral drugs with diverse action modes are urgently required to overcome the challenges of viral mutation and drug resistance, and targeted protein degradation strategies constitute excellent candidates for this purpose. Herein, the first degradation of the influenza virus polymerase acidic (PA) protein using small-molecule degraders developed by hydrophobic tagging (HyT) technology to effectively combat the influenza virus was reported. The SAR results revealed that compound 19b with Boc2-(L)-Lys demonstrated excellent inhibitory activity against A/WSN/33/H1N1 (EC50 = 0.015 μM) and amantadine-resistant strain (A/PR/8/H1N1), low cytotoxicity, high selectivity, substantial degradation ability, and good drug-like properties. Mechanistic studies demonstrated that the proteasome system and autophagic lysosome pathway were the potential drivers of these HyT degraders. Thus, this study provides a powerful tool for investigating the targeted degradation of influenza virus proteins and for antiviral drug development.
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Affiliation(s)
- Xiaoyu Ma
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xueyun Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Feifei Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenting Zou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Junrui Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lilan Xin
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Pei He
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jinsen Liang
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhichao Xu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Chune Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Bing Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University, Wuhan 430071, China
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Le NTN, Han CL, Delila L, Nebie O, Chien HT, Wu YW, Buée L, Blum D, Burnouf T. Proteomics of human platelet lysates and insight from animal studies on platelet protein diffusion to hippocampus upon intranasal administration. APL Bioeng 2024; 8:026111. [PMID: 38726021 PMCID: PMC11080963 DOI: 10.1063/5.0196553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Human platelet lysates (HPLs) from allogeneic platelet concentrates (PCs) are biomaterials, which are rich in various trophic factors, increasingly used in regenerative medicine and biotherapy. Understanding how preparation methods influence the HPL protein profile, biological function, and clinical outcomes is crucial. Our study sheds light on the proteomes and functionality of different HPLs, with the aim of advancing their scientifically grounded clinical applications. To achieve this, PCs suspended in plasma underwent three distinct processing methods, resulting in seven HPL types. We used three characterization techniques: label-free proteomics and tandem mass tag (TMT)-based quantitative proteomics, both before and after the immunodepletion of abundant plasma proteins. Bioinformatic tools assessed the proteome, and western blotting validated our quantitative proteomics data. Subsequent pre-clinical studies with fluorescent labeling and label-free proteomics were used as a proof of concept for brain diffusion. Our findings revealed 1441 proteins detected using the label-free method, 952 proteins from the TMT experiment before and after depletion, and 1114 proteins from the subsequent TMT experiment on depleted HPLs. Most detected proteins were cytoplasmic, playing key roles in catalysis, hemostasis, and immune responses. Notably, the processing methodologies significantly influenced HPL compositions, their canonical pathways, and, consequently, their functionality. Each HPL exhibited specific abundant proteins, providing valuable insight for tailored clinical applications. Immunoblotting results for selected proteins corroborated our quantitative proteomics data. The diffusion and differential effects to the hippocampus of a neuroprotective HPL administered intranasally to mice were demonstrated. This proteomics study advances our understanding of HPLs, suggesting ways to standardize and customize their production for better clinical efficacy in regenerative medicine and biotherapy. Proteomic analyses also offered objective evidence that HPPL, upon intranasal delivery, not only effectively diffuses to the hippocampus but also alters protein expression in mice, bolstering its potential as a treatment for memory impairments.
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Affiliation(s)
- Nhi Thao Ngoc Le
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Liling Delila
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei, Taiwan
| | | | - Hsin-Tung Chien
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei, Taiwan
| | - Yu-Wen Wu
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei, Taiwan
| | | | - David Blum
- Authors to whom correspondence should be addressed: and . Tel.: +886 988 925 235
| | - Thierry Burnouf
- Authors to whom correspondence should be addressed: and . Tel.: +886 988 925 235
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You G, Li Z, Li L, Xu C. Overexpression of RBM15 modulated the effect of trophoblast cells by promoting the binding ability between YTHDF2 and the CD82 3'UTR to decrease the expression of CD82. Heliyon 2024; 10:e30702. [PMID: 38765115 PMCID: PMC11098837 DOI: 10.1016/j.heliyon.2024.e30702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024] Open
Abstract
Background Pre-eclampsia (PE) is a syndrome with no specific pathological mechanism and is specific to pregnancy. The combined analysis of proteomics and transcriptomics possesses many benefits for treating this disease. m6A modification plays a major role in PE; however, mechanism have not been studied clearly. This study investigated the potential mechanism underlying the role of m6A in PE. Methods Mass spectrometry-based label-free quantitative proteomics and transcriptomics experiments were conducted on the placenta of patients with pre-eclampsia and normal pregnancies, and the two omics were followed by joint analysis. Total m6A modification in placental tissues, HTR8/SVneo cells, and JEG-3 cells was measured by dot blot. The levels of RBM15 and CD82 in tissues and cells were detected using qPCR. The protein levels of G3BP1, RBM15, MMP-2, YTHDF2, and MMP-9 were measured by western blotting. The function, migration, and invasion characteristics of HTR8/SVneo and JEG-3 cells were measured using Transwell assays. SRAMP predicted the m6A modification site in the CD82 mRNA 3'UTR, and this was confirmed using luciferase activity and YTHDF2-RIP. Results m6A modification was promoted in the PE group, and the RBM15 abundance was increased. Overexpression of RBM15 increased m6A modification. However, overexpression of RBM15 suppressed the expression of MMP-2 and MMP-9 and also the migratory and invasive capabilities of HTR8/SVneo and JEG-3 cells. CD82 expression levels were decreased in PE, and CD82 expression was confirmed via qPCR, western blotting and immunofluorescence. Furthermore, RBM15 overexpression reduced CD82 mRNA and protein levels. Luciferase activity and YTHDF2-RIP results verified that overexpression of RBM15 promoted the binding ability between YTHDF2 and the CD82 3'UTR, thereby decreasing CD82 expression. Finally, CD82 overexpression reversed the effect of RBM15 overexpression on the expression of MMP-2 and MMP-9 and on the migratory and invasive capabilities of the cells. Conclusions Overexpression of RBM15 hindered the migratory and invasive capabilities of trophoblasts, while concurrently enhancing m6A modification. The potential mechanism was that overexpression of RBM15 promoted the binding capability between YTHDF2 and CD82 3'UTR and decrease the expression of CD82. Thus, this study provides a theoretical basis for the treatment of PE.
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Affiliation(s)
| | | | - Ling Li
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, PR China
| | - Chengfang Xu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, PR China
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Fu G, Augspurger K, Sakizadeh J, Reck J, Bower R, Tritschler D, Gui L, Nicastro D, Porter ME. The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dynein b and reveals axoneme asymmetries involved in ciliary waveform. Mol Biol Cell 2024; 35:ar72. [PMID: 38568782 PMCID: PMC11151096 DOI: 10.1091/mbc.e23-11-0439] [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: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Cilia generate three-dimensional waveforms required for cell motility and transport of fluid, mucus, and particles over the cell surface. This movement is driven by multiple dynein motors attached to nine outer doublet microtubules that form the axoneme. The outer and inner arm dyneins are organized into 96-nm repeats tandemly arrayed along the length of the doublets. Motility is regulated in part by projections from the two central pair microtubules that contact radial spokes located near the base of the inner dynein arms in each repeat. Although much is known about the structures and protein complexes within the axoneme, many questions remain about the regulatory mechanisms that allow the cilia to modify their waveforms in response to internal or external stimuli. Here, we used Chlamydomonas mbo (move backwards only) mutants with altered waveforms to identify at least two conserved proteins, MBO2/CCDC146 and FAP58/CCDC147, that form part of a L-shaped structure that varies between doublet microtubules. Comparative proteomics identified additional missing proteins that are altered in other motility mutants, revealing overlapping protein defects. Cryo-electron tomography and epitope tagging revealed that the L-shaped, MBO2/FAP58 structure interconnects inner dynein arms with multiple regulatory complexes, consistent with its function in modifying the ciliary waveform.
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Affiliation(s)
- Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Katherine Augspurger
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jason Sakizadeh
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jaimee Reck
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E. Porter
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
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11
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Jorgensen AN, Rashdan NA, Rao KNS, Delgadillo LF, Kolluru GK, Krzywanski DM, Pattillo CB, Kevil CG, Nam HW. Neurogranin expression regulates mitochondrial function and redox balance in endothelial cells. Redox Biol 2024; 70:103085. [PMID: 38359746 PMCID: PMC10878108 DOI: 10.1016/j.redox.2024.103085] [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: 01/20/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024] Open
Abstract
Endothelial dysfunction and endothelial activation are common early events in vascular diseases and can arise from mitochondrial dysfunction. Neurogranin (Ng) is a 17kD protein well known to regulate intracellular Ca2+-calmodulin (CaM) complex signaling, and its dysfunction is significantly implicated in brain aging and neurodegenerative diseases. We found that Ng is also expressed in human aortic endothelial cells (HAECs), and depleting Ng promotes Ca2+-CaM complex-dependent endothelial activation and redox imbalances. Endothelial-specific Ng knockout (Cre-CDH5-Ngf/f) mice demonstrate a significant delay in the flow-mediated dilation (FMD) response. Therefore, it is critical to characterize how endothelial Ng expression regulates reactive oxygen species (ROS) generation and affects cardiovascular disease. Label-free quantification proteomics identified that mitochondrial dysfunction and the oxidative phosphorylation pathway are significantly changed in the aorta of Cre-CDH5-Ngf/f mice. We found that a significant amount of Ng is expressed in the mitochondrial fraction of HAECs using western blotting and colocalized with the mitochondrial marker, COX IV, using immunofluorescence staining. Seahorse assay demonstrated that a lack of Ng decreases mitochondrial respiration. Treatment with MitoEbselen significantly restores the oxygen consumption rate in Ng knockdown cells. With the RoGFP-Orp1 approach, we identified that Ng knockdown increases mitochondrial-specific hydrogen peroxide (H2O2) production, and MitoEbselen treatment significantly reduced mitochondrial ROS (mtROS) levels in Ng knockdown cells. These results suggest that Ng plays a significant role in mtROS production. We discovered that MitoEbselen treatment also rescues decreased eNOS expression and nitric oxide (NO) levels in Ng knockdown cells, which implicates the critical role of Ng in mtROS-NO balance in the endothelial cells.
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Affiliation(s)
- Ashton N Jorgensen
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Nabil A Rashdan
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - K N Shashanka Rao
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Luisa F Delgadillo
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Gopi K Kolluru
- Department of Pathology, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - David M Krzywanski
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Christopher B Pattillo
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Christopher G Kevil
- Department of Pathology, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA
| | - Hyung W Nam
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center, Shreveport, LA, 71103, USA.
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12
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Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems. J Proteome Res 2024; 23:999-1013. [PMID: 38354288 PMCID: PMC10913063 DOI: 10.1021/acs.jproteome.3c00714] [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: 10/30/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.
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Affiliation(s)
- Mengxun Shi
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Caroline A. Evans
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Josie L. McQuillan
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Josselin Noirel
- GBCM
Laboratory (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, 2 rue Conté, Paris 75003, France
| | - Jagroop Pandhal
- Department
of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
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13
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Liu Y, Wang X, Sheng Y, Jin H, Han L, Xu J, Fu Q, Liu J, Ji F, Ding H, Xu X, Wu K, Zhang P, Wang G. Recurrence of macular edema in patients with branch retinal vein occlusion: a proteomic study. BMC Ophthalmol 2024; 24:82. [PMID: 38388341 PMCID: PMC10882909 DOI: 10.1186/s12886-024-03359-z] [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: 12/28/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Branch retinal vein occlusion (BRVO) is a common retinal vascular disease leading to severe vision loss and blindness. This study aimed to investigate and reveal the pathophysiological mechanisms underlying macular edema (ME) recurrence in patients with BRVO through a proteomic approach. METHODS We detected proteins in the aqueous humor of 14 untreated, four refractory, and four post-operative patients with BRVO-ME and 12 age-matched cataract controls using four-dimensional label-free proteomic and bioinformatics analyses. RESULTS In total, 84 proteins exhibited significant differential expression between the BRVO and control samples (fold change [FC] ≥ 1.2 and adjusted p-value < 0.05). Compared to the control group, 43 and 41 proteins were upregulated and downregulated, respectively, in the BRVO group. These proteins were involved in cell adhesion, visual perception, retina homeostasis, and platelet activation. Several significantly enriched signaling pathways included complement and coagulation cascades and platelet activation. In the protein-protein interaction networks generated using the search tool for retrieval of interacting genes (STRING), the fibrinogen alpha chain and fibrinogen beta chain constituted a tightly connected cluster. Many common protein expression trends, such as the fibrinogen alpha chain and fibrinogen beta chain, were observed in both the recurrent and refractory groups. Differentially expressed proteins in the two groups were involved in complement activation, acute-phase response, platelet activation, and platelet aggregation. Important signaling pathways include the complement and coagulation cascades, and platelet activation. Protein-protein interaction analysis suggested that the fibrinogen alpha chain and fibrinogen beta chain constituted a tightly connected cluster. The expression of some differentially expressed proteins shared by the BRVO and the recurrent and refractory groups was reversed in the post-operative group. CONCLUSIONS Our study is the first to analyze the proteomics of recurrent, refractory, and post-operative groups treated for BRVO-ME, and may potentially provide novel therapeutic interventions for the recurrence of ME.
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Affiliation(s)
- Yin Liu
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Xiaohu Wang
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Yonghong Sheng
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Haili Jin
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Linfeng Han
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Jun Xu
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Qingqing Fu
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Jing Liu
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Feng Ji
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - He Ding
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - Xiaochen Xu
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China
| | - KunChao Wu
- Department of Ophthalmology, First People's Hospital of Guiyang, Guiyang, China.
| | - Pengfei Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
| | - Guoping Wang
- Wuhu Eye Hospital, No. 378, Santan Road, Yijiang District, Wuhu, Anhui Province, 241000, China.
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14
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Banerjee S, Hatimuria M, Sarkar K, Das J, Pabbathi A, Sil PC. Recent Contributions of Mass Spectrometry-Based "Omics" in the Studies of Breast Cancer. Chem Res Toxicol 2024; 37:137-180. [PMID: 38011513 DOI: 10.1021/acs.chemrestox.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".
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Affiliation(s)
- Subhrajit Banerjee
- Department of Physiology, Surendranath College, University of Calcutta, Kolkata 700009, India
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Madushmita Hatimuria
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Kasturi Sarkar
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Joydeep Das
- Department of Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India
| | - Ashok Pabbathi
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Parames C Sil
- Department of Molecular Medicine Bose Institute, Kolkata 700054, India
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15
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Woo DU, Lee Y, Min CW, Kim ST, Kang YJ. RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis. Sci Rep 2024; 14:3671. [PMID: 38351208 PMCID: PMC10864295 DOI: 10.1038/s41598-024-54151-4] [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: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Rice, feeding a significant portion of the world, poses unique proteomic challenges critical to agricultural research and global food security. The complexity of the rice proteome, influenced by various genetic and environmental factors, demands specialized analytical approaches for effective study. The central challenges in rice proteomics lie in developing custom methods suited to the unique aspects of rice biology. These include data preprocessing, method selection, and result validation, all of which are essential for advancing rice research. Our aim is to decode these proteomic intricacies to facilitate breakthroughs in strain improvement, disease resistance, and yield optimization, all vital for combating global food insecurity. To achieve this, we have created the RiceProteomeDB (RPDB), a React + Django database, offering a streamlined and comprehensive platform for the analysis of rice proteomics data. RiceProteomeDB (RPDB) simplifies proteomics data management and analysis. It offers features for data organization, preprocessing, method selection, result validation, and data sharing. Researchers can access processed rice proteomics data, conduct analyses, and explore experimental conditions. The user-friendly web interface enhances navigation and interaction. RPDB fosters collaboration by enabling data sharing and proper acknowledgment of sources, contributing to proteomics research and knowledge dissemination. Availability and implementation: Web application: http://riceproteome.plantprofile.net/ . The web application's source code, user's manual, and sample data: https://github.com/dongu7610/Riceproteome .
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Affiliation(s)
- Dong U Woo
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Yejin Lee
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Milyang, 50463, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Milyang, 50463, Republic of Korea
| | - Yang Jae Kang
- Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
- Division of Life Science Department, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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16
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Li FG, Shi XY, Yang L, Lu X, Qi Y, Li P, Yang H, Gao W. Quantitative proteomics based bioactive proteins discovery and quality control of medicinal leeches. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117117. [PMID: 37659761 DOI: 10.1016/j.jep.2023.117117] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leech, a classical traditional Chinese medicine for promoting blood circulation and removing blood stasis, is mainly used in the clinical treatment of cardiovascular and cerebrovascular diseases. The discovery of activity proteins or peptides in the dead and dried medicinal leech is an important task with great challenges. AIM OF THE STUDY The aim of this study was to provide a basic proteome profile and help further discover active proteins and quality control for medicinal leeches, which would also provide insight into the research of animal medicines. MATERIALS AND METHODS Seventeen batches of dried medicinal leeches covering three species were collected from medicinal markets, which were authenticated by DNA barcoding. Then the proteome of different species leeches was profiled to reveal the significantly different proteins using label-free proteomics. The characteristic peptides were screened out based on biological pathways analysis, which were further absolutely quantified using the developed stable isotope-labeled based parallel reaction monitoring method. RESULTS Seventeen batches of leech materials were Whitmania pigra Whitman (WP), Whitmania laevis Whitman (WL) and Poecilobdella manillensis Lesson (PM), respectively. A total of 1,035 proteins (452 in WP, 425 in WL and 158 in PM) were identified. Among them, 90 overlapping proteins were mainly concentrated in diverse metabolic pathways and primarily localized in the cytoplasm and mitochondrial inner membrane, which mainly related to ATP binding, catalytic activity and structural molecular activity. In total of 51 uniquely expressed proteins (21 in WP, 23 in WL and 7 in PM), associated with multiple key signaling pathways, including Rap1, cGMP-PKG, PI3K-Akt, Wnt and HIF-1, etc., relevant to treating cardiovascular diseases, diabetes, cancer and even a variety of neurodegenerative diseases. Three proteins with potential bioactivities, including Neurohemerythrin, Hirudin and Eglin C, were selected as the quality makers and then quantified based on the characteristic peptides. CONCLUSIONS This work profiled the proteome of three species of leeches, and addressed potential active proteins of the medicinal leech, which would help to provide the potential molecular mechanisms involved in disease treatment. The proteomics-based approach developed in this work is not only useful for the discovery of proteins with potential bioactivities but also helpful for the bioactivity relevant quality control of animal medicines.
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Affiliation(s)
- Fu-Gui Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xin-Yue Shi
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Liu Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Yan Qi
- Yangshengtang Pharmaceutical Co., Ltd, Hangzhou, 310000, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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17
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Powers J, Zhang X, Reyes AV, Zavaliev R, Xu SL, Dong X. Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574047. [PMID: 38260692 PMCID: PMC10802274 DOI: 10.1101/2024.01.03.574047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for both basal and systemic acquired resistance (SAR). SA activates these immune responses by reprogramming up to 20% of the transcriptome through the function of NPR1. However, components in the NPR1-signaling hub, which appears as nuclear condensates, and the NPR1- signaling cascade remained elusive due to difficulties in studying transcriptional cofactors whose chromatin associations are often indirect and transient. To overcome this challenge, we applied TurboID to divulge the NPR1-proxiome, which detected almost all known NPR1-interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, NPR1-proxiome shares a striking similarity to GBPL3-proxiome involved in SA synthesis, except associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise greenCUT&RUN analyses showed that, upon SA-induction, NPR1 initiates the transcriptional cascade primarily through association with TGA TFs to induce expression of secondary TFs, predominantly WRKYs. WRKY54 and WRKY70 then play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, a loss of NPR1 condensate formation decreases its chromatin-association and transcriptional activity, indicating the importance of condensates in organizing the NPR1- signaling hub and initiating the transcriptional cascade. This study demonstrates how combinatorial applications of TurboID and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades.
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Affiliation(s)
- Jordan Powers
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Xing Zhang
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Andres V. Reyes
- Carnegie Institute for Science, Stanford University, Stanford, CA 94305, USA
| | - Raul Zavaliev
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Shou-Ling Xu
- Carnegie Institute for Science, Stanford University, Stanford, CA 94305, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
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18
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Li J. Proteomic Analyses of the Mouse Brain. Methods Mol Biol 2024; 2794:105-120. [PMID: 38630224 DOI: 10.1007/978-1-0716-3810-1_10] [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: 04/19/2024]
Abstract
Proteomics is a scientific field that aims to identify and characterize all proteins within a biological system, including their posttranslational modifications (PTMs), quantitative changes, and protein-protein interactions. Over the last two decades, proteomic approaches have been widely used in neuroscience research, providing multidimensional insights into the biology and pathology of the brain.Here, we present a basic protocol for profiling protein expression in the mouse brain, which involves total protein extraction, fractionation, digestion, and identification through liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). This method is compatible with many prevalent techniques used for protein quantitation, PTM analysis, and protein-protein interaction mapping.
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Affiliation(s)
- Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, China.
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19
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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20
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Terhaar HM, Henriksen MDL, Mehaffy C, Hess A, McMullen RJ. The use of shotgun label-free quantitative proteomic mass spectrometry to evaluate the inflammatory response in aqueous humor from horses with uveitis compared to ophthalmologically healthy horses. Vet Ophthalmol 2024; 27:40-52. [PMID: 37144658 DOI: 10.1111/vop.13107] [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: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVE The objective of this study was to use shotgun label-free tandem mass spectrometry (LF-MS/MS) to evaluate aqueous humor (AH) from horses with uveitis (UH) compared to ophthalmologically healthy horses (HH). ANIMALS STUDIED Twelve horses diagnosed with uveitis based on ophthalmic examination and six ophthalmologically healthy horses (postmortem) purchased for teaching purposes. PROCEDURES All horses received a complete ophthalmic examination and physical exam. Aqueous paracentesis was performed on all horses and AH total protein concentrations were measured with nanodrop (TPn) and refractometry (TPr). AH samples were analyzed with shotgun LF-MS/MS and proteomic data were compared between groups using Wilcoxon rank-sum test. RESULTS A total of 147 proteins were detected, 11 proteins had higher abundance in UH, and 38 proteins had lower abundance in UH. Proteins with higher abundance included apolipoprotein E, alpha-2-macroglobulin (A2M), alpha-2-HS-glycoprotein, prothrombin, fibrinogen, complement component 4 (C4), joining chain for IgA and IgM, afamin, and amine oxidase. There were positive correlations between TPn (p = .003) and TPr (p = .0001) compared to flare scores. CONCLUSION Differential abundance of A2M, prothrombin, fibrinogen, and C4 indicate upregulation of the complement and coagulation cascade in equine uveitis. Proinflammatory cytokines and the complement cascade have potential as therapeutic targets for equine uveitis.
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Affiliation(s)
- Hannah M Terhaar
- Comparative Ophthalmology, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michala de Linde Henriksen
- Comparative Ophthalmology, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Ann Hess
- Department of Statistics, College of Natural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Richard J McMullen
- Equine Ophthalmology, Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, JT Vaughan Large Animal Teaching Hospital, Auburn, Alabama, USA
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21
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FNU PIJ, Tanim-Al-Hassan M, Yaroshuk T, Ai Y, Chen H. Absolute Quantitation of Peptides and Proteins by Coulometric Mass Spectrometry After Derivatization. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 495:117153. [PMID: 38009161 PMCID: PMC10673616 DOI: 10.1016/j.ijms.2023.117153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Peptide/protein quantitation using mass spectrometry (MS) is advantageous due to its high sensitivity. Traditional absolute peptide quantitation methods rely on making calibration curves using peptide standards or isotope-labelled peptide standards, which are expensive and take time to synthesize. A method which can eliminate the need for using standards would be beneficial. Recently, we developed coulometric mass spectrometry (CMS) which can be used to quantify peptides that are oxidizable (e.g., those containing tyrosine or tryptophan), without using peptide standard. The method is based on electrochemical oxidation of peptides followed by MS to measure the oxidation yield. However, it cannot be directly used to quantify peptides without oxidizable residues. To extend this method for quantifying peptides/proteins in general, in this study, we adopted a derivatization strategy, in which a target peptide is first tagged with an electroactive reagent such as monocarboxymethylene blue NHS ester (MCMB-NHS ester), followed with quantitation by CMS. To illustrate the power of this method, we have analyzed peptides MG and RPPGFSPFR. The quantification error was less than 5%. Using RPPGFSPFR as an example, the quantitation sensitivity of the technique was found to be 0.25 pmol. Furthermore, we also used the strategy to quantify proteins cytochrome C and β-casein with an error of 2-26%.
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Affiliation(s)
- Praneeth Ivan Joel FNU
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Md. Tanim-Al-Hassan
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Timothy Yaroshuk
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
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22
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Li Z, Weller CA, Shah S, Johnson N, Hao Y, Roberts J, Bereda C, Klaisner S, Machado P, Fratta P, Petrucelli L, Prudencio M, Oskarsson B, Staff NP, Dickson DW, Cookson MR, Ward ME, Singleton AB, Nalls MA, Qi YA. ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571327. [PMID: 38168437 PMCID: PMC10760195 DOI: 10.1101/2023.12.12.571327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe , accompanied by a web interface.
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23
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Mateos Guerrero D, Martínez-Cruz M, Pérez-Campos E, García-Guerrero M, de los Santos-Romero R, Solórzano-Mata C, Sánchez-Salgado JL, Pereyra Morales MA, Lugo A, Torres-Rivera A, Alpuche J. Molecular signature of the ontogenic development of the prawn Macrobrachium tenellum. PeerJ 2023; 11:e16344. [DOI: 10.7717/peerj.16344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024] Open
Abstract
The prawn Macrobrachium tenellum shows aquaculture potential due to its well-defined reproductive cycle linked to female nutritional requirements. Significant changes occur in egg composition during the 16 to 17-day embryo development. Understanding the ontogenic proteins is crucial for developmental insights and controlled reproduction. We employed free-label quantitative proteomics to analyze egg peptides at the initial and final stages of wild females. Using the emPAI protocol and Proteome Discoverer 2.0, we identified 89 differentially expressed proteins in M. tenellum eggs. Of these, 27 were exclusive to early-stage development and three to late-stage. Abundant proteins included Vitellogenin, glyceraldehyde-3-phosphate dehydrogenase, histone 4, beta-actin, and hemocyanin. Gene Ontology analysis revealed 518 terms across molecular functions, biological processes, and cellular components using the GoRetriever tool of AgBase and the CateGOrizer tool of the Animal Genome Research Program. Carbohydrate metabolism was significant in early-stage development, with glyceraldehyde-3-phosphate dehydrogenase being the second most abundant protein. Proteins involved in ATP synthesis and cytoplasmic proteins associated with catalytic and binding activities related to primary metabolism were also detected. Our study elucidates the role of Vitellogenin in lipid transport activity and its potential involvement in the juvenile hormone feedback pathway. This pathway includes farnesoic acid O-methyltransferase and juvenile hormone epoxide oxidase, regulating protein biosynthesis, molt cycles (including chitinase activity), and potentially influencing controlled reproduction. Our proteomic analysis provides insights into the molecular mechanisms driving Ontogenic development in Macrobrachium tenellum, with implications for controlled reproduction strategies and advancements in aquaculture practices.
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Affiliation(s)
- Dulce Mateos Guerrero
- IT Oaxaca, Tecnológico Nacional de México, Oaxaca de Juarez, Oaxaca, Mexico
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juarez, Oaxaca, Mexico
| | | | | | - Marcelo García-Guerrero
- Laboratorio de Crustáceos Dulceacuicolas, CIIDIR-Oaxaca Instituto Politécnico Nacional, Oaxaca de Juarez, Oaxaca, Mexico
| | | | - Carlos Solórzano-Mata
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juarez, Oaxaca, Mexico
| | - José Luís Sánchez-Salgado
- Facultad de Medicina, Departamento de Bioquímica, Universidad Nacional Autonoma de México, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | - Mohamed Ali Pereyra Morales
- Facultad de Medicina, Departamento de Bioquímica, Universidad Nacional Autonoma de México, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | - Agustin Lugo
- CONACYT–Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juarez, Oaxaca, Mexico
| | - Anayetzin Torres-Rivera
- Tecnológico de Estudios Superiores de Huixquilucan, TecNM, Huixquilucan, Estado de México, Mexico
| | - Juan Alpuche
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca de Juarez, Oaxaca, Mexico
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24
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Petersen M, Chorzalska A, Pardo M, Rodriguez A, Morgan J, Ahsan N, Zhao TC, Liang O, Kotula L, Bertone P, Gruppuso PA, Dubielecka PM. Proximity proteomics reveals role of Abelson interactor 1 in the regulation of TAK1/RIPK1 signaling. Mol Oncol 2023; 17:2356-2379. [PMID: 36635880 PMCID: PMC10620119 DOI: 10.1002/1878-0261.13374] [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: 11/30/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
Dysregulation of the adaptor protein Abelson interactor 1 (ABI1) is linked to malignant transformation. To interrogate the role of ABI1 in cancer development, we mapped the ABI1 interactome using proximity-dependent labeling (PDL) with biotin followed by mass spectrometry. Using a novel PDL data filtering strategy, considering both peptide spectral matches and peak areas of detected peptides, we identified 212 ABI1 proximal interactors. These included WAVE2 complex components such as CYFIP1, NCKAP1, or WASF1, confirming the known role of ABI1 in the regulation of actin-polymerization-dependent processes. We also identified proteins associated with the TAK1-IKK pathway, including TAK1, TAB2, and RIPK1, denoting a newly identified function of ABI1 in TAK1-NF-κB inflammatory signaling. Functional assays using TNFα-stimulated, ABI1-overexpressing or ABI1-deficient cells showed effects on the TAK1-NF-kB pathway-dependent signaling to RIPK1, with ABI1-knockout cells being less susceptible to TNFα-induced, RIPK1-mediated, TAK1-dependent apoptosis. In sum, our PDL-based strategy enabled mapping of the ABI1 proximal interactome, thus revealing a previously unknown role of this adaptor protein in TAK1/RIPK1-based regulation of cell death and survival.
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Affiliation(s)
- Max Petersen
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Division of Biology and Medicine, Department of Pathology and Laboratory MedicineBrown UniversityProvidenceRIUSA
| | - Anna Chorzalska
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - Makayla Pardo
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - Anaelena Rodriguez
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
| | - John Morgan
- Flow Cytometry and Cell Sorting Core FacilityRoger Williams Medical CenterProvidenceRIUSA
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core FacilityRhode Island HospitalProvidenceRIUSA
- Department of Chemistry and BiochemistryThe University of OklahomaNormanOKUSA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research CenterThe University of OklahomaNormanOKUSA
| | - Ting C. Zhao
- Department of SurgeryRhode Island Hospital and Warren Alpert Medical School of Brown UniversityProvidenceRIUSA
| | - Olin Liang
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
| | - Leszek Kotula
- Department of UrologySUNY Upstate Medical UniversitySyracuseNYUSA
- Department of Biochemistry and Molecular BiologySUNY Upstate Medical UniversitySyracuseNYUSA
- Upstate Cancer CenterSUNY Upstate Medical UniversitySyracuseNYUSA
| | - Paul Bertone
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
| | - Philip A. Gruppuso
- Division of Pediatric EndocrinologyRhode Island Hospital and Warren Alpert Medical School of Brown UniversityProvidenceRIUSA
| | - Patrycja M. Dubielecka
- Department of Medicine, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
- Division of Hematology/OncologyRhode Island HospitalProvidenceRIUSA
- Division of Biology and Medicine, Department of Pathology and Laboratory MedicineBrown UniversityProvidenceRIUSA
- Legorreta Cancer Center, Alpert Medical SchoolBrown UniversityProvidenceRIUSA
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25
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Zhang T, Zheng H, Lu D, Guan G, Li D, Zhang J, Liu S, Zhao J, Guo JT, Lu F, Chen X. RNA binding protein TIAR modulates HBV replication by tipping the balance of pgRNA translation. Signal Transduct Target Ther 2023; 8:346. [PMID: 37699883 PMCID: PMC10497612 DOI: 10.1038/s41392-023-01573-7] [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: 01/30/2023] [Revised: 06/20/2023] [Accepted: 07/23/2023] [Indexed: 09/14/2023] Open
Abstract
The pregenomic RNA (pgRNA) of hepatitis B virus (HBV) serves not only as a bicistronic message RNA to translate core protein (Cp) and DNA polymerase (Pol), but also as the template for reverse transcriptional replication of viral DNA upon packaging into nucleocapsid. Although it is well known that pgRNA translates much more Cp than Pol, the molecular mechanism underlying the regulation of Cp and Pol translation efficiency from pgRNA remains elusive. In this study, we systematically profiled HBV nucleocapsid- and pgRNA-associated cellular proteins by proteomic analysis and identified TIA-1-related protein (TIAR) as a novel cellular protein that binds pgRNA and promotes HBV DNA replication. Interestingly, loss- and gain-of-function genetic analyses showed that manipulation of TIAR expression did not alter the levels of HBV transcripts nor the secretion of HBsAg and HBeAg in human hepatoma cells supporting HBV replication. However, Ribo-seq and PRM-based mass spectrometry analyses demonstrated that TIAR increased the translation of Pol but decreased the translation of Cp from pgRNA. RNA immunoprecipitation (RIP) and pulldown assays further revealed that TIAR directly binds pgRNA at the 5' stem-loop (ε). Moreover, HBV replication or Cp expression induced the increased expression and redistribution of TIAR from the nucleus to the cytoplasm of hepatocytes. Our results thus imply that TIAR is a novel cellular factor that regulates HBV replication by binding to the 5' ε structure of pgRNA to tip the balance of Cp and Pol translation. Through induction of TIAR translocation from the nucleus to the cytoplasm, Cp indirectly regulates the Pol translation and balances Cp and Pol expression levels in infected hepatocytes to ensure efficient viral replication.
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Affiliation(s)
- Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Huiling Zheng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Danjuan Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Guiwen Guan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Deyao Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jing Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shuhong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Jingmin Zhao
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Ju-Tao Guo
- Department of Experimental Therapeutics, Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Peking University Hepatology Institute, Peking University People's Hospital, Beijing, 100044, China.
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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26
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Cunningham J, Sfakianos AP, Kritsiligkou P, Kershaw C, Whitmarsh A, Hubbard S, Ashe M, Grant C. Paralogous translation factors target distinct mRNAs to differentially regulate tolerance to oxidative stress in yeast. Nucleic Acids Res 2023; 51:8820-8835. [PMID: 37449412 PMCID: PMC10484682 DOI: 10.1093/nar/gkad568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
Translation initiation factor 4G (eIF4G) is an integral component of the eIF4F complex which is key to translation initiation for most eukaryotic mRNAs. Many eIF4G isoforms have been described in diverse eukaryotic organisms but we currently have a poor understanding of their functional roles and whether they regulate translation in an mRNA specific manner. The yeast Saccharomyces cerevisiae expresses two eIF4G isoforms, eIF4G1 and eIF4G2, that have previously been considered as functionally redundant with any phenotypic differences arising due to alteration in eIF4G expression levels. Using homogenic strains that express eIF4G1 or eIF4G2 as the sole eIF4G isoforms at comparable expression levels to total eIF4G, we show that eIF4G1 is specifically required to mediate the translational response to oxidative stress. eIF4G1 binds the mRNA cap and remains associated with actively translating ribosomes during oxidative stress conditions and we use quantitative proteomics to show that eIF4G1 promotes oxidative stress-specific proteome changes. eIF4G1, but not eIF4G2, binds the Slf1 LARP protein which appears to mediate the eIF4G1-dependent translational response to oxidative stress. We show similar isoform specific roles for eIF4G in human cells suggesting convergent evolution of multiple eIF4G isoforms offers significant advantages especially where translation must continue under stress conditions.
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Affiliation(s)
- Joanne Cunningham
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Aristeidis P Sfakianos
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Paraskevi Kritsiligkou
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Christopher J Kershaw
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Alan J Whitmarsh
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Mark P Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Chris M Grant
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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27
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Nava-Galeana J, Núñez C, Bustamante VH. Proteomic analysis reveals the global effect of the BarA/SirA-Csr regulatory cascade in Salmonella Typhimurium grown in conditions that favor the expression of invasion genes. J Proteomics 2023; 286:104960. [PMID: 37451358 DOI: 10.1016/j.jprot.2023.104960] [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: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
In many bacteria, the BarA/SirA and Csr regulatory systems control expression of genes encoding a wide variety of cellular functions. The BarA/SirA two-component system induces the expression of CsrB and CsrC, two small non-coding RNAs that sequester CsrA, a protein that binds to target mRNAs and thus negatively or positively regulates their expression. BarA/SirA and CsrB/C induce expression of the Salmonella Pathogenicity Island 1 (SPI-1) genes required for Salmonella invasion of host cells. To further investigate the regulatory role of the BarA/SirA and Csr systems in Salmonella, we performed LC-MS/MS proteomic analysis using the WT S. Typhimurium strain and its derived ΔsirA and ΔcsrB ΔcsrC mutants grown in SPI-1-inducing conditions. The expression of 164 proteins with a wide diversity, or unknown, functions was significantly affected positively or negatively by the absence of SirA and/or CsrB/C. Interestingly, 19 proteins were identified as new targets for SirA-CsrB/C. Our results support that SirA and CsrB/C act in a cascade fashion to regulate gene expression in S. Typhimurium in the conditions tested. Notably, our results show that SirA-CsrB/C-CsrA controls expression of proteins required for the replication of Salmonella in the intestinal lumen, in an opposite way to its control exerted on the SPI-1 proteins. SIGNIFICANCE: The BarA/SirA and Csr global regulatory systems control a wide range of cellular processes, including the expression of virulence genes. For instance, in Salmonella, BarA/SirA and CsrB/C positively regulate expression of the SPI-1 genes, which are required for Salmonella invasion to host cells. In this study, by performing a proteomic analysis, we identified 164 proteins whose expression was positively or negatively controlled by SirA and CsrB/C in SPI-1-inducing conditions, including 19 new possible targets of these systems. Our results support the action of SirA and CsrB/C in a cascade fashion to control different cellular processes in Salmonella. Interestingly, our data indicate that SirA-CsrB/C-CsrA controls inversely the expression of proteins required for invasion of the intestinal epithelium and for replication in the intestinal lumen, which suggests a role for this regulatory cascade as a molecular switch for Salmonella virulence. Thus, our study further expands the insight into the regulatory mechanisms governing the virulence and physiology of an important pathogen.
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Affiliation(s)
- Jessica Nava-Galeana
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Víctor H Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
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28
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Kourti M, Aivaliotis M, Hatzipantelis E. Proteomics in Childhood Acute Lymphoblastic Leukemia: Challenges and Opportunities. Diagnostics (Basel) 2023; 13:2748. [PMID: 37685286 PMCID: PMC10487225 DOI: 10.3390/diagnostics13172748] [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: 06/30/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children and one of the success stories in cancer therapeutics. Risk-directed therapy based on clinical, biologic and genetic features has played a significant role in this accomplishment. Despite the observed improvement in survival rates, leukemia remains one of the leading causes of cancer-related deaths. Implementation of next-generation genomic and transcriptomic sequencing tools has illustrated the genomic landscape of ALL. However, the underlying dynamic changes at protein level still remain a challenge. Proteomics is a cutting-edge technology aimed at deciphering the mechanisms, pathways, and the degree to which the proteome impacts leukemia subtypes. Advances in mass spectrometry enable high-throughput collection of global proteomic profiles, representing an opportunity to unveil new biological markers and druggable targets. The purpose of this narrative review article is to provide a comprehensive overview of studies that have utilized applications of proteomics in an attempt to gain insight into the pathogenesis and identification of biomarkers in childhood ALL.
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Affiliation(s)
- Maria Kourti
- Third Department of Pediatrics, School of Medicine, Aristotle University and Hippokration General Hospital, 54642 Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Emmanouel Hatzipantelis
- Children & Adolescent Hematology-Oncology Unit, Second Department of Pediatrics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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29
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [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: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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30
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Rodina A, Xu C, Digwal CS, Joshi S, Patel Y, Santhaseela AR, Bay S, Merugu S, Alam A, Yan P, Yang C, Roychowdhury T, Panchal P, Shrestha L, Kang Y, Sharma S, Almodovar J, Corben A, Alpaugh ML, Modi S, Guzman ML, Fei T, Taldone T, Ginsberg SD, Erdjument-Bromage H, Neubert TA, Manova-Todorova K, Tsou MFB, Young JC, Wang T, Chiosis G. Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation. Nat Commun 2023; 14:3742. [PMID: 37353488 PMCID: PMC10290137 DOI: 10.1038/s41467-023-39241-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based 'omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.
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Affiliation(s)
- Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chao Xu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yogita Patel
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Anand R Santhaseela
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sadik Bay
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Swathi Merugu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Aftab Alam
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chenghua Yang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liza Shrestha
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yanlong Kang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Justina Almodovar
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Maimonides Medical Center, Brooklyn, NY, USA
| | - Mary L Alpaugh
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Rowan University, Glassboro, NJ, USA
| | - Shanu Modi
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Monica L Guzman
- Department of Medicine, Division of Hematology Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stephen D Ginsberg
- Departments of Psychiatry, Neuroscience & Physiology & the NYU Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, 10962, USA
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Katia Manova-Todorova
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Meng-Fu Bryan Tsou
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jason C Young
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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31
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Czaplewska P, Bogucka A, Macur K, Rybicka M, Rychłowski M, Fiołka MJ. Proteomic response of A549 lung cancer cell line to protein-polysaccharide complex Venetin-1 isolated from earthworm coelomic fluid. Front Mol Biosci 2023; 10:1128320. [PMID: 37377864 PMCID: PMC10292018 DOI: 10.3389/fmolb.2023.1128320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Earthworms' celomic fluid has long attracted scientists' interest due to their toxic properties. It has been shown that the elimination of coelomic fluid cytotoxicity to normal human cells was crucial for the generation of the non-toxic Venetin-1 protein-polysaccharide complex, which exhibits selective activity against Candida albicans cells as well as A549 non-small cell lung cancer cells. To find the molecular mechanisms behind the anti-cancer properties of the preparation, this research investigated the proteome response of A549 cells to the presence of Venetin-1. The sequential window acquisition of all theoretical mass spectra (SWATH-MS) methodology was used for the analysis, which allows for a relative quantitative analysis to be carried out without radiolabelling. The results showed that the formulation did not induce significant proteome responses in normal BEAS-2B cells. In the case of the tumour line, 31 proteins were up regulated, and 18 proteins down regulated. Proteins with increased expression in neoplastic cells are mainly associated with the mitochondrion, membrane transport and the endoplasmic reticulum. In the case of altered proteins, Venetin-1 interferes with proteins that stabilise the structures, i.e., keratin, glycolysis/gluconeogenesis and metabolic processes.
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Affiliation(s)
- Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
- Institute of Biochemistry, Justus Liebig University of Giessen, Giessen, Germany
| | - Katarzyna Macur
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Magda Rybicka
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Michał Rychłowski
- Intercollegiate Faculty of Biotechnology, The University of Gdansk, Gdańsk, Poland
| | - Marta J. Fiołka
- Department of Immunobiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
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Smith CF, Nikolakis ZL, Ivey K, Perry BW, Schield DR, Balchan NR, Parker J, Hansen KC, Saviola AJ, Castoe TA, Mackessy SP. Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake. BMC Biol 2023; 21:136. [PMID: 37280596 DOI: 10.1186/s12915-023-01626-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (Crotalus viridis viridis) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom. RESULTS Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition. CONCLUSIONS Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the cascading influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.
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Affiliation(s)
- Cara F Smith
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Kathleen Ivey
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
- Current address: Department of Ecology & Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309, USA
| | - Neil R Balchan
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
| | - Joshua Parker
- Fresno City College, 1101 E. University Avenue, Fresno, CA, 93741, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA.
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Bai M, Deng J, Dai C, Pfeuffer J, Sachsenberg T, Perez-Riverol Y. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis. J Proteome Res 2023. [PMID: 37220883 DOI: 10.1021/acs.jproteome.2c00812] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.
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Affiliation(s)
- Mingze Bai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Jingwen Deng
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Chengxin Dai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Julianus Pfeuffer
- Algorithmic Bioinformatics, Freie Universität Berlin, Berlin 14195, Germany
- Visualization and Data Analysis, Zuse Institute Berlin, Berlin 14195, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72076, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hixton, Cambridge CB10 1SD, United Kingdom
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34
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Niimi A, Limsirichaikul S, Kano K, Mizutani Y, Takeuchi T, Sawangsri P, Tran DQ, Kawamoto Y, Suzuki M. LASP1, CERS6, and Actin Form a Ternary Complex That Promotes Cancer Cell Migration. Cancers (Basel) 2023; 15:2781. [PMID: 37345118 DOI: 10.3390/cancers15102781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
CERS6 is associated with metastasis and poor prognosis in non-small cell lung cancer (NSCLC) patients through d18:1/C16:0 ceramide (C16 ceramide)-mediated cell migration, though the detailed mechanism has not been elucidated. In the present study, examinations including co-immunoprecipitation, liquid chromatography, and tandem mass spectrometry analysis were performed to identify a novel binding partner of CERS6. Among the examined candidates, LASP1 was a top-ranked binding partner, with the LIM domain possibly required for direct interaction. In accord with those findings, CERS6 and LASP1 were found to co-localize on lamellipodia in several lung cancer cell lines. Furthermore, silencing of CERS6 and/or LASP1 significantly suppressed cell migration and lamellipodia formation, whereas ectopic addition of C16 ceramide partially rescued those phenotypes. Both LASP1 and CERS6 showed co-immunoprecipitation with actin, with those interactions markedly reduced when the LASP1-CERS6 complex was abolished. Based on these findings, it is proposed that LASP1-CERS6 interaction promotes cancer cell migration.
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Affiliation(s)
- Atsuko Niimi
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
| | - Siripan Limsirichaikul
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
- Department of Biopharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Keiko Kano
- Institute of Transformative Bio-Molecules (WPI-ItbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yasuyoshi Mizutani
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
| | - Toshiyuki Takeuchi
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
| | - Patinya Sawangsri
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
| | - Dat Quoc Tran
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
| | - Yoshiyuki Kawamoto
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai 487-8501, Japan
| | - Motoshi Suzuki
- Department of Molecular Oncology, Fujita Health University, Toyoake 470-1192, Japan
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35
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Gok MO, Connor OM, Wang X, Menezes CJ, Llamas CB, Mishra P, Friedman JR. The outer mitochondrial membrane protein TMEM11 demarcates spatially restricted BNIP3/BNIP3L-mediated mitophagy. J Cell Biol 2023; 222:e202204021. [PMID: 36795401 PMCID: PMC9960330 DOI: 10.1083/jcb.202204021] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 11/30/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023] Open
Abstract
Mitochondria play critical roles in cellular metabolism and to maintain their integrity, they are regulated by several quality control pathways, including mitophagy. During BNIP3/BNIP3L-dependent receptor-mediated mitophagy, mitochondria are selectively targeted for degradation by the direct recruitment of the autophagy protein LC3. BNIP3 and/or BNIP3L are upregulated situationally, for example during hypoxia and developmentally during erythrocyte maturation. However, it is not well understood how they are spatially regulated within the mitochondrial network to locally trigger mitophagy. Here, we find that the poorly characterized mitochondrial protein TMEM11 forms a complex with BNIP3 and BNIP3L and co-enriches at sites of mitophagosome formation. We find that mitophagy is hyper-active in the absence of TMEM11 during both normoxia and hypoxia-mimetic conditions due to an increase in BNIP3/BNIP3L mitophagy sites, supporting a model that TMEM11 spatially restricts mitophagosome formation.
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Affiliation(s)
- Mehmet Oguz Gok
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Olivia M. Connor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xun Wang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cameron J. Menezes
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Claire B. Llamas
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan R. Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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36
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Yang M, Unsihuay D, Hu H, Meke FN, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023; 95:5214-5222. [PMID: 36917636 PMCID: PMC11330692 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.
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Affiliation(s)
- Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hang Hu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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37
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Massudi H, Luo JS, Holien JK, Gadde S, Krishan S, Herath M, Koach J, Stevenson BW, Gorman MA, Venkat P, Mayoh C, Luo XQ, Parker MW, Cheung BB, Marshall GM. Inhibitors of the Oncogenic PA2G4-MYCN Protein-Protein Interface. Cancers (Basel) 2023; 15:cancers15061822. [PMID: 36980710 PMCID: PMC10046377 DOI: 10.3390/cancers15061822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
MYCN is a major oncogenic driver for neuroblastoma tumorigenesis, yet there are no direct MYCN inhibitors. We have previously identified PA2G4 as a direct protein-binding partner of MYCN and drive neuroblastoma tumorigenesis. A small molecule known to bind PA2G4, WS6, significantly decreased tumorigenicity in TH-MYCN neuroblastoma mice, along with the inhibition of PA2G4 and MYCN interactions. Here, we identified a number of novel WS6 analogues, with 80% structural similarity, and used surface plasmon resonance assays to determine their binding affinity. Analogues #5333 and #5338 showed direct binding towards human recombinant PA2G4. Importantly, #5333 and #5338 demonstrated a 70-fold lower toxicity for normal human myofibroblasts compared to WS6. Structure-activity relationship analysis showed that a 2,3 dimethylphenol was the most suitable substituent at the R1 position. Replacing the trifluoromethyl group on the phenyl ring at the R2 position, with a bromine or hydrogen atom, increased the difference between efficacy against neuroblastoma cells and normal myofibroblast toxicity. The WS6 analogues inhibited neuroblastoma cell phenotype in vitro, in part through effects on apoptosis, while their anti-cancer effects required both PA2G4 and MYCN expression. Collectively, chemical inhibition of PA2G4-MYCN binding by WS6 analogues represents a first-in-class drug discovery which may have implications for other MYCN-driven cancers.
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Affiliation(s)
- Hassina Massudi
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Jie-Si Luo
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Jessica K. Holien
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Satyanarayana Gadde
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Sukriti Krishan
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Mika Herath
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Jessica Koach
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Brendan W. Stevenson
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Michael A. Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Pooja Venkat
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2750, Australia
| | - Xue-Qun Luo
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510060, China
| | - Michael W. Parker
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Belamy B. Cheung
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW 2750, Australia
- Correspondence: (B.B.C.); (G.M.M.); Tel.: +61-(02)-9385-2450 (B.B.C.); +61-(02)-9382-1721 (G.M.M.); Fax: +61-(02)-9662-6584 (B.B.C.); +61-(02)-9382-1789 (G.M.M.)
| | - Glenn M. Marshall
- Children’s Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2750, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
- Correspondence: (B.B.C.); (G.M.M.); Tel.: +61-(02)-9385-2450 (B.B.C.); +61-(02)-9382-1721 (G.M.M.); Fax: +61-(02)-9662-6584 (B.B.C.); +61-(02)-9382-1789 (G.M.M.)
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38
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Nguyen M, Zimmer A. A reflection on the improvement of Chinese Hamster ovary cell-based bioprocesses through advances in proteomic techniques. Biotechnol Adv 2023; 65:108141. [PMID: 37001570 DOI: 10.1016/j.biotechadv.2023.108141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Chinese hamster ovary (CHO) cells are the preferred mammalian host for the large-scale production of recombinant proteins in the biopharmaceutical industry. Research endeavors have been directed to the optimization of CHO-based bioprocesses to increase protein quantity and quality, often in an empirical manner. To provide a rationale for those achievements, a myriad of CHO proteomic studies has arisen in recent decades. This review gives an overview of significant advances in LC-MS-based proteomics and sheds light on CHO proteomic studies, with a particular focus on CHO cells with superior bioprocessing phenotypes (growth, viability, titer, productivity and cQA), that have exploited novel proteomic or sub-omic techniques. These proteomic findings expand the current knowledge and understanding about the underlying protein clusters, protein regulatory networks and biological pathways governing such phenotypic changes. The proteomic studies, highlighted herein, will help in the targeted modulation of these cell factories to the desired needs.
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39
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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40
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Huang YZ, Xie YS, Li YX, Zhao MY, Sun N, Qi H, Dong XP. Quality assessment of variable collagen tissues of sea cucumber (Stichopus japonicus) body wall under different heat treatment durations by label-Free proteomics analysis. Food Res Int 2023; 165:112540. [PMID: 36869547 DOI: 10.1016/j.foodres.2023.112540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Accepted: 01/22/2023] [Indexed: 02/05/2023]
Abstract
The microstructure of the body wall, body wall composition, and collagen fibers of sea cucumber (Stichopus japonicus) under different heating times (1 h, 4 h, 12 h, and 24 h) was investigated based on heat treatment at 80 °C. A Label-Free proteomics technique was applied to study the proteomic changes in the body wall of sea cucumbers under 4 and 12 h of heat treatment. Compared with the fresh group, 981 proteins were found to be differentially expressed proteins (DEPs) after heat treatment at 80 °C (4 h), and 1110 DEPs were observed after heat treatment at the same temperature for 12 h. There were 69 DEPs associated with mutable collagenous tissues (MCTs) structures. The results of correlation analysis showed that 55 DEPs were correlated with sensory properties, among which A0A2G8KRV2 was significantly correlated with hardness and SEM image texture features (SEM_Energy, SEM_Correlation, SEM_Homogeneity, and SEM_Contrast). These findings could be conducive to further comprehension of the structural changes and mechanisms of quality loss in the body wall of sea cucumbers at different heat treatment times.
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Affiliation(s)
- Yi-Zhen Huang
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Yi-Sha Xie
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Yan-Xin Li
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Mei-Yu Zhao
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Na Sun
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Hang Qi
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China
| | - Xiu-Ping Dong
- Academy of Food Interdisciplinary Science, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China; National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Liaoning Province Collaborative Innovation Center for Marine Food Deep Processing, Dalian 116034, Liaoning, China.
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Li Y, Zhang Z, Jiang S, Xu F, Tulum L, Li K, Liu S, Li S, Chang L, Liddell M, Tu F, Gu X, Carmichael PL, White A, Peng S, Zhang Q, Li J, Zuo T, Kukic P, Xu P. Using transcriptomics, proteomics and phosphoproteomics as new approach methodology (NAM) to define biological responses for chemical safety assessment. CHEMOSPHERE 2023; 313:137359. [PMID: 36427571 DOI: 10.1016/j.chemosphere.2022.137359] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Omic-based technologies are of particular interest and importance for hazard identification and health risk characterization of chemicals. Their application in the new approach methodologies (NAMs) anchored on cellular toxicity pathways is based on the premise that any apical health endpoint change must be underpinned by some alterations at the omic levels. In the present study we examined the cellular responses to two chemicals, caffeine and coumarin, by generating and integrating multi-omic data from multi-dose and multi-time point transcriptomic, proteomic and phosphoproteomic experiments. We showed that the methodology presented here was able to capture the complete chain of events from the first chemical-induced changes at the phosphoproteome level, to changes in gene expression, and lastly to changes in protein abundance, each with vastly different points of departure (PODs). In HepG2 cells we found that the metabolism of lipids and general cellular stress response to be the dominant biological processes in response to caffeine and coumarin exposure, respectively. The phosphoproteomic changes were detected early in time, at very low doses and provided a fast, adaptive cellular response to chemical exposure with 7-37-fold lower points of departure comparing to the transcriptomics. Changes in protein abundance were found much less frequently than transcriptomic changes. While challenges remain, our study provides strong and novel evidence supporting the notion that these three omic technologies can be used in an integrated manner to facilitate a more complete understanding of pathway perturbations and POD determinations for risk assessment of chemical exposures.
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Affiliation(s)
- Yuan Li
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Songhao Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Feng Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Liz Tulum
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Kaixuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Shu Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Suzhen Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Mark Liddell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Fengjuan Tu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Xuelan Gu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Paul Lawford Carmichael
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Andrew White
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Tao Zuo
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China.
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Ping Xu
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
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Rende U, Ahn SB, Adhikari S, Moh ESX, Pollock CA, Saad S, Guller A. Deciphering the Kidney Matrisome: Identification and Quantification of Renal Extracellular Matrix Proteins in Healthy Mice. Int J Mol Sci 2023; 24:ijms24032827. [PMID: 36769148 PMCID: PMC9917693 DOI: 10.3390/ijms24032827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Precise characterization of a tissue's extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules' activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome.
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Affiliation(s)
- Umut Rende
- ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Seong Beom Ahn
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Edward S. X. Moh
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol A. Pollock
- Department of Medicine, Kolling Institute of Medical Research, University of Sydney, St. Leonards, NSW 2065, Australia
| | - Sonia Saad
- Department of Medicine, Kolling Institute of Medical Research, University of Sydney, St. Leonards, NSW 2065, Australia
| | - Anna Guller
- ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia
- Correspondence:
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Kano K, Noda S, Sato S, Kuwata K, Mishiro‐Sato E. An efficient in‐gel digestion method on small amounts of protein sample from large intact gel pieces. SEPARATION SCIENCE PLUS 2023. [DOI: 10.1002/sscp.202200121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Keiko Kano
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Saki Noda
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Shinya Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Keiko Kuwata
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Emi Mishiro‐Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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Meng P, Shao Y, Xiong Y, Zhang L, Bao H, Lu H. Peptide- and Protein-Level Combined Strategy for Analyzing Newly Synthesized Proteins by Integrating Tandem Orthogonal Proteolysis with Cleavable Bioorthogonal Tagging. Anal Chem 2023; 95:628-637. [PMID: 36549687 DOI: 10.1021/acs.analchem.2c01537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A newly synthesized proteome reflects perturbations sensitively and maintains homeostasis in cells. To investigate the low abundant newly synthesized proteins (NSPs) from a complex background proteome, an enrichment process with high selectivity and reliability is essential. Here, we have developed a strategy to realize comprehensive analysis of NSPs by integrating tandem orthogonal proteolysis (TOP) with cleavable bioorthogonal tagging (CBOT) called TOP-CBOT. A solid-phase-conjugated probe with a clickable moiety and a protease-cleavable site was designed, which allowed NSPs to be covalently captured along with tandem release by trypsin and orthogonal tobacco etch virus (TEV) protease. Our method has integrated the advantages of protein-level and peptide-level enrichment. Trypsin digests larger number of peptides from the recovered proteins for NSPs identification and quantification, while the specific tag-contained peptides from TEV data set enabled further NSPs confirmation. Integrating information from two complementary data sets, the reliability in NSPs identification and quantitation were remarkably enhanced. A total of 3699 proteins were recovered in the trypsin data set. Additionally, 1931 proteins were confirmed as NSPs with 5019 identified peptides in the TEV data set, over 90% of which were overlapped with the tryptic data set. Our strategy was further applied to profile NSP degradation kinetics during rapamycin-induced macroautophagy. The newly synthesized proteome displayed varied alteration of degradation rates among stimulation and more than half of NSPs showed decreased half-lives during autophagy.
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Affiliation(s)
- Peiyi Meng
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China
| | - Yuyin Shao
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Yingying Xiong
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Huimin Bao
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China
| | - Haojie Lu
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China.,Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
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Chen M, Assis DM, Benet M, McClung CM, Gordon EA, Ghose S, Dupard SJ, Willetts M, Taron CH, Samuelson JC. Comparative site-specific N-glycoproteome analysis reveals aberrant N-glycosylation and gives insights into mannose-6-phosphate pathway in cancer. Commun Biol 2023; 6:48. [PMID: 36639722 PMCID: PMC9839730 DOI: 10.1038/s42003-023-04439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
N-glycosylation is implicated in cancers and aberrant N-glycosylation is recognized as a hallmark of cancer. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 displays hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells. This comparative site-specific N-glycoproteome analysis provides a pool of potential N-glycosylation-related cancer biomarkers, but also gives insights into the M6P pathway in cancer.
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Affiliation(s)
- Minyong Chen
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Diego M. Assis
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Matthieu Benet
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Colleen M. McClung
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Elizabeth A. Gordon
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Shourjo Ghose
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Steven J. Dupard
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Matthew Willetts
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Christopher H. Taron
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - James C. Samuelson
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
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Wani S, Humaira, Farooq I, Ali S, Rehman MU, Arafah A. Proteomic profiling and its applications in cancer research. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Correlation between aortic valve protein levels and vector flow mapping of wall shear stress and oscillatory shear index in patients supported with continuous-flow left ventricular assist devices. J Heart Lung Transplant 2023; 42:64-75. [PMID: 36400676 DOI: 10.1016/j.healun.2022.09.017] [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: 01/09/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Continuous-flow left ventricular assist devices commonly lead to aortic regurgitation, which results in decreased pump efficiency and worsening heart failure. We hypothesized that non-physiological wall shear stress and oscillatory shear index alter the abundance of structural proteins in aortic valves of left ventricular assist device (LVAD) patients. METHODS Doppler images of aortic valves of patients undergoing heart transplants were obtained. Eight patients had been supported with LVADs, whereas 10 were not. Aortic valve tissue was collected and protein levels were analyzed using mass spectrometry. Echocardiographic images were analyzed and wall shear stress and oscillatory shear index were calculated. The relationship between normalized levels of individual proteins and in vivo echocardiographic measurements was evaluated. RESULTS Of the 57 proteins of interest, there was a strong negative correlation between levels of 15 proteins and the wall shear stress (R < -0.500, p ≤ 0.05), and a moderate negative correlation between 16 proteins and wall shear stress (R -0.500 to -0.300, p ≤ 0.05). Gene ontology analysis demonstrated clusters of proteins involved in cellular structure. Proteins negatively correlated with WSS included those with cytoskeletal, actin/myosin, cell-cell junction and extracellular functions. C: In aortic valve tissue, 31 proteins were identified involved in cellular structure and extracellular junctions with a negative correlation between their levels and wall shear stress. These findings suggest an association between the forces acting on the aortic valve (AV) and leaflet protein abundance, and may form a mechanical basis for the increased risk of aortic leaflet degeneration in LVAD patients.
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Gregori J, Sánchez À, Villanueva J. msmsEDA & msmsTests: Label-Free Differential Expression by Spectral Counts. Methods Mol Biol 2023; 2426:197-242. [PMID: 36308691 DOI: 10.1007/978-1-0716-1967-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
msmsTests is an R/Bioconductor package providing functions for statistical tests in label-free LC-MS/MS data by spectral counts. These functions aim at discovering differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package. The three models admit blocking factors to control for nuisance variables. To assure a good level of reproducibility a post-test filter is available, where (1) a minimum effect size considered biologically relevant, and (2) a minimum expression of the most abundant condition, may be set. A companion package, msmsEDA, proposes functions to explore datasets based on msms spectral counts. The provided graphics help in identifying outliers, the presence of eventual batch factors, and check the effects of different normalizing strategies. This protocol illustrates the use of both packages on two examples: A purely spike-in experiment of 48 human proteins in a standard yeast cell lysate; and a cancer cell-line secretome dataset requiring a biological normalization.
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Affiliation(s)
- Josep Gregori
- Vall Hebron Research Institute (VHIR), Barcelona, Spain.
| | - Àlex Sánchez
- VHIR, Barcelona, Spain
- Department of Genetics Statistics and Microbiology, UB, Barcelona, Spain
| | - Josep Villanueva
- Tumor Biomarkers Lab, Vall Hebron Institute of Oncology, Barcelona, Spain
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50
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Nisa MU, Farooq S, Ali S, Eachkoti R, Rehman MU, Hafiz S. Proteomics: A modern tool for identifying therapeutic targets in different types of carcinomas. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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