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Yan L, Han X, Zhang M, Fu Y, Yang F, Li Q, Cheng T. Integrative analysis of TBI data reveals Lgmn as a key player in immune cell-mediated ferroptosis. BMC Genomics 2023; 24:747. [PMID: 38057699 DOI: 10.1186/s12864-023-09842-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Traumatic brain injury (TBI) is a central nervous system disease caused by external trauma, which has complex pathological and physiological mechanisms. The aim of this study was to explore the correlation between immune cell infiltration and ferroptosis post-TBI. METHODS This study utilized the GEO database to download TBI data and performed differentially expressed genes (DEGs) and ferroptosis-related differentially expressed genes (FRDEGs) analysis. DEGs were further analyzed for enrichment using the DAVID 6.8. Immunoinfiltration cell analysis was performed using the ssGSEA package and the Timer2.0 tool. The WGCNA analysis was then used to explore the gene modules in the data set associated with differential expression of immune cell infiltration and to identify the hub genes. The tidyverse package and corrplot package were used to calculate the correlations between hub genes and immune cell infiltration and ferroptosis-marker genes. The miRDB and TargetScan databases were used to predict complementary miRNAs for the Hub genes selected from the WGCNA analysis, and the DIANA-LncBasev3 tool was used to identify target lncRNAs for the miRNAs, constructing an mRNA-miRNA-lncRNA regulatory network. RESULTS A total of 320 DEGs and 21 FRDEGs were identified in GSE128543. GO and KEGG analyses showed that the DEGs after TBI were primarily associated with inflammation and immune response. Xcell and ssGSEA immune infiltration cell analysis showed significant infiltration of T cell CD4+ central memory, T cell CD4+ Th2, B cell memory, B cell naive, monocyte, macrophage, and myeloid dendritic cell activated. The WGCNA analysis identified two modules associated with differentially expressed immune cells and identified Lgmn as a hub gene associated with immune infiltrating cells. Lgmn showed significant correlation with immune cells and ferroptosis-marker genes, including Gpx4, Hspb1, Nfe2l2, Ptgs2, Fth1, and Tfrc. Finally, an mRNA-miRNA-lncRNA regulatory network was constructed using Lgmn. CONCLUSION Our results indicate that there is a certain correlation between ferroptosis and immune infiltrating cells in brain tissue after TBI, and that Lgmn plays an important role in this process.
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Affiliation(s)
- Liyan Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiaonan Han
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Mingkang Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yikun Fu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Fei Yang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Qian Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| | - Tian Cheng
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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Baskerville MJ, Kovalyova Y, Mejías-Luque R, Gerhard M, Hatzios SK. Isotope tracing reveals bacterial catabolism of host-derived glutathione during Helicobacter pylori infection. PLoS Pathog 2023; 19:e1011526. [PMID: 37494402 PMCID: PMC10406306 DOI: 10.1371/journal.ppat.1011526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 07/01/2023] [Indexed: 07/28/2023] Open
Abstract
Mammalian cells synthesize the antioxidant glutathione (GSH) to shield cellular biomolecules from oxidative damage. Certain bacteria, including the gastric pathogen Helicobacter pylori, can perturb host GSH homeostasis. H. pylori infection significantly decreases GSH levels in host tissues, which has been attributed to the accumulation of reactive oxygen species in infected cells. However, the precise mechanism of H. pylori-induced GSH depletion remains unknown, and tools for studying this process during infection are limited. We developed an isotope-tracing approach to quantitatively monitor host-derived GSH in H. pylori-infected cells by mass spectrometry. Using this method, we determined that H. pylori catabolizes reduced GSH from gastric cells using γ-glutamyl transpeptidase (gGT), an enzyme that hydrolyzes GSH to glutamate and cysteinylglycine (Cys-Gly). gGT is an established virulence factor with immunomodulatory properties that is required for H. pylori colonization in vivo. We found that H. pylori internalizes Cys-Gly in a gGT-dependent manner and that Cys-Gly production during H. pylori infection is coupled to the depletion of intracellular GSH from infected cells. Consistent with bacterial catabolism of host GSH, levels of oxidized GSH did not increase during H. pylori infection, and exogenous antioxidants were unable to restore the GSH content of infected cells. Altogether, our results indicate that H. pylori-induced GSH depletion proceeds via an oxidation-independent mechanism driven by the bacterial enzyme gGT, which fortifies bacterial acquisition of nutrients from the host. Additionally, our work establishes a method for tracking the metabolic fate of host-derived GSH during infection.
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Affiliation(s)
- Maia J. Baskerville
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Yekaterina Kovalyova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Raquel Mejías-Luque
- Institute of Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich, Germany
- German Centre for Infection Research, Munich, Germany
| | - Markus Gerhard
- Institute of Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich, Germany
- German Centre for Infection Research, Munich, Germany
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
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Chen Y, Cao X, Loh KH, Slavoff SA. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochem Soc Trans 2023; 51:1071-1082. [PMID: 37171061 PMCID: PMC10317152 DOI: 10.1042/bst20221074] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Thousands of unannotated small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been revealed in mammalian genomes. While hundreds of mammalian smORF- and alt-ORF-encoded proteins (SEPs and alt-proteins, respectively) affect cell proliferation, the overwhelming majority of smORFs and alt-ORFs remain uncharacterized at the molecular level. Complicating the task of identifying the biological roles of smORFs and alt-ORFs, the SEPs and alt-proteins that they encode exhibit limited sequence homology to protein domains of known function. Experimental techniques for the functionalization of these gene classes are therefore required. Approaches combining chemical labeling and quantitative proteomics have greatly advanced our ability to identify and characterize functional SEPs and alt-proteins in high throughput. In this review, we briefly describe the principles of proteomic discovery of SEPs and alt-proteins, then summarize how these technologies interface with chemical labeling for identification of SEPs and alt-proteins with specific properties, as well as in defining the interactome of SEPs and alt-proteins.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ken H. Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, U.S.A
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, U.S.A
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, U.S.A
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, U.S.A
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Bird LE, Edgington-Mitchell LE, Newton HJ. Eat, prey, love: Pathogen-mediated subversion of lysosomal biology. Curr Opin Immunol 2023; 83:102344. [PMID: 37245414 DOI: 10.1016/j.coi.2023.102344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/23/2023] [Accepted: 04/30/2023] [Indexed: 05/30/2023]
Abstract
The mammalian lysosome is classically considered the 'garbage can' of the cell, contributing to clearance of infection through its primary function as a degradative organelle. Intracellular pathogens have evolved several strategies to evade contact with this harsh environment through subversion of endolysosomal trafficking or escape into the cytosol. Pathogens can also manipulate pathways that lead to lysosomal biogenesis or alter the abundance or activity of lysosomal content. This pathogen-driven subversion of lysosomal biology is highly dynamic and depends on a range of factors, including cell type, stage of infection, intracellular niche and pathogen load. The growing body of literature in this field highlights the nuanced and complex relationship between intracellular pathogens and the host lysosome, which is critical for our understanding of infection biology.
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Affiliation(s)
- Lauren E Bird
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC 3800, Australia
| | | | - Hayley J Newton
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC 3800, Australia.
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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7
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Elamin T, Brandstetter H, Dall E. Legumain Activity Is Controlled by Extended Active Site Residues and Substrate Conformation. Int J Mol Sci 2022; 23:12548. [PMID: 36293424 PMCID: PMC9604545 DOI: 10.3390/ijms232012548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Legumain is a lysosomal cysteine protease with strict specificity for cleaving after asparagine residues. By sequence comparison, legumain belongs to MEROPS clan CD of the cysteine proteases, which indicates its structural and mechanistic relation to caspases. Contrasting caspases, legumain harbors a pH-dependent ligase activity in addition to the protease activity. Although we already have a significant body of knowledge on the catalytic activities of legumain, many mechanistic details are still elusive. In this study, we provide evidence that extended active site residues and substrate conformation are steering legumain activities. Biochemical experiments and bioinformatics analysis showed that the catalytic Cys189 and His148 residues are regulated by sterically close Glu190, Ser215 and Asn42 residues. While Glu190 serves as an activity brake, Ser215 and Asn42 have a favorable effect on legumain protease activity. Mutagenesis studies using caspase-9 as model enzyme additionally showed that a similar Glu190 activity brake is also implemented in the caspases. Furthermore, we show that the substrate's conformational flexibility determines whether it will be hydrolyzed or ligated by legumain. The functional understanding of the extended active site residues and of substrate prerequisites will allow us to engineer proteases with increased enzymatic activity and better ligase substrates, with relevance for biotechnological applications.
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Affiliation(s)
| | | | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
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