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Pandi K, Angabo S, Makkawi H, Benyamini H, Elgavish S, Nussbaum G. P. gingivalis-Induced TLR2 Interactome Analysis Reveals Association with PARP9. J Dent Res 2024; 103:329-338. [PMID: 38344758 DOI: 10.1177/00220345231222181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobic bacterium strongly associated with periodontal disease. Toll-like receptor 2 (TLR2) is indispensable for the host response to P. gingivalis, but P. gingivalis escapes from immune clearance via TLR2-dependent activation of phosphoinositide-3-kinase (PI3K). To probe the TLR2-dependent escape pathway of P. gingivalis, we analyzed the TLR2 interactome induced following P. gingivalis infection or activation by a synthetic lipopeptide TLR2/1 agonist on human macrophages overexpressing TLR2. Interacting proteins were stabilized by cross-linking and then immunoprecipitated and analyzed by mass spectrometry. In total, 792 proteins were recovered and network analysis enabled mapping of the TLR2 interactome at baseline and in response to infection. The P. gingivalis infection-induced TLR2 interactome included the poly (ADP-ribose) polymerase family member mono-ADP-ribosyltransferase protein 9 (PARP9) and additional members of the PARP9 complex (DTX3L and NMI). PARP9 and its complex members are highly upregulated in macrophages exposed to P. gingivalis or to the synthetic TLR2/1 ligand Pam3Cys-Ser-(Lys)4 (PAM). Consistent with its known role in virally induced interferon production, PARP9 knockdown blocked type I interferon (IFN-I) production in response to P. gingivalis and reduced inflammatory cytokine production. We found that P. gingivalis drives signal transducer and activation of transcription (STAT) 1 (S727) phosphorylation through TLR2-PARP9, explaining PARP9's role in the induction of IFN-I downstream of TLR2. Furthermore, PARP9 knockdown reduced PI3K activation by P. gingivalis, leading to improved macrophage bactericidal activity. In summary, PARP9 is a novel TLR2 interacting partner that enables IFN-I induction and P. gingivalis immune escape in macrophages downstream of TLR2 sensing.
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Affiliation(s)
- K Pandi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - S Angabo
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - H Makkawi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - H Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - S Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - G Nussbaum
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
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2
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Yang X, Xiaoping W, Nan D, Jian Z, Xiaofeng L, Liwei Y, Zhao M, Wang F. Proteomic and bioinformatic analysis of human endometrium from polycystic ovarian syndrome with and without insulin resistance. Gynecol Endocrinol 2023; 39:2173948. [PMID: 36750132 DOI: 10.1080/09513590.2023.2173948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Objective: The aim of this study was to investigate the endometrial proteomic profiles of patients with polycystic ovary syndrome (PCOS) with and without insulin resistance (IR). Method of Study: We collected 40 endometrial samples, including PCOS-IR (n = 21), PCOS-non-IR (n = 12), and control (n = 7). Data-independent acquisition (DIA)-based proteomics method is used to identify the expressed proteins among the three groups. The correlation between pregnancy outcomes and identified proteins was analyzed by Lasso regression. Results: A total of 5331 proteins were identified, while 275 proteins were differentially expressed in the PCOS vs. control group and 215 proteins were differentially expressed in the PCOS-IR vs. PCOS-non-IR group. Platelet degranulation, neutrophil degranulation, and very long-chain fatty acid catabolic processes have been found to play important roles in the endometrium of patients with PCOS-IR. Lasso regression analysis found that ACTR1A, TSC22D2, CKB, ABRAXAS2, and TAGLN2 were associated with miscarriage in patients with PCOS. ACTR1A and CKB were higher in the PCOS-IR group and were positively correlated with HOMA-IR (p < .05). Conclusion: In this study, a panel of proteins was found to be differently expressed in the endometrium. ACTR1A and CKB may be considered as PCOS-IR candidate biomarkers.
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Affiliation(s)
- Xin Yang
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Wang Xiaoping
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Ding Nan
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Zhang Jian
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Li Xiaofeng
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yuan Liwei
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Mengni Zhao
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
| | - Fang Wang
- Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou, China
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Matthews CEP, Fussner LA, Yaeger M, Aloor JJ, Reece SW, Kilburg-Basnyat BJ, Varikuti S, Luo B, Inks M, Sergin S, Schmidt CA, Neufer PD, Pennington ER, Fisher-Wellman KH, Chowdhury SM, Fessler MB, Fenton JI, Anderson EJ, Shaikh SR, Gowdy KM. The prohibitin complex regulates macrophage fatty acid composition, plasma membrane packing, and lipid raft-mediated inflammatory signaling. Prostaglandins Leukot Essent Fatty Acids 2023; 190:102540. [PMID: 36706677 PMCID: PMC9992117 DOI: 10.1016/j.plefa.2023.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/28/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Prohibitins (PHB1 and PHB2) are ubiquitously expressed proteins which play critical roles in multiple biological processes, and together form the ring-like PHB complex found in phospholipid-rich cellular compartments including lipid rafts. Recent studies have implicated PHB1 as a mediator of fatty acid transport as well as a membrane scaffold mediating B lymphocyte and mast cell signal transduction. However, the specific role of PHBs in the macrophage have not been characterized, including their role in fatty acid uptake and lipid raft-mediated inflammatory signaling. We hypothesized that the PHB complex regulates macrophage inflammatory signaling through the formation of lipid rafts. To evaluate our hypothesis, RAW 264.7 macrophages were transduced with shRNA against PHB1, PHB2, or scrambled control (Scr), and then stimulated with lipopolysaccharide (LPS) or tumor necrosis factor-alpha (TNF-α), which activate lipid raft-dependent receptor signaling (CD14/TLR4 and TNFR1, respectively). PHB1 knockdown was lethal, whereas PHB2 knockdown (PHB2kd), which also resulted in decreased PHB1 expression, led to attenuated nuclear factor-kappa-B (NF-κB) activation and subsequent cytokine and chemokine production. PHB2kd macrophages also had decreased cell surface TNFR1, CD14, TLR4, and lipid raft marker ganglioside GM1 at baseline and post-stimuli. Post-LPS, PHB2kd macrophages did not increase the concentration of cellular saturated, monounsaturated, and polyunsaturated fatty acids. This was accompanied by decreased lipid raft formation and modified plasma membrane molecular packing, further supporting the PHB complex's importance in lipid raft formation. Taken together, these data suggest a critical role for PHBs in regulating macrophage inflammatory signaling via maintenance of fatty acid composition and lipid raft structure. SUMMARY: Prohibitins are proteins found in phospholipid-rich cellular compartments, including lipid rafts, that play important roles in signaling, transcription, and multiple other cell functions. Macrophages are key cells in the innate immune response and the presence of membrane lipid rafts is integral to signal transduction, but the role of prohibitins in macrophage lipid rafts and associated signaling is unknown. To address this question, prohibitin knockdown macrophages were generated and responses to lipopolysaccharide and tumor necrosis factor-alpha, which act through lipid raft-dependent receptors, were analyzed. Prohibitin knockdown macrophages had significantly decreased cytokine and chemokine production, transcription factor activation, receptor expression, lipid raft assembly and membrane packing, and altered fatty acid remodeling. These data indicate a novel role for prohibitins in macrophage inflammatory signaling through regulation of fatty acid composition and lipid raft formation.
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Affiliation(s)
- Christine E Psaltis Matthews
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Lynn A Fussner
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Michael Yaeger
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Jim J Aloor
- Diabetes and Obesity Institute, Department of Physiology, East Carolina University, Greenville, NC, United States
| | - Sky W Reece
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Brita J Kilburg-Basnyat
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Sanjay Varikuti
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Bin Luo
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Morgan Inks
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Selin Sergin
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Cameron A Schmidt
- Diabetes and Obesity Institute, Department of Physiology, East Carolina University, Greenville, NC, United States
| | - P Darrell Neufer
- Diabetes and Obesity Institute, Department of Physiology, East Carolina University, Greenville, NC, United States
| | - Edward Ross Pennington
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Kelsey H Fisher-Wellman
- Diabetes and Obesity Institute, Department of Physiology, East Carolina University, Greenville, NC, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, United States
| | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, United States
| | - Jenifer I Fenton
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Ethan J Anderson
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, FOE Diabetes Research Center, University of Iowa, Iowa City, IA, United States
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Kymberly M Gowdy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States.
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Kamal AHM, Chakrabarty JK, Chowdhury SM. Lipopolysaccharide and statin-mediated immune-responsive protein networks revealed in macrophages through affinity purification spacer-arm controlled cross-linking (AP-SPACC) proteomics. Mol Omics 2023; 19:48-59. [PMID: 36377691 DOI: 10.1039/d2mo00224h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Toll-like receptor 4 (TLR4), a pattern recognition receptor, is activated by lipopolysaccharides (LPS) and induces the MyD88 pathway, which subsequently produces pro-inflammatory cytokines through activation of transcriptional nuclear factor (NF)-κB. Statins have been widely prescribed to reduce cholesterol synthesis for patients with cardiovascular disease. Statins may have pleiotropic effects, which include anti- and pro-inflammatory effects on cells. The molecular mechanism of the sequential influence of LPS and statin on the innate immune system remains unknown. We employed affinity purification-spacer-arm controlled cross-linking (AP-SPACC) MS-based proteomics analysis to identify the LPS- and statin-LPS-responsive proteins and their networks. LPS-stimulated RAW 264.7 macrophage cells singly and combined with the drug statin used in this study. Two chemical cross-linkers with different spacer chain lengths were utilized to stabilize the weak and transient interactors. Proteomic analysis identified 1631 differentially expressed proteins. We identified 151 immune-response proteins through functional enrichment analysis and visualized their interaction networks. Selected candidate protein-coding genes were validated, specifically squamous cell carcinoma antigens recognized by T cells 3, sphingosine-1-phosphate lyase 1, Ras-related protein Rab-35, and tumor protein D52 protein-coding genes through transcript-level expression analysis. The expressions of those genes were significantly increased upon statin treatment and decreased in LPS-stimulated macrophage cells. Therefore, we presumed that the expression changes of genes occurred due to immune response during activation of inflammation. These results highlight the immune-responsive proteins network, providing a new platform for novel investigations and discovering future therapeutic targets for inflammatory diseases.
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Affiliation(s)
- Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA. .,Advanced Technology Cores, Dan L Duncan Comprehensive Cancer Center, Metabolomics Core, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA. .,Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, 10027, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, TX, 76019, USA.
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5
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Mehta A, Kamal AHM, Cornelius S, Chowdhury SM. Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics. Methods Mol Biol 2023; 2690:255-267. [PMID: 37450153 DOI: 10.1007/978-1-0716-3327-4_22] [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: 07/18/2023]
Abstract
Protein-protein interactions (PPIs) are the physical interactions formed among proteins. These interactions are primarily functional, i.e., they arise from specific biomolecular events, and each interaction interface serves a specific purpose. A significant number of methods have been developed for protein interactions in the field of proteomics in the last decade. Advanced mass spectrometry technology significantly contributed to the development of these methods. The rapid advancement of groundbreaking MS technology has greatly aided the mapping of protein interaction from large-data sets comprehensively. This chapter describes the affinity purification (AP) mass spectrometry (MS)-based methods combined with chemical cross-linking (XL) of protein complexes. This chapter includes sample preparation methods involving cell culture, cell treatments with ligands, drugs, and cross-linkers, protein extractions, affinity purification, sodium dodecyl sulfate (SDS) polyacrylamide gel separation, in-solution or in-gel digestion, liquid-chromatography, and mass spectrometry analysis of samples (LC-MS/MS). Application of a cleavable cross-linker, dual cleavable cross-linking technology (DUCCT) in combination with the affinity purification (AP) method has also been described. Methods for data analysis using unmodified and cross-linked peptide analysis are discussed.
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Affiliation(s)
- Ashima Mehta
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Abu Hena Mostafa Kamal
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas, Arlington, TX, USA.
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6
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Shahinuzzaman ADA, Kamal AHM, Chakrabarty JK, Rahman A, Chowdhury SM. Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics. Proteomes 2022; 10:proteomes10030031. [PMID: 36136309 PMCID: PMC9506174 DOI: 10.3390/proteomes10030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/14/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is a receptor on an immune cell that can recognize the invasion of bacteria through their attachment with bacterial lipopolysaccharides (LPS). Hence, LPS is a pro-immune response stimulus. On the other hand, statins are lipid-lowering drugs and can also lower immune cell responses. We used human embryonic kidney (HEK 293) cells engineered to express HA-tagged TLR-4 upon treatment with LPS, statin, and both statin and LPS to understand the effect of pro- and anti-inflammatory responses. We performed a monoclonal antibody (mAb) directed co-immunoprecipitation (CO-IP) of HA-tagged TLR4 and its interacting proteins in the HEK 293 extracted proteins. We utilized an ETD cleavable chemical cross-linker to capture weak and transient interactions with TLR4 protein. We tryptic digested immunoprecipitated and cross-linked proteins on beads, followed by liquid chromatography–mass spectrometry (LC-MS/MS) analysis of the peptides. Thus, we utilized the label-free quantitation technique to measure the relative expression of proteins between treated and untreated samples. We identified 712 proteins across treated and untreated samples and performed protein network analysis using Ingenuity Pathway Analysis (IPA) software to reveal their protein networks. After filtering and evaluating protein expression, we identified macrophage myristoylated alanine-rich C kinase substrate (MARCKSL1) and creatine kinase proteins as a potential part of the inflammatory networks of TLR4. The results assumed that MARCKSL1 and creatine kinase proteins might be associated with a statin-induced anti-inflammatory response due to possible interaction with the TLR4.
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Affiliation(s)
- A. D. A. Shahinuzzaman
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Advanced Technology Cores, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jayanta K. Chakrabarty
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Aurchie Rahman
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Correspondence: ; Tel.: +1-817-272-5439
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7
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Motkowski R, Alifier M, Abramowicz P, Konstantynowicz J, Mikołuć B, Stasiak-Barmuta A. Innate and Acquired Cellular Immunity in Children with Familial Hypercholesterolemia Treated with Simvastatin. J Clin Med 2022; 11:jcm11102924. [PMID: 35629051 PMCID: PMC9147505 DOI: 10.3390/jcm11102924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/03/2022] Open
Abstract
The aim of this cross-sectional study was to assess the influence of simvastatin treatment in children with familial hypercholesterolemia (FH) on parameters of cellular immunity. Twenty-six children with FH were included, of which thirteen were treated with 10 mg simvastatin for at least 26 weeks, and thirteen were age- and sex-matched with a low-cholesterol diet only. Total WBC count and lipid profile were measured. Flow cytometry was used to identify lymphocyte subsets and determine the expression of adhesion molecules (AM) and toll-like receptors (TLRs) on leukocytes. No differences were found in the basic values of peripheral blood count and subpopulations of lymphocytes between groups. The percentage of granulocytes with the expression of AM was higher in those treated with statins. The TLR-2 expression on granulocytes and monocytes showed higher values, whereas the TLR-4 expression was lower on lymphocytes and granulocytes in simvastatin-treated children. Treatment with simvastatin in children with FH is not associated with alterations in the amounts of granulocytes and monocytes. There is no association between statin treatment and the pattern of peripheral blood lymphocyte subpopulations. The role of AM and TLRs needs further investigation, given the effect of statins on the innate immunity may be important for their efficacy and safety during growth.
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Affiliation(s)
- Radosław Motkowski
- Department of Pediatrics, Rheumatology, Immunology and Metabolic Bone Diseases, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.A.); (J.K.); (B.M.)
- Correspondence: ; Tel.: +48-85-7450-622; Fax: +48-85-7450-644
| | - Marek Alifier
- Department of Clinical Immunology, Medical University of Bialystok, 15-274 Bialystok, Poland;
| | - Paweł Abramowicz
- Department of Pediatrics, Rheumatology, Immunology and Metabolic Bone Diseases, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.A.); (J.K.); (B.M.)
| | - Jerzy Konstantynowicz
- Department of Pediatrics, Rheumatology, Immunology and Metabolic Bone Diseases, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.A.); (J.K.); (B.M.)
| | - Bożena Mikołuć
- Department of Pediatrics, Rheumatology, Immunology and Metabolic Bone Diseases, Medical University of Bialystok, 15-274 Bialystok, Poland; (P.A.); (J.K.); (B.M.)
| | - Anna Stasiak-Barmuta
- Department of Clinical Immunology, Medical University of Bialystok, 15-274 Bialystok, Poland;
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8
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Fang Z, Wanigasekara MSK, Yepremyan A, Lam B, Thapa P, Foss FW, Chowdhury SM. Mass Spectrometry-Cleavable Protein N-Terminal Tagging Strategy for System-Level Protease Activity Profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:189-197. [PMID: 34928623 DOI: 10.1021/jasms.1c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteolysis is one of the most important protein post-translational modifications (PTMs) that influences the functions, activities, and structures of nearly all proteins during their lifetime. To facilitate the targeted identification of low-abundant proteolytic products, we devised a strategy incorporating a novel biotinylated reagent PFP (pentafluorophenyl)-Rink-biotin to specifically target, enrich and identify proteolytic N-termini. Within the PFP-Rink-biotin reagent, a mass spectrometry (MS)-cleavable feature was designed to assist in the unambiguous confirmation of the enriched proteolytic N-termini. The proof-of-concept study was performed with multiple standard proteins whose N-termini were successfully modified, enriched and identified by a signature ion (SI) in the MS/MS fragmentation, along with the determination of N-terminal peptide sequences by multistage tandem MS of the complementary fragment generated after the cleavage of MS-cleavable bond. For large-scale application, the enrichment and identification of protein N-termini from Escherichia coli cells were demonstrated, facilitated by an in-house developed NTermFinder bioinformatics workflow. We believe this approach will be beneficial in improving the confidence of identifying proteolytic substrates in a native cellular environment.
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Affiliation(s)
- Zixiang Fang
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Maheshika S K Wanigasekara
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Akop Yepremyan
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Brandon Lam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Pawan Thapa
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Frank W Foss
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington Texas 76019, United States
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9
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Paggi RA, De Castro RE, Cerletti M. In Vivo Protein Cross-Linking and Coimmunoprecipitation in Haloferax volcanii. Methods Mol Biol 2022; 2522:301-317. [PMID: 36125758 DOI: 10.1007/978-1-0716-2445-6_19] [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: 06/15/2023]
Abstract
Coimmunoprecipitation is a powerful and commonly used method to identify protein-protein interactions in a physiological context. Here, we report a coimmunoprecipitation protocol that was adapted and optimized for the haloarchaeon Haloferax volcanii to identify interacting partners to the LonB protease. This protocol includes the in vivo cross-linking of H. volcanii proteins using two different crosslinker agents, dithiobis(succinimidyl propionate) and formaldehyde, followed by immunoprecipitation with anti-LonB antibody conjugated to Protein A - Sepharose beads. Tryptic on-bead protein digestion was performed combined with Mass Spectrometry analysis of peptides for the identification and quantification of LonB ligands.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina.
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10
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Guo D, Zhao G, Li G, Wang C, Wang H, Liu Z, Xu B, Guo X. Identification of a mitogen-activated protein kinase kinase (AccMKK4) from Apis cerana cerana and its involvement in various stress responses. INSECT MOLECULAR BIOLOGY 2021; 30:325-339. [PMID: 33538052 DOI: 10.1111/imb.12698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/03/2020] [Accepted: 01/25/2021] [Indexed: 05/19/2023]
Abstract
The mitogen-activated protein kinase (MAPK) cascade pathway is a ubiquitous signal transduction pathway in eukaryotes that regulates a variety of immune responses. This study accomplished the first isolation of an AccMKK4 gene from Apis cerana cerana and explored its function. Yeast two-hybrid experiments proved that AccMKK4 can interact with Accp38b, and the silencing of AccMKK4 in honeybees downregulated the expression level of Accp38b, which suggests that AccMKK4 might participate in the oxidative stress response through the p38 MAPK pathway. Tissue-specific expression levels of AccMKK4 analysis showed that AccMKK4 in the thorax, particularly muscle tissue, was higher than that in other tissues. The qRT-PCR results from different conditions demonstrated that AccMKK4 responds to various environmental stresses. After AccMKK4 silencing, the transcription level of some antioxidant genes and the activity of antioxidant-related enzymes are reduced, which indicated that AccMKK4 plays an important role in resistance against oxidative stress caused by external stimuli. In summary, our findings indicate that AccMKK4 probably plays an indispensable role in the response of honeybees to environmental stress and might aid for further research on the role of the MAPK cascade pathway in the antioxidant defence mechanisms of insects.
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Affiliation(s)
- D Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, PR China
| | - G Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, PR China
| | - G Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, PR China
| | - C Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, PR China
| | - H Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, PR China
| | - Z Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, PR China
| | - B Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, PR China
| | - X Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, PR China
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Lei S, Zhang Y. Identification of the key genes and pathways involved in B cells in primary Sjögren' s syndrome. Bioengineered 2021; 12:2055-2073. [PMID: 34034637 PMCID: PMC8806908 DOI: 10.1080/21655979.2021.1930753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Primary Sjögren’ s syndrome (pSS) is a relatively common autoimmune disease, which mainly involves the exocrine glands, causing dry eye, dryness of mouth, fatigue and pain in the joints, thus severely affecting the normal lives of patients. B cell populations are considered to play an important role in their pathogenesis and pSS patients are generally characterized by exhibiting biological signs of B cell activation. Moreover, another important characterized change in the peripheral blood of pSS patients is found to be the decreased number of circulating memory B cells. However, the mechanisms underlying the B cell activation and the decreased level of circulating memory B cells in pSS patients are still unclear. Therefore, we identified key genes and pathways involved in B cells in pSS through a combination of several bioinformatic approaches including Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and weighted gene co-expression network analysis (WGCNA) using gene expression data of pSS patients and controls from an open database Gene Expression Omnibus (GEO). The results may provide some novel insights into the pathogenesis of pSS. Moreover, we constructed and validated a diagnostic model for pSS by using the expression patterns of these key genes, which may assist clinicians in diagnosing pSS.
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Affiliation(s)
- Shizhen Lei
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yi Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
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Kosuge H, Nakakido M, Nagatoishi S, Fukuda T, Bando Y, Ohnuma SI, Tsumoto K. Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR. J Biol Chem 2021; 296:100278. [PMID: 33428936 PMCID: PMC7948961 DOI: 10.1016/j.jbc.2021.100278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 01/19/2023] Open
Abstract
Proline and arginine-rich end leucine-rich repeat protein (PRELP) is a member of the small leucine-rich repeat proteoglycans (SLRPs) family. Levels of PRELP mRNA are downregulated in many types of cancer, and PRELP has been reported to have suppressive effects on tumor cell growth, although the molecular mechanism has yet to be fully elucidated. Given that other SLRPs regulate signaling pathways through interactions with various membrane proteins, we reasoned that PRELP likely interacts with membrane proteins to maintain cellular homeostasis. To identify membrane proteins that interact with PRELP, we carried out coimmunoprecipitation coupled with mass spectrometry (CoIP-MS). We prepared membrane fractions from Expi293 cells transfected to overexpress FLAG-tagged PRELP or control cells and analyzed samples precipitated with anti-FLAG antibody by mass spectrometry. Comparison of membrane proteins in each sample identified several that seem to interact with PRELP; among them, we noted two growth factor receptors, insulin-like growth factor I receptor (IGFI-R) and low-affinity nerve growth factor receptor (p75NTR), interactions with which might help to explain PRELP's links to cancer. We demonstrated that PRELP directly binds to extracellular domains of these two growth factor receptors with low micromolar affinities by surface plasmon resonance analysis using recombinant proteins. Furthermore, cell-based analysis using recombinant PRELP protein showed that PRELP suppressed cell growth and affected cell morphology of A549 lung carcinoma cells, also at micromolar concentration. These results suggest that PRELP regulates cellular functions through interactions with IGFI-R and p75NTR and provide a broader set of candidate partners for further exploration.
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Affiliation(s)
- Hirofumi Kosuge
- School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | - Shin-Ichi Ohnuma
- The Institute of Ophthalmology, University College London, London, United Kingdom
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, Tokyo, Japan; The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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Zacharias AO, Fang Z, Rahman A, Talukder A, Cornelius S, Chowdhury SM. Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks. J Sep Sci 2020; 44:310-322. [DOI: 10.1002/jssc.202000930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Adway O. Zacharias
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Zixiang Fang
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Aurchie Rahman
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Akash Talukder
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Sharel Cornelius
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry University of Texas at Arlington Arlington Texas USA
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Zhao B, Reilly CP, Davis C, Matouschek A, Reilly JP. Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms. J Proteome Res 2020; 19:2758-2771. [PMID: 32496805 DOI: 10.1021/acs.jproteome.0c00111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple ion fragmentation methods involving collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) with regular and very high energy settings, and electron-transfer dissociation with supplementary HCD (EThcD) are implemented to improve the confidence of cross-link identifications. Three different S. cerevisiae proteasome samples cross-linked by diethyl suberthioimidate (DEST) or bis(sulfosuccinimidyl)suberate (BS3) are analyzed. Two approaches are introduced to combine interpretations from the above four methods. Working with cleavable cross-linkers such as DEST, the first approach searches for cross-link diagnostic ions and consistency among the best interpretations derived from all four MS2 spectra associated with each precursor ion. Better agreement leads to a more definitive identification. Compatible with both cleavable and noncleavable cross-linkers such as BS3, the second approach multiplies scoring metrics from a number of fragmentation experiments to derive an overall best match. This significantly increases the scoring gap between the target and decoy matches. The validity of cross-links fragmented by HCD alone and identified by Kojak, MeroX, pLink, and Xi was evaluated using multiple fragmentation data. Possible ways to improve the identification credibility are discussed. Data are available via ProteomeXchange with identifier PXD018310.
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Affiliation(s)
- Bingqing Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Colin P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Caroline Davis
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James P Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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