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Alicehajic A, Duivenvoorden AAM, Lenaerts K. Unveiling the molecular complexity of intestinal ischemia-reperfusion injury through omics technologies. Proteomics 2024; 24:e2300160. [PMID: 38477684 DOI: 10.1002/pmic.202300160] [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: 11/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Intestinal ischemia-reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores the extent to which omics technologies-transcriptomics, proteomics, metabolomics, and metagenomics-have already contributed to deciphering the molecular mechanisms contributing to intestinal IR injury, in in vivo and in vitro animal and human models, and in clinical samples. Recent breakthroughs involve applying omics methodologies on exosomes, organoids, and single cells, shedding light on promising avenues and valuable targets to reduce intestinal IR injury. Future directions aimed at expediting clinical translation are discussed as well and include multi-omics data integration to facilitate the identification of key regulatory nodes driving intestinal IR injury and advancing human organoid models based on the novel insights by single-cell omics technologies, offering hope for clinical application of therapeutic strategies in the years to come.
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Affiliation(s)
- Anja Alicehajic
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Annet Adriana Maria Duivenvoorden
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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2
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Passos JRS, Guerreiro DD, Otávio KS, Dos Santos-Neto PC, Souza-Neves M, Cuadro F, Nuñez-Olivera R, Crispo M, Vasconcelos FR, Bezerra MJB, Silva RF, Lima LF, Figueiredo JR, Bustamante-Filho IC, Menchaca A, Moura AA. How in vitro maturation changes the proteome of ovine cumulus-oocyte complexes? Mol Reprod Dev 2022; 89:459-470. [PMID: 35901249 DOI: 10.1002/mrd.23638] [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: 02/16/2022] [Revised: 05/29/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022]
Abstract
The present study evaluated the effects of in vitro maturation (IVM) on the proteome of cumulus-oocyte complexes (COCs) from ewes. Extracted COC proteins were analyzed by LC-MS/MS. Differences in protein abundances (p < 0.05) and functional enrichments in immature versus in vitro-matured COCs were evaluated using bioinformatics tools. There were 2550 proteins identified in the COCs, with 89 and 87 proteins exclusive to immature and mature COCs, respectively. IVM caused downregulation of 84 and upregulation of 34 proteins. Major upregulated proteins in mature COCs were dopey_N domain-containing protein, structural maintenance of chromosomes protein, ubiquitin-like modifier-activating enzyme 2. Main downregulated proteins in mature COCs were immunoglobulin heavy constant mu, inter-alpha-trypsin inhibitor heavy chain 2, alpha-2-macroglobulin. Proteins exclusive to mature COCs and upregulated after IVM related to immune response, complement cascade, vesicle-mediated transport, cell cycle, and extracellular matrix organization. Proteins of immature COCs and downregulated after IVM were linked to metabolic processes, immune response, and complement cascade. KEGG pathways and miRNA-regulated genes attributed to downregulated and mature COC proteins related to complement and coagulation cascades, metabolism, humoral response, and B cell-mediated immunity. Thus, IVM influenced the ovine COC proteome. This knowledge supports the future development of efficient IVM protocols for Ovis aries.
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Affiliation(s)
- José Renato S Passos
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Denise D Guerreiro
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Kamila S Otávio
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | | | - Marcela Souza-Neves
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - Federico Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | | | - Martina Crispo
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fábio R Vasconcelos
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Maria Julia B Bezerra
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Renato F Silva
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, Brazil
| | - Laritza F Lima
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, Brazil
| | - José Ricardo Figueiredo
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, Brazil
| | | | - Alejo Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay.,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria, Montevideo, Uruguay
| | - Arlindo A Moura
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
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3
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Passos JRS, Guerreiro DD, Otávio KS, Dos Santos-Neto PC, Souza-Neves M, Cuadro F, Nuñez-Olivera R, Crispo M, Bezerra MJB, Silva RF, Lima LF, Figueiredo JR, Bustamante-Filho IC, Menchaca A, Moura AA. Global proteomic analysis of pre-implantational ovine embryos produced in-vitro. Reprod Domest Anim 2022; 57:784-797. [PMID: 35377953 DOI: 10.1111/rda.14122] [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: 02/15/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
The present study was conducted to characterize the major proteome of pre-implantation (D6) ovine embryos produced in vitro. COCs were aspirated from antral follicles (2-6 mm), matured and fertilized in vitro, and cultured until day six. Proteins were extracted separately from three pools of 45 embryos and separately run in SDS-PAGE. Proteins from each pool were individually subjected to in-gel digestion followed by LC-MS/MS. Three "raw. files" and protein lists were produced by Pattern Lab software but only proteins present in all three lists were used for the bioinformatics analyses. https://david.ncifcrf.govThere were 2,262 proteins identified in the 6-day old ovine embryos, including albumin, zona pellucida glycoprotein 2, 3 and 4, peptidyl arginine deiminase 6, actin cytoplasmic 1, gamma-actin 1, pyruvate kinase, heat shock protein 90 and protein disulfide isomerase, among others. Major biological processes linked to the sheep embryo proteome were translation, protein transport and protein stabilization, and molecular functions, defined as ATP binding, oxygen carrier activity and oxygen binding. There were 42 enriched functional clusters according to the 2,147 genes (UniProt database). Ten selected clusters with potential association with embryo development included translation, structural constituent of ribosomes, ribosomes, nucleosomes, structural constituent of the cytoskeleton, microtubule-based process, translation initiation factor activity, regulation of translational initiation, cell body and nucleotide biosynthetic process. The most representative KEEG pathways were ribosome, oxidative phosphorylation, glutathione metabolism, gap junction, mineral absorption, DNA replication and cGMP-PKG signaling pathway. Analyses of functional clusters clearly showed differences associated with the proteome of pre-implantation (D6) sheep embryos generated after in vitro fertilization in comparison with in vivo counterparts (Sanchez et al., 2021; https://doi.org/10.1111/rda.13897), confirming that the quality of in vitro derived blastocysts are unlike those produced in vivo. The present study portrays the first comprehensive overview of the proteome of pre-implantational ovine embryos grown in vitro.
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Affiliation(s)
- J R S Passos
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - D D Guerreiro
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - K S Otávio
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - P C Dos Santos-Neto
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - M Souza-Neves
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - F Cuadro
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - R Nuñez-Olivera
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay
| | - M Crispo
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - M J B Bezerra
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
| | - R F Silva
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - L F Lima
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - J R Figueiredo
- Laboratory of Manipulation of Oocyte and Preantral Follicles (LAMOFOPA), Ceará State University, Fortaleza, CE, Brazil
| | - I C Bustamante-Filho
- Laboratório de Biotecnologia, Universidade do Vale do Taquari, Lajeado, RS, Brazil
| | - A Menchaca
- Instituto de Reproducción Animal Uruguay, Fundación IRAUy, Montevideo, Uruguay.,Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria, Montevideo, Uruguay
| | - A A Moura
- Laboratory of Animal Physiology, Department of Animal Science, Federal University of Ceará, Fortaleza, CE, Brazil
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Piccolo EB, Thorp EB, Sumagin R. Functional implications of neutrophil metabolism during ischemic tissue repair. Curr Opin Pharmacol 2022; 63:102191. [PMID: 35276496 PMCID: PMC8995387 DOI: 10.1016/j.coph.2022.102191] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 12/11/2022]
Abstract
Immune cell mobilization and their accumulation in the extravascular space is a key consequence of tissue injury. Maladaptive trafficking and immune activation following reperfusion of ischemic tissue can exacerbate tissue repair. After ischemic injury such as myocardial infarction (MI), PMNs are the first cells to arrive at the sites of insult and their response is critical for the sequential progression of ischemia from inflammation to resolution and finally to tissue repair. However, PMN-induced inflammation can also be detrimental to cardiac function and ultimately lead to heart failure. In this review, we highlight the role of PMNs during key cellular and molecular events of ischemic heart failure. We address new research on PMN metabolism, and how this orchestrates diverse functions such as PMN chemotaxis, degranulation, and phagocytosis. Particular focus is given to PMN metabolism regulation by mitochondrial function and mTOR kinase activity.
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Affiliation(s)
- Enzo B Piccolo
- Department of Pathology, Northwestern University Feinberg School of Medicine, 300 East Superior St, Chicago, IL, 60611, USA
| | - Edward B Thorp
- Department of Pathology, Northwestern University Feinberg School of Medicine, 300 East Superior St, Chicago, IL, 60611, USA.
| | - Ronen Sumagin
- Department of Pathology, Northwestern University Feinberg School of Medicine, 300 East Superior St, Chicago, IL, 60611, USA.
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Sanchez DJD, Vasconcelos FR, Teles-Filho ACA, Viana AGA, Martins AMA, Sousa MV, Castro MS, Ricart CA, Fontes W, Bertolini M, Bustamante-Filho IC, Moura AA. Proteomic profile of pre-implantational ovine embryos produced in vivo. Reprod Domest Anim 2021; 56:586-603. [PMID: 33460477 DOI: 10.1111/rda.13897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
The present study was conducted to decipher the proteome of in vivo-produced pre-implantation ovine embryos. Ten locally adapted Morana Nova ewes received hormonal treatment and were inseminated 12 hr after ovulation. Six days later, 54 embryos (morula and blastocyst developmental state) were recovered from eight ewes and pooled to obtain sufficient protein for proteomic analysis. Extracted embryo proteins were analysed by LC-MS/MS, followed by identification based on four database searches (PEAKS, Proteome Discoverer software, SearchGUI software, PepExplorer). Identified proteins were analysed for gene ontology terms, protein clusters and interactions. Genes associated with the ovine embryo proteome were screened for miRNA targets using data sets of TargetScan (http://www.targetscan.org) and mIRBase (http://www.mirbase.org) servers. There were 667 proteins identified in the ovine embryos. Biological processes of such proteins were mainly related to cellular process and regulation, and molecular functions, to binding and catalytic activity. Analysis of the embryo proteins revealed 49 enriched functional clusters, linked to energy metabolism (TCA cycle, pyruvate and glycolysis metabolism), zona pellucida (ZP), MAPK signalling pathway, tight junction, binding of sperm to ZP, translation, proteasome, cell cycle and calcium/phospholipid binding. Sixteen miRNAs were related to 25 pre-implantation ovine embryo genes, all conserved in human, bovine and ovine species. The interaction network generated by miRNet showed four key miRNAs (hsa-mir-106b-5p; hsa-mir-30-5p; hsa-mir-103a-5p and hsa-mir-106a-5p) with potential interactions with embryo-expressed genes. Functional analysis of the network indicated that miRNAs modulate genes related to cell cycle, regulation of stem cell and embryonic cell differentiation, among others. Retrieved miRNAs also modulate the expression of genes involved in cell signalling pathways, such as MAPK, Wnt, TGF-beta, p53 and Toll-like receptor. The current study describes the first major proteomic profile of 6-day-old ovine embryos produced in vivo, setting a comprehensive foundation for our understanding of embryo physiology in the ovine species.
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Affiliation(s)
- Deisy J D Sanchez
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Fabio R Vasconcelos
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | | | - Arabela G A Viana
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Aline M A Martins
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Marcelo V Sousa
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Mariana S Castro
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Carlos A Ricart
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, University of Brasília, Brasília, Brazil
| | - Marcelo Bertolini
- The School of Veterinay Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
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6
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Freire MS, Oliveira NG, Lima SMF, Porto WF, Martins DCM, Silva ON, Chaves SB, Sousa MV, Ricart CAO, Castro MS, Fontes W, Franco OL, Rezende TMB. IL-4 absence triggers distinct pathways in apical periodontitis development. J Proteomics 2020; 233:104080. [PMID: 33338687 DOI: 10.1016/j.jprot.2020.104080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 12/18/2022]
Abstract
Dental pulp is a specialized tissue able to respond to infectious processes. Nevertheless, infection progress and root canal colonization trigger an immune-inflammatory response in tooth-surrounding tissues, leading to apical periodontitis and bone tissue destruction, further contributing to tooth loss. In order to shed some light on the effects of IL-4 on periradicular pathology development modulation, microtomographic, histological and proteomic analyses were performed using 60 mice, 30 wild type and 30 IL-4-/-. For that, 5 animals were used for microtomographic and histological analysis, and another 5 for proteomic analysis for 0, 7 and 21 days with/without pulp exposure. The periapical lesions were established in WT and IL-4-/- mice without statistical differences in their volume, and the value of p < 0.05 was adopted as significant in microtomographic and histological analyses. Regarding histological analysis, IL-4-/- mice show aggravation of pulp inflammation compared to WT. By using proteomic analysis, we have identified 32 proteins with increased abundance and 218 proteins with decreased abundance in WT animals after 21 days of pulp exposure, compared to IL-4-/- animals. However, IL-4-/- mice demonstrated faster development of apical periodontitis. These animals developed a compensatory mechanism to overcome IL-4 absence, putatively based on the identification of upregulated proteins related to immune system signaling pathways. Significance: IL-4 might play a protective role in diseases involving bone destruction and its activity may contribute to host protection, mainly due to its antiosteoclastogenic action.
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Affiliation(s)
- Mirna S Freire
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Curso de Odontologia, Centro Universitário do Planalto Central Apparecido dos Santos, UNICEPLAC, Brasília, DF, Brazil
| | - Nelson G Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Stella M F Lima
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Curso de Odontologia, Universidade Católica de Brasília, UCB, Brasília, DF, Brazil
| | - William F Porto
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Porto Reports, Brasília, DF, Brazil
| | - Danilo C M Martins
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, UnB, Brasília, DF, Brazil
| | - Osmar N Silva
- Programa de Pós-graduacao em Ciências Farmacêuticas. Centro Universitário de Anápolis - UniEVANGELICA, Anápolis, GO, Brazil
| | - Sacha B Chaves
- Departamento de nanotecnologia, Universidade de Brasília, Brazil
| | - Marcelo V Sousa
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brazil
| | - Carlos A O Ricart
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brazil
| | - Mariana S Castro
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brazil
| | - Wagner Fontes
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brazil
| | - Octavio L Franco
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade de Brasília, Brasília, DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, UnB, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil.
| | - Taia M B Rezende
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Curso de Odontologia, Universidade Católica de Brasília, UCB, Brasília, DF, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, UnB, Brasília, DF, Brazil.
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7
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Tahir M, Arshid S, Fontes B, S. Castro M, Sidoli S, Schwämmle V, Luz IS, Roepstorff P, Fontes W. Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases. Int J Mol Sci 2020; 21:ijms21165799. [PMID: 32823483 PMCID: PMC7460855 DOI: 10.3390/ijms21165799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/11/2020] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Intestinal ischemia reperfusion injury (iIRI) is a severe clinical condition presenting high morbidity and mortality worldwide. Some of the systemic consequences of IRI can be prevented by applying ischemic preconditioning (IPC), a series of short ischemia/reperfusion events preceding the major ischemia. Although neutrophils are key players in the pathophysiology of ischemic injuries, neither the dysregulation presented by these cells in iIRI nor the protective effect of iIPC have their regulation mechanisms fully understood. Protein phosphorylation, as well as the regulation of the respective phosphatases and kinases are responsible for regulating a large number of cellular functions in the inflammatory response. Moreover, in previous work we found hydrolases and transferases to be modulated in iIR and iIPC, suggesting the possible involvement of phosphatases and kinases in the process. Therefore, in the present study, we analyzed the phosphoproteome of neutrophils from rats submitted to mesenteric ischemia and reperfusion, either submitted or not to IPC, compared to quiescent controls and sham laparotomy. Proteomic analysis was performed by multi-step enrichment of phosphopeptides, isobaric labeling, and LC-MS/MS analysis. Bioinformatics was used to determine phosphosite and phosphopeptide abundance and clustering, as well as kinases and phosphatases sites and domains. We found that most of the phosphorylation-regulated proteins are involved in apoptosis and migration, and most of the regulatory kinases belong to CAMK and CMGC families. An interesting finding revealed groups of proteins that are modulated by iIR, but such modulation can be prevented by iIPC. Among the regulated proteins related to the iIPC protective effect, Vamp8 and Inpp5d/Ship are discussed as possible candidates for control of the iIR damage.
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Affiliation(s)
- Muhammad Tahir
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Samina Arshid
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Laboratory of Surgical Physiopathology (LIM-62), Faculty of Medicine, University of São Paulo, São Paulo 01246903, Brazil;
| | - Belchor Fontes
- Laboratory of Surgical Physiopathology (LIM-62), Faculty of Medicine, University of São Paulo, São Paulo 01246903, Brazil;
| | - Mariana S. Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Isabelle S. Luz
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (S.S.); (V.S.); (P.R.)
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia 70910-900, Brazil; (M.T.); (S.A.); (M.S.C.); (I.S.L.)
- Correspondence:
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8
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Cassatella MA, Östberg NK, Tamassia N, Soehnlein O. Biological Roles of Neutrophil-Derived Granule Proteins and Cytokines. Trends Immunol 2019; 40:648-664. [PMID: 31155315 DOI: 10.1016/j.it.2019.05.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Neutrophils, the most abundant white blood cells in human circulation, entertain intense interactions with other leukocyte subsets, platelets, and stromal cells. Molecularly, such interactions are typically communicated through proteins generated during granulopoiesis, stored in granules, or produced on demand. Here, we provide an overview of the mammalian regulation of granule protein production in the bone marrow and the de novo synthesis of cytokines by neutrophils recruited to tissues. In addition, we discuss some of the known biological roles of these protein messengers, and how neutrophil-borne granule proteins and cytokines can synergize to modulate inflammation and tumor development. Decoding the neutrophil interactome is important for therapeutically neutralizing individual proteins to putatively dampen inflammation, or for delivering modified neutrophil-borne proteins to boost host defense.
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Affiliation(s)
| | - Nataliya K Östberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Oliver Soehnlein
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden; Institute for Cardiovascular Prevention (IPEK), Klinikum der LMU, München, Germany; German Centre for Cardiovascular Research (DZHK), Partner site, Munich, Germany.
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9
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Improving deep proteome and PTMome coverage using tandem HILIC-HPRP peptide fractionation strategy. Anal Bioanal Chem 2018; 411:459-469. [PMID: 30456605 DOI: 10.1007/s00216-018-1462-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/04/2018] [Accepted: 10/30/2018] [Indexed: 01/03/2023]
Abstract
Despite being orthogonal to reverse-phase separation and valuable for posttranslational modification (PTM) pre-enrichment, hydrophilic interaction liquid chromatography (HILIC) has not been widely adopted for large-scale proteomic applications. Here, we first evaluated the performance of HILIC in comparison with the popular high-pH reverse-phase (HPRP) separation, as the first dimension for tryptic peptide fractionation in a shotgun workflow to characterize the complex 293T cell proteome. The data indicated that the complementary nature of HILIC and HPRP for peptide separation was mainly due to different hydrophobicity preferences. Realizing that uncaptured components from one mode can be resolved in the other mode, we then designed and compared two multidimensional separation schemes using HILIC and HPRP in tandem for peptide prefractionation, in terms of identification efficiency and coverage at peptide, protein, and PTM levels. A total of 22,604 and 23,566 peptides corresponding to 4481 and 4436 proteins from 293T cell lysate were detected using HILIC-HPRP- and HPRP-HILIC-based shotgun proteomics workflow, respectively. In addition, without assistance of enrichment techniques, the tandem fractionation methods aided to identify 46 different PTMs from over 10,000 of spectra using blind modification search algorithm. We concluded that HILIC is a valuable alternative option for peptide prefractionation in a large-scale proteomic study, but can be further augmented with the use of a secondary HPRP separation.
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Proteomic landscape of seminal plasma associated with dairy bull fertility. Sci Rep 2018; 8:16323. [PMID: 30397208 PMCID: PMC6218504 DOI: 10.1038/s41598-018-34152-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022] Open
Abstract
Male fertility is the ability of sperm to fertilize the egg and sustain embryo development. Several factors determine the fertilizing capacity of mammalian sperm, including those intrinsic to sperm and components of the seminal plasma. The present study analyzed the seminal fluid proteome of Bos taurus and potential associations between proteins and fertility scores. Mass spectrometry coupled with nano HPLC allowed the identification of 1,159 proteins in the dairy bull seminal plasma. There were 50 and 29 seminal proteins more abundant in high (HF) low fertility (LF) bulls, respectively. Based on multivariate analysis, C-type natriuretic peptide, TIMP-2, BSP5 and sulfhydryl oxidase indicated relationship with HF bulls. Clusterin, tissue factor pathway inhibitor 2, galectin-3-binding protein and 5′-nucleotidase were associated with LF bulls. Abundance of NAD(P)(+)-arginine ADP-ribosyltransferase, prosaposin and transmembrane protein 2 proteins had the highest positive correlations with fertility ranking. Quantities of vitamin D-binding protein, nucleotide exchange factor SIL1 and galectin-3-binding protein showed the highest negative correlations with fertility ranking. A fertility ranking score was calculated and the relationship with these proteins was significant (Spearman’s rho = 0.94). The present findings represent a major and novel contribution to the study of bovine seminal proteins. Indicators of fertility can be used to improve reproductive biotechnologies.
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