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Watral J, Formanowicz D, Perek B, Kostka-Jeziorny K, Podkowińska A, Tykarski A, Luczak M. Comprehensive proteomics of monocytes indicates oxidative imbalance functionally related to inflammatory response in chronic kidney disease-related atherosclerosis. Front Mol Biosci 2024; 11:1229648. [PMID: 38389898 PMCID: PMC10882078 DOI: 10.3389/fmolb.2024.1229648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Atherosclerosis-induced cardiovascular events are the leading cause of mortality in chronic kidney disease (CKD) patients. Monocytes are involved in the formation of atherosclerotic plaques and mediate in the overproduction of ROS, promoting inflammation and oxidative stress. However, the relationship between monocytes, inflammation, and oxidative status in CKD-associated atherosclerosis has not been thoroughly investigated. Monocytes and plasma derived from two groups of CKD patients with varying degrees of atherosclerosis and two groups of patients with cardiovascular disease (CVD) and non-CKD atherosclerosis were analyzed. This study was designed to perform a comprehensive proteomic analysis of monocytes in combination with functional bioinformatics. In addition, a targeted investigation of oxidative stress- and inflammatory-related factors to explore CKD-associated atherosclerosis was applied. Dysregulation of proteins involved in lipid oxidation, cell survival, ROS synthesis and metabolism, and inflammatory responses has been revealed. The characteristic disturbances in the monocyte proteome changed with the progression of CKD. A closer examination of oxidative stress's triggers, mediators, and effects on protein and lipid levels showed alterations in the oxidative imbalance between CKD and CVD. CKD monocytes demonstrated a significant increase of oxidized glutathione without changing the level of its reduced form. Evaluation of enzymatic antioxidants, sources of ROS, and modifications caused by ROS also revealed significant alterations between the study groups. In CKD, inflammation and oxidative imbalance correlated and drove each other. However, in CVD, oxidative stress-related factors were associated with each other but not to inflammatory proteins. Moreover, lipid abnormalities were more specific to classical CVD and unrelated to CKD. Such a comprehensive characterization of monocytes and oxidative stress in CKD and CVD patients has never been presented so far. Obtained results support the involvement of distinct mechanisms underlying the acceleration of atherosclerotic and non-atherosclerotic CKD.
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Affiliation(s)
- Joanna Watral
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Dorota Formanowicz
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Bartłomiej Perek
- Department of Cardiac Surgery and Transplantology, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Kostka-Jeziorny
- Department of Hypertensiology, Angiology and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Andrzej Tykarski
- Department of Hypertensiology, Angiology and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Magdalena Luczak
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
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Luo Z, Yu X, Wang C, Zhao H, Wang X, Guan X. Trimethylamine N-oxide promotes oxidative stress and lipid accumulation in macrophage foam cells via the Nrf2/ABCA1 pathway. J Physiol Biochem 2024; 80:67-79. [PMID: 37932654 DOI: 10.1007/s13105-023-00984-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/04/2023] [Indexed: 11/08/2023]
Abstract
Recently, trimethylamine N-oxide (TMAO) has been considered a risk factor for cardiovascular disease and has a proatherogenic effect. Many studies have found that TMAO is involved in plaque oxidative stress and lipid metabolism, but the specific mechanism is still unclear. In our study, meta-analysis and bioinformatic analysis were firstly conducted in the database, and found that the effect of high plasma TMAO levels on promoting atherosclerotic plaque may be related to the expression of key antioxidant genes nuclear factor erytheroid-derived-2-like 2 (NFE2L2/Nrf2) decreased. Next, we assessed the role of Nrf2-mediated signaling pathway in TMAO-treated foam cells. Our results showed that TMAO can inhibit the expression of Nrf2 and its downstream antioxidant response element such as heme oxygenase-1 (HO-1) and glutathione peroxidase4 (GPX4), resulting in increased production of reactive oxygen species and decreased activity of superoxide dismutase, promoting oxidative stress. And TMAO can also promote lipid accumulation in foam cells by inhibiting cholesterol efflux protein expression. In addition, upregulation of Nrf2 expression partially rescues TMAO-induced oxidative stress and reduces ATP-binding cassette A1 (ABCA1)-mediated lipid accumulation. Therefore, TMAO promotes oxidative stress and lipid accumulation in macrophage foam cells through the Nrf2/ABCA1 pathway, which may provide a potential mechanism for the proatherogenic effect of TMAO.
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Affiliation(s)
- ZhiSheng Luo
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China
| | - XiaoChen Yu
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Chao Wang
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China
| | - HaiYan Zhao
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China
| | - Xinming Wang
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China
| | - XiuRu Guan
- Department of Laboratory Diagnostics, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, NanGang, Harbin, Heilongjiang, 150001, People's Republic of China.
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Raíssa-Oliveira B, Lara-Ribeiro AC, Rezende-Ribeiro J, Bahia ABQ, Verano-Braga T. Cardioproteomics: Insights on Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:159-171. [PMID: 38409420 DOI: 10.1007/978-3-031-50624-6_8] [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: 02/28/2024]
Abstract
Cardiovascular diseases (CVDs) remain a global health challenge and are the leading cause of deaths worldwide. Proteomics has emerged as a valuable tool for unraveling the complex molecular mechanisms underlying CVDs, offering insights into biomarker discovery, drug targets, and personalized medicine. This review explores key breakthroughs in proteomic applications related to CVDs, mainly coronary artery disease (CAD), ischemic heart diseases such as myocardial infarction (MI), and cardiomyopathies. Notable findings include potential biomarkers, therapeutic targets, and insights into disease pathogenesis. The review highlights the importance of proteomics in advancing our understanding of CVDs and shaping future therapeutic approaches.
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Affiliation(s)
- Brenda Raíssa-Oliveira
- Núcleo de Proteômica Funcional (NPF), Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- INCT-Nanobiofar, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Carolina Lara-Ribeiro
- Núcleo de Proteômica Funcional (NPF), Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- INCT-Nanobiofar, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Júlia Rezende-Ribeiro
- Núcleo de Proteômica Funcional (NPF), Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- INCT-Nanobiofar, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Beatriz Queiroz Bahia
- Núcleo de Proteômica Funcional (NPF), Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- INCT-Nanobiofar, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago Verano-Braga
- Núcleo de Proteômica Funcional (NPF), Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
- INCT-Nanobiofar, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:cancers15020555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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Gharban HAJ, AL-Shaeli SJJ, Hussen TJ. Molecular genotyping, histopathological and immunohistochemical studies of bovine papillomatosis. Open Vet J 2023; 13:26-41. [PMID: 36777440 PMCID: PMC9897500 DOI: 10.5455/ovj.2023.v13.i1.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/10/2022] [Indexed: 02/05/2023] Open
Abstract
Background Bovine papillomatosis (BP) is considered the most common health problem in large cattle farms. Aim This study attempts to confirm clinically suspected BP in cattle by polymerase chain reaction (PCR) assay, histopathology, immunohistochemistry (IHC), and genotyping analysis of local isolates. Methods According to morphological appearance and lesion features, a cross sectional study of 54 clinically diagnosed BP cattle was assigned to this current investigation from May to August (2021) in Al-Kut district (Wasit Province, Iraq) private veterinary clinics using purposive sampling technique based on set criteria. The cattle were diagnosed clinically, and the tissues were collected and some fixed in 10% neutral buffered formalin and other stored frozen and examined by histopathological technique, IHC, and PCR assays. Results Using PCR assay, all cattle were positive for the BPV L1 gene. According to detect the L1 gene, analysis of the phylogenetic tree showed that local BPV cattle isolates were closely related to the NCBI-BLAST BPV type-1 and type-2 of the Polish equine isolate (KF284133.1) and BPV Brazilian Bostaurus isolate (MH187961.1), respectively. Histological detection showed there were acanthosis, hyperkeratosis, epidermal thickening, severe infiltration of mononuclear cells, massive hemorrhage, dermal fibroplasias, multifocal spongiosis, moderate neovascularization, moderate to severe elongation of the retention ridge towards the dermis, parakeratosis, rings of calcification, and necrosis with nuclear pyknosis of some spinosum cells. Immunohistochemical findings of tumor necrosis factor-alpha, epidermal growth factor receptor and Fascin showed a significant variation in values of immunoreaction in the dermis and epidermis. These results ranged from negative (0) to mild positive (+1) to moderate positive (+2) reactions. Conclusion The study provided essential molecular and genotyping data to improve our knowledge by emphasizing the crucial of IHC as an elegant diagnostic method to detect cellular alterations.
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Affiliation(s)
- Hasanain A. J. Gharban
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Wasit, Kut, Iraq
| | - Sattar J. J. AL-Shaeli
- Department of Medical Basic Sciences, College of Dentistry, University of Wasit, Kut, Iraq,Corresponding Author: Sattar J. J. AL-Shaeli. Department of Medical Basic Sciences, College of Dentistry, University of Wasit, Kut, Iraq.
| | - Talal Jabal Hussen
- Department of Medical Basic Sciences, College of Dentistry, University of Wasit, Kut, Iraq
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Volk RF, Montaño JL, Warrington SE, Hofmann KL, Zaro BW. Proteomic characterization of phagocytic primary human monocyte-derived macrophages. RSC Chem Biol 2022; 3:783-793. [PMID: 35755185 PMCID: PMC9175098 DOI: 10.1039/d2cb00076h] [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: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 11/21/2022] Open
Abstract
Macrophages play a vital role in the innate immune system, identifying and destroying unwanted cells. However, it has been difficult to attain a comprehensive understanding of macrophage protein abundance due to technical limitations. In addition, it remains unclear how changes in proteome composition are linked to phagocytic activity. In this study we developed methods to derive human macrophages and prepare them for mass spectrometry analysis in order to more-deeply understand the proteomic consequences of macrophage stimulation. Interferon gamma (IF-g), an immune stimulating cytokine, was used to induce macrophage activation, increasing phagocytosis of cancer cells by 2-fold. These conditions were used to perform comparative shotgun proteomics between resting macrophages and stimulated macrophages with increased phagocytic activity. Our analysis revealed that macrophages bias their protein production toward biological processes associated with phagocytosis and antigen processing in response to stimulation. We confirmed our findings by antibody-based western blotting experiments, validating both previously reported and novel proteins of interest. In addition to whole protein changes, we evaluated active protein synthesis by treating cells with the methionine surrogate probe homopropargylglycine (HPG). We saw increased rates of HPG incorporation during phagocytosis-inducing stimulation, suggesting protein synthesis rates are altered by stimulation. Together our findings provide the most comprehensive proteomic insight to date into primary human macrophages. We anticipate that this data can be used as a launchpoint to generate new hypotheses about innate immune function.
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Affiliation(s)
- Regan F Volk
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - José L Montaño
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Sara E Warrington
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Katherine L Hofmann
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
| | - Balyn W Zaro
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Quantitative Biosciences Institute, and Helen Diller Family Comprehensive Cancer Centre, University of California San Francisco CA USA
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Proteogenomics Analysis Reveals Novel Micropeptides in Primary Human Immune Cells. IMMUNO 2022. [DOI: 10.3390/immuno2020018] [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] Open
Abstract
Short open reading frames (sORFs) encoding functional peptides have emerged as important mediators of biological processes. Recent studies indicate that sORFs of long non-coding RNAs (lncRNAs) can encode functional micropeptides regulating immunity and inflammation. However, large-scale identification of potential micropeptide-encoding sequences is a significant challenge. We present a data analysis pipeline that uses immune cell-derived mass spectrometry-based proteomic data reanalyzed using a rigorous proteogenomics-based workflow. Our analysis resulted in the identification of 2815 putative lncRNA-encoded micropeptides across three human immune cell types. Stringent score cut-off and manual verification confidently identified 185 high-confidence putative micropeptide-coding events, of which a majority have not been reported previously. Functional validation revealed the expression and localization of lnc-MKKS in both nucleus and cytoplasmic compartments. Our pilot analysis serves as a resource for future studies focusing on the role of micropeptides in immune cell response.
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