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Schwab SK, Harris PS, Michel C, McGinnis CD, Nahomi RB, Assiri MA, Reisdorph R, Henriksen K, Orlicky DJ, Levi M, Rosenberg A, Nagaraj RH, Fritz KS. Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue. Proteomics Clin Appl 2024:e202400018. [PMID: 38923810 DOI: 10.1002/prca.202400018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
PURPOSE Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end-stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post-translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism. EXPERIMENTAL DESIGN A novel extraction and LC-MS/MS approach was adapted to quantify sites of lysine acetylation from formalin-fixed paraffin-embedded (FFPE) kidney tissue and from patients with DKD and non-diabetic donors (n = 5 and n = 7, respectively). RESULTS Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis. CONCLUSIONS AND CLINICAL RELEVANCE A quantitative acetylomics platform was developed for protein biomarker discovery in formalin-fixed and paraffin-embedded biopsies of kidney transplant patients suffering from DKD.
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Affiliation(s)
- Stefanie K Schwab
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Peter S Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cole Michel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Courtney D McGinnis
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rooban B Nahomi
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mohammed A Assiri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Richard Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kammi Henriksen
- Department of Pathology, University of Chicago Medical Center, Chicago, Illinois, USA
| | - David J Orlicky
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Avi Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ram H Nagaraj
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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2
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Comparative Transcriptomics and Proteomics of Cancer Cell Lines Cultivated by Physiological and Commercial Media. Biomolecules 2022; 12:biom12111575. [DOI: 10.3390/biom12111575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
Aiming to reduce the gap between in vitro and in vivo environment, a complex culture medium, Plasmax, was introduced recently, which includes nutrients and metabolites with concentrations normally found in human plasma. Herein, to study the influence of this medium on cellular behaviors, we utilized Plasmax to cultivate two cancer cell lines, including one breast cancer cell line, MDA-MB-231BR, and one brain cancer cell line, CRL-1620. Cancer cells were harvested and prepared for transcriptomics and proteomics analyses to assess the discrepancies caused by the different nutritional environments of Plasmax and two commercial media: DMEM, and EMEM. Total RNAs of cells were extracted using mammalian total RNA extract kits and analyzed by next-generation RNA sequencing; proteomics analyses were performed using LC-MS/MS. Gene oncology and pathway analysis were employed to study the affected functions. The cellular invasion and cell death were inhibited in MDA-MB-231BR cell line when cultured in Plasmax compared to DMEM and EMEM, whereas the invasion, migration and protein synthesis of CRL-1620 cell line were activated in Plasmax in relative to both commercial media. The expression changes of some proteins were more significant compared to their corresponding transcripts, indicating that Plasmax has more influence upon regulatory processes of proteins after translation. This work provides complementary information to the original study of Plasmax, aiming to facilitate the selection of appropriate media for in vitro cancer cell studies.
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Gutaj P, Matysiak J, Matuszewska E, Jaskiewicz K, Kamińska D, Światły-Błaszkiewicz A, Szczapa T, Kalantarova A, Gajecka M, Wender-Ozegowska E. Maternal serum proteomic profiles of pregnant women with type 1 diabetes. Sci Rep 2022; 12:8696. [PMID: 35610262 PMCID: PMC9130255 DOI: 10.1038/s41598-022-12221-5] [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: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Despite improvement in the care of diabetes over the years, pregnancy complicated by type 1 diabetes (T1DM) is still associated with adverse maternal and neonatal outcomes. To date, proteomics studies have been conducted to identify T1DM biomarkers in non-pregnant women, however, no studies included T1DM pregnant women. In this study serum proteomic profiling was conducted in pregnant women with T1DM in the late third trimester. Serum samples were collected from 40 women with T1DM and 38 healthy controls within 3 days before delivery at term pregnancy. Significant differences between serum proteomic patterns were revealed, showing discriminative peaks for complement C3 and C4-A, kininogen-1, and fibrinogen alpha chain. Quantification of selected discriminative proteins by ELISA kits was also performed. The serum concentration of kininogen-1 was significantly lower in women with T1DM than in controls. There were no significant differences in serum concentrations of complement C3 and complement C4-A between study groups. These data indicate that pregnant women with T1DM have a distinct proteomic profile involving proteins in the coagulation and inflammatory pathways. However, their utility as biomarkers of pregnancy complications in women with T1DM warrants further investigation.
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Affiliation(s)
- Paweł Gutaj
- Department of Reproduction, Poznan University of Medical Sciences, 61-701, Poznan, Poland.
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Eliza Matuszewska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Katarzyna Jaskiewicz
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Dorota Kamińska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Agata Światły-Błaszkiewicz
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089, Bydgoszcz, Poland
| | - Tomasz Szczapa
- Department of Neonatology, Neonatal Biophysical Monitoring and Cardiopulmonary Therapies Research Unit, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | | | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Ewa Wender-Ozegowska
- Department of Reproduction, Poznan University of Medical Sciences, 61-701, Poznan, Poland
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Investigation of proteins important for microcirculation using in vivo microdialysis after glucose provocation: a proteomic study. Sci Rep 2021; 11:19093. [PMID: 34580391 PMCID: PMC8476624 DOI: 10.1038/s41598-021-98672-8] [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: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022] Open
Abstract
Insulin has metabolic and vascular effects in the human body. What mechanisms that orchestrate the effects in the microcirculation, and how the responds differ in different tissues, is however not fully understood. It is therefore of interest to search for markers in microdialysate that may be related to the microcirculation. This study aims to identify proteins related to microvascular changes in different tissue compartments after glucose provocation using in vivo microdialysis. Microdialysis was conducted in three different tissue compartments (intracutaneous, subcutaneous and intravenous) from healthy subjects. Microdialysate was collected during three time periods; recovery after catheter insertion, baseline and glucose provocation, and analyzed using proteomics. Altogether, 126 proteins were detected. Multivariate data analysis showed that the differences in protein expression levels during the three time periods, including comparison before and after glucose provocation, were most pronounced in the intracutaneous and subcutaneous compartments. Four proteins with vascular effects were identified (angiotensinogen, kininogen-1, alpha-2-HS-glycoprotein and hemoglobin subunit beta), all upregulated after glucose provocation compared to baseline in all three compartments. Glucose provocation is known to cause insulin-induced vasodilation through the nitric oxide pathway, and this study indicates that this is facilitated through the interactions of the RAS (angiotensinogen) and kallikrein-kinin (kininogen-1) systems.
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Imasawa T, Claverol S, Lacombe D, Amoedo ND, Rossignol R. Proteomic Study of Low-Birth-Weight Nephropathy in Rats. Int J Mol Sci 2021; 22:10294. [PMID: 34638634 PMCID: PMC8508940 DOI: 10.3390/ijms221910294] [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: 08/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023] Open
Abstract
The hyperfiltration theory has been used to explain the mechanism of low birth weight (LBW)-related nephropathy. However, the molecular changes in the kidney proteome have not been defined in this disease, and early biomarkers are lacking. We investigated the molecular pathogenesis of LBW rats obtained by intraperitoneal injection of dexamethasone into pregnant animals. Normal-birth-weight (NBW) rats were used as controls. When the rats were four weeks old, the left kidneys were removed and used for comprehensive label-free proteomic studies. Following uninephrectomy, all rats were fed a high-salt diet until 9 weeks of age. Differences in the molecular composition of the kidney cortex were observed at the early step of LBW nephropathy pathogenesis. Untargeted quantitative proteomics showed that proteins involved in energy metabolism, such as oxidative phosphorylation (OXPHOS), the TCA cycle, and glycolysis, were specifically downregulated in the kidneys of LBW rats at four weeks. No pathological changes were detected at this early stage. Pathway analysis identified NEFL2 (NRF2) and RICTOR as potential upstream regulators. The search for biomarkers identified components of the mitochondrial respiratory chain, namely, ubiquinol-cytochrome c reductase complex subunits (UQCR7/11) and ATP5I/L, two components of mitochondrial F1FO-ATP synthase. These findings were further validated by immunohistology. At later stages of the disease process, the right kidneys revealed an increased frequency of focal segmental glomerulosclerosis lesions, interstitial fibrosis and tubular atrophy. Our findings revealed proteome changes in LBW rat kidneys and revealed a strong downregulation of specific mitochondrial respiratory chain proteins, such as UQCR7.
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Affiliation(s)
- Toshiyuki Imasawa
- Kidney Center, National Hospital Organization Chiba-Higashi National Hospital, Chiba 260-8712, Japan
- Rare Diseases, Genetics and Metabolism, University of Bordeaux, INSERM U1211, 33000 Bordeaux, France;
- Department of Biology and Medical Sciences, University of Bordeaux, 33000 Bordeaux, France;
| | - Stéphane Claverol
- Department of Biology and Medical Sciences, University of Bordeaux, 33000 Bordeaux, France;
- Functional Genomics Center, Proteomics Department, University of Bordeaux, 33000 Bordeaux, France
| | - Didier Lacombe
- Rare Diseases, Genetics and Metabolism, University of Bordeaux, INSERM U1211, 33000 Bordeaux, France;
- Department of Biology and Medical Sciences, University of Bordeaux, 33000 Bordeaux, France;
| | | | - Rodrigue Rossignol
- Rare Diseases, Genetics and Metabolism, University of Bordeaux, INSERM U1211, 33000 Bordeaux, France;
- Department of Biology and Medical Sciences, University of Bordeaux, 33000 Bordeaux, France;
- CELLOMET, CHU Pellegrin, 33300 Bordeaux, France;
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Bin-Jaliah I, Hewett PW, Al-Hashem F, Haidara MA, Abdel Kader DH, Morsy MD, Al-Ani B. Insulin protects against type 1 diabetes mellitus-induced aortopathy associated with the inhibition of biomarkers of vascular injury in rats. Arch Physiol Biochem 2021; 127:266-272. [PMID: 31250674 DOI: 10.1080/13813455.2019.1632900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND We sought to investigate the protective effect of insulin against type 1 diabetes mellitus (T1DM)-induced aortic injury (aortopathy) associated with the inhibition of biomarkers of vascular injury. MATERIAL AND METHODS T1DM was induced in rats by streptozotocin (STZ) (65 mg/kg), and the protection group started insulin treatment 2 days post diabetic induction and continued until being sacrificed at week 8. RESULTS Aortopathy was developed in the diabetic rats as demonstrated by profound alterations to the aorta ultrastructure, which was substantially protected by insulin. In addition, insulin significantly inhibited diabetes-induced dyslipidaemia, soluble vascular cell adhesion molecule-1 (sVCAM-1) and soluble intercellular adhesion molecule-1 (sICAM-1), oxidative stress, and inflammation. However, blood levels of these biomarkers in the insulin-treated group were still significant (p < .05) compared with the control group, whereas insulin treatment returned blood glucose and triglyceride to control levels. CONCLUSIONS We demonstrate effective protection by insulin against T1DM-induced aortopathy in rats, which is associated with the inhibition of vascular injury biomarkers.
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Affiliation(s)
- Ismaeel Bin-Jaliah
- Department of Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Peter W Hewett
- Institute of Cardiovascular Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fahaid Al-Hashem
- Department of Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Mohamed A Haidara
- Department of Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
- Department of Physiology, Kasr al-Aini Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Dina H Abdel Kader
- Department of Medical Histology, Kasr al-Aini Faculty of Medicine, Cairo University, Cairo, Egypt
| | - M D Morsy
- Department of Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
- Department of Physiology, College of Medicine, Menoufia University, Shibin el Kom, Egypt
| | - Bahjat Al-Ani
- Department of Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
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7
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MALDI-TOF Protein Profiling Reflects Changes in Type 1 Diabetes Patients Depending on the Increased Amount of Adipose Tissue, Poor Control of Diabetes and the Presence of Chronic Complications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052263. [PMID: 33668851 PMCID: PMC7967698 DOI: 10.3390/ijerph18052263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 11/18/2022]
Abstract
Introduction: Protein profiling allows the determination of the presence of proteins marking various stages of the disease, and differentiates between people at risk of various diseases. In type 1 diabetes, protein profiling had been previously used to find blood markers other than islet autoantibodies to indicate the pancreatic beta cell destruction process and to reflect the progression of type 1 diabetes mellitus (T1DM). However, T1DM is an auto-immune disease and its clinical presentation changes in time of its duration. The aim of the study: To find differences in protein profiles in patients with type 1 diabetes according to diabetes control (HbA1c > 7%) and with presence of diabetic complications or obesity. It may help to identify subgroups of patients who may need a better clinical supervision and individualized treatment. Material and methods: A group of 103 patients with auto-immunologically confirmed T1DM, and meeting the following inclusion criteria: Caucasian race, duration of diabetes >5 years, were used in the study. Criteria of exclusion: past or present cancer (treated with chemo-/radiotherapy), diseases of the liver (ALT > 3 × ULN) except for people with simple hepatic steatosis, chronic renal disease (eGFR < 30 mL/1.73 m2/min), and acute inflammation (CRP > 5 mg/dL). The study group was divided in terms of the presence of chronic complications, obesity, or poor metabolic control (HbA1c > 7%). Protein profiling was completed by using the MALDI-TOF MS (matrix-assisted laser desorption/ionization-time of flight mass spectrometry) analyzer. Results: Differentiating proteins were identified in all of the groups. The groups burdened with complications, obesity, and poor metabolic control were characterized by increased levels of fibrinogen, complement C4 and C3. Conclusion: The groups of type 1 diabetes patients burdened with complications, obesity, and poor metabolic control were characterized by increased levels of fibrinogen, complement C4 and C3. Further detailed studies are necessary to determine more subtle changes in the proteomic profile of patients with type 1 diabetes.
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8
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Yadav SPS, Sandoval RM, Zhao J, Huang Y, Wang E, Kumar S, Campos-Bilderback SB, Rhodes G, Mechref Y, Molitoris BA, Wagner MC. Mechanism of how carbamylation reduces albumin binding to FcRn contributing to increased vascular clearance. Am J Physiol Renal Physiol 2021; 320:F114-F129. [PMID: 33283642 PMCID: PMC7847050 DOI: 10.1152/ajprenal.00428.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/12/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease results in high serum urea concentrations leading to excessive protein carbamylation, primarily albumin. This is associated with increased cardiovascular disease and mortality. Multiple methods were used to address whether carbamylation alters albumin metabolism. Intravital two-photon imaging of the Munich Wistar Frömter (MWF) rat kidney and liver allowed us to characterize filtration and proximal tubule uptake and liver uptake. Microscale thermophoresis enabled quantification of cubilin (CUB7,8 domain) and FcRn binding. Finally, multiple biophysical methods including dynamic light scattering, small-angle X-ray scattering, LC-MS/MS and in silico analyses were used to identify the critical structural alterations and amino acid modifications of rat albumin. Carbamylation of albumin reduced binding to CUB7,8 and FcRn in a dose-dependent fashion. Carbamylation markedly increased vascular clearance of carbamylated rat serum albumin (cRSA) and altered distribution of cRSA in both the kidney and liver at 16 h post intravenous injection. By evaluating the time course of carbamylation and associated charge, size, shape, and binding parameters in combination with in silico analysis and mass spectrometry, the critical binding interaction impacting carbamylated albumin's reduced FcRn binding was identified as K524. Carbamylation of RSA had no effect on glomerular filtration or proximal tubule uptake. These data indicate urea-mediated time-dependent carbamylation of albumin lysine K524 resulted in reduced binding to CUB7,8 and FcRn that contribute to altered albumin transport, leading to increased vascular clearance and increased liver and endothelial tissue accumulation.
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MESH Headings
- Animals
- Chromatography, Liquid
- Disease Models, Animal
- Glomerular Filtration Rate
- Histocompatibility Antigens Class I/metabolism
- Kidney Tubules, Proximal/metabolism
- Kidney Tubules, Proximal/physiopathology
- Liver/metabolism
- Lysine
- Male
- Microscopy, Fluorescence, Multiphoton
- Protein Binding
- Protein Carbamylation
- Rats, Inbred Strains
- Rats, Sprague-Dawley
- Receptors, Cell Surface/metabolism
- Receptors, Fc/metabolism
- Renal Insufficiency, Chronic/metabolism
- Renal Insufficiency, Chronic/pathology
- Renal Insufficiency, Chronic/physiopathology
- Scattering, Small Angle
- Serum Albumin/metabolism
- Tandem Mass Spectrometry
- Time Factors
- X-Ray Diffraction
- Rats
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Affiliation(s)
- Shiv Pratap S Yadav
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ruben M Sandoval
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Exing Wang
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, Texas
| | - Sudhanshu Kumar
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Silvia B Campos-Bilderback
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - George Rhodes
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Bruce A Molitoris
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Mark C Wagner
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
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Hariri MA, Jaffa MA, Saoud R, Zhao J, Zhu R, Jaffa AA, El-Achkar GA, Moussa M, Kobeissy F, Hassan A, Ziyadeh FN, Mechref Y, Jaffa AA. Vascular Cells Proteome Associated with Bradykinin and Leptin Inflammation and Oxidative Stress Signals. Antioxidants (Basel) 2020; 9:antiox9121251. [PMID: 33316969 PMCID: PMC7764689 DOI: 10.3390/antiox9121251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/13/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023] Open
Abstract
Among the primary contributors to cardiovascular diseases are inflammation and oxidative imbalance within the vessel walls as well as the fibrosis of rat aortic smooth muscle cell (RASMC). Bradykinin (BK) and leptin are inflammatory modulators that are linked to vascular injury. In this study, we employed tandem LC-MS/MS to identify protein signatures that encompass protein abundance in RASMC treated with BK or leptin followed by systems biology analyses to gain insight into the biological pathways and processes linked to vascular remodeling. In the study, 1837 proteins were identified in control untreated RASMC. BK altered the expression of 72 (4%) and 120 (6.5%) proteins, whereas leptin altered the expression of 189 (10.2%) and 127 (6.5%) proteins after 24 and 48 h, respectively, compared to control RASMC. BK increased the protein abundance of leptin receptor, transforming growth factor-β. On the other hand, leptin increased the protein abundance of plasminogen activator inhibitor 1 but decreased the protein abundance of cofilin. BK and leptin induced the expression of inflammatory cytokines such as tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) and pathway analysis revealed the activation of mitogen-activated protein kinases (MAPKs) and AKT pathways. The proteome profile in response to BK and leptin revealed mechanistic interplay of multiple processes that modulate inflammation and oxidative stress signals in the vasculature.
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Affiliation(s)
- Moustafa Al Hariri
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Miran A. Jaffa
- Epidemiology and Population Health Department, Faculty of Health Sciences, American University of Beirut, Beirut 11-0236, Lebanon;
| | - Richard Saoud
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.Z.); (R.Z.)
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.Z.); (R.Z.)
| | - Aneese A. Jaffa
- Faculty of Arts and Sciences, American University of Beirut, Beirut 11-0236, Lebanon;
| | - Ghewa A. El-Achkar
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Mayssam Moussa
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Anwarul Hassan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar;
| | - Fuad N. Ziyadeh
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.Z.); (R.Z.)
- Correspondence: (Y.M.); (A.A.J.); Tel.: +1812-219-1972 (Y.M.); +961-1-350000 (A.A.J.)
| | - Ayad A. Jaffa
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 11-0236, Lebanon; (M.A.H.); (R.S.); (G.A.E.-A.); (M.M.); (F.K.); (F.N.Z.)
- Correspondence: (Y.M.); (A.A.J.); Tel.: +1812-219-1972 (Y.M.); +961-1-350000 (A.A.J.)
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10
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Saoud R, Jaffa MA, Habib A, Zhao J, Al Hariri M, Zhu R, Hasan A, Ziyadeh FN, Kobeissy F, Mechref Y, Jaffa AA. Modulation of proteomic and inflammatory signals by Bradykinin in podocytes. J Adv Res 2020; 24:409-422. [PMID: 32518694 PMCID: PMC7270529 DOI: 10.1016/j.jare.2020.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 01/19/2023] Open
Abstract
Podocyte damage is one of the hallmarks of diabetic nephropathy leading to proteinuria and kidney damage. The underlying mechanisms of podocyte injury are not well defined. Bradykinin (BK) was shown to contribute to diabetic kidney disease. Here, we evaluated the temporal changes in proteome profile and inflammatory signals of podocytes in response to BK (10−7M). Protein profile was evaluated by liquid chromatography mass Spectrometry (LC-MS/MS) analysis. Proteome profile analysis of podocytes treated with BK (10−7M) for 3 and 6 h, revealed 61 proteins that were differentially altered compared to unstimulated control podocytes. Pathway enrichment analysis suggested inhibition of cell death pathways, engagement of cytoskeletal elements and activation of inflammatory pathways. One of the inflammatory proteins that was identified to be induced by BK treatment is Prostaglandin (PG) H Synthase-2 (Cyclooxygenase-2, COX-2). In addition, BK significantly induced the production and release of PGE2 and this effect was inhibited by both COX-2 and MEK Kinase inhibitors, demonstrating that the production of PGE2 by BK is mediated via COX-2 and MAPK-dependent mechanisms. These findings provide a global understanding of the effector modulated proteome in response to BK and also reveal BK as an important modulator of inflammation and a potential player in podocyte injury.
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Affiliation(s)
- Richard Saoud
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Miran A Jaffa
- Epidemiology and Population Health Department, Faculty of Health Sciences, American University of Beirut, Lebanon
| | - Aida Habib
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon.,INSERM-U1149, Centre de Recherche sur l'Inflammation, Sorbonne Paris Cité, Laboratoire d'Excellence Inflamex, Faculté de Médecine, Site Xavier Bichat, Université de Paris, France
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Moustafa Al Hariri
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Qatar
| | - Fuad N Ziyadeh
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon.,Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Lebanon
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Ayad A Jaffa
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
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11
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Magnadóttir B, Uysal-Onganer P, Kraev I, Svansson V, Hayes P, Lange S. Deiminated proteins and extracellular vesicles - Novel serum biomarkers in whales and orca. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100676. [PMID: 32114311 DOI: 10.1016/j.cbd.2020.100676] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/16/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
Peptidylarginine deiminases (PADs) are a family of phylogenetically conserved calcium-dependent enzymes which cause post-translational protein deimination. This can result in neoepitope generation, affect gene regulation and allow for protein moonlighting via functional and structural changes in target proteins. Extracellular vesicles (EVs) carry cargo proteins and genetic material and are released from cells as part of cellular communication. EVs are found in most body fluids where they can be useful biomarkers for assessment of health status. Here, serum-derived EVs were profiled, and post-translationally deiminated proteins and EV-related microRNAs are described in 5 ceataceans: minke whale, fin whale, humpback whale, Cuvier's beaked whale and orca. EV-serum profiles were assessed by transmission electron microscopy and nanoparticle tracking analysis. EV profiles varied between the 5 species and were identified to contain deiminated proteins and selected key inflammatory and metabolic microRNAs. A range of proteins, critical for immune responses and metabolism were identified to be deiminated in cetacean sera, with some shared KEGG pathways of deiminated proteins relating to immunity and physiology, while some KEGG pathways were species-specific. This is the first study to characterise and profile EVs and to report deiminated proteins and putative effects of protein-protein interaction networks via such post-translationald deimination in cetaceans, revealing key immune and metabolic factors to undergo this post-translational modification. Deiminated proteins and EVs profiles may possibly be developed as new biomarkers for assessing health status of sea mammals.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK.
| | - Vilhjálmur Svansson
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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12
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Phillips RA, Kraev I, Lange S. Protein Deimination and Extracellular Vesicle Profiles in Antarctic Seabirds. BIOLOGY 2020; 9:E15. [PMID: 31936359 PMCID: PMC7168935 DOI: 10.3390/biology9010015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/19/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Pelagic seabirds are amongst the most threatened of all avian groups. They face a range of immunological challenges which seem destined to increase due to environmental changes in their breeding and foraging habitats, affecting prey resources and exposure to pollution and pathogens. Therefore, the identification of biomarkers for the assessment of their health status is of considerable importance. Peptidylarginine deiminases (PADs) post-translationally convert arginine into citrulline in target proteins in an irreversible manner. PAD-mediated deimination can cause structural and functional changes in target proteins, allowing for protein moonlighting in physiological and pathophysiological processes. PADs furthermore contribute to the release of extracellular vesicles (EVs), which play important roles in cellular communication. In the present study, post-translationally deiminated protein and EV profiles of plasma were assessed in eight seabird species from the Antarctic, representing two avian orders: Procellariiformes (albatrosses and petrels) and Charadriiformes (waders, auks, gulls and skuas). We report some differences between the species assessed, with the narrowest EV profiles of 50-200 nm in the northern giant petrel Macronectes halli, and the highest abundance of larger 250-500 nm EVs in the brown skua Stercorarius antarcticus. The seabird EVs were positive for phylogenetically conserved EV markers and showed characteristic EV morphology. Post-translational deimination was identified in a range of key plasma proteins critical for immune response and metabolic pathways in three of the bird species under study; the wandering albatross Diomedea exulans, south polar skua Stercorarius maccormicki and northern giant petrel. Some differences in Gene Ontology (GO) biological and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for deiminated proteins were observed between these three species. This indicates that target proteins for deimination may differ, potentially contributing to a range of physiological functions relating to metabolism and immune response, as well as to key defence mechanisms. PAD protein homologues were identified in the seabird plasma by Western blotting via cross-reaction with human PAD antibodies, at an expected 75 kDa size. This is the first study to profile EVs and to identify deiminated proteins as putative novel plasma biomarkers in Antarctic seabirds. These biomarkers may be further refined to become useful indicators of physiological and immunological status in seabirds-many of which are globally threatened.
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Affiliation(s)
- Richard A. Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge CB3 0ET, UK;
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
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13
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Magnadóttir B, Hayes P, Hristova M, Bragason BT, Nicholas AP, Dodds AW, Guðmundsdóttir S, Lange S. Post-translational protein deimination in cod (Gadus morhua L.) ontogeny novel roles in tissue remodelling and mucosal immune defences? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:157-170. [PMID: 29908202 DOI: 10.1016/j.dci.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Peptidylarginine deiminases (PADs) are calcium dependent enzymes with physiological and pathophysiological roles conserved throughout phylogeny. PADs promote post-translational deimination of protein arginine to citrulline, altering the structure and function of target proteins. Deiminated proteins were detected in the early developmental stages of cod from 11 days post fertilisation to 70 days post hatching. Deiminated proteins were present in mucosal surfaces and in liver, pancreas, spleen, gut, muscle, brain and eye during early cod larval development. Deiminated protein targets identified in skin mucosa included nuclear histones; cytoskeletal proteins such as tubulin and beta-actin; metabolic and immune related proteins such as galectin, mannan-binding lectin, toll-like receptor, kininogen, Beta2-microglobulin, aldehyde dehydrogenase, bloodthirsty and preproapolipoprotein A-I. Deiminated histone H3, a marker for anti-pathogenic neutrophil extracellular traps, was particularly elevated in mucosal tissues in immunostimulated cod larvae. PAD-mediated protein deimination may facilitate protein moonlighting, allowing the same protein to exhibit a range of biological functions, in tissue remodelling and mucosal immune defences in teleost ontogeny.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX, London, UK.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
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14
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Thippakorn C, Schaduangrat N, Nantasenamat C. Proteomic and bioinformatic discovery of biomarkers for diabetic nephropathy. EXCLI JOURNAL 2018; 17:312-330. [PMID: 29805343 PMCID: PMC5962897 DOI: 10.17179/excli2018-1150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/12/2018] [Indexed: 11/13/2022]
Abstract
Diabetes is associated with numerous metabolic and vascular risk factors that contribute to a high rate of micro-vascular and macro-vascular disorders leading to mortality and morbidity from diabetic complications. In this case, the major cause of death in overall diabetic patients results from diabetic nephropathy (DN) or renal failure. The risk factors and mechanisms that correspond to the development of DN are not fully understood and so far, no specific and sufficient diagnostic biomarkers are currently available other than micro- or macroalbuminuria. Therefore, this review describes current and novel protein biomarkers in the context of DN as well as probable proteins biomarkers associated with pathological processes for the early stage of DN via proteomics data together with bioinformatics. In addition, the mechanisms involved in early development of diabetic vascular disorders and complications resulting from glucose induced oxidative stress will also be explored.
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Affiliation(s)
- Chadinee Thippakorn
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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