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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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Wang L, Tian R, Wang G, Zhao M, Zhang Y, Li J. Proteomic analysis of fetal skin by iTRAQ reveals molecular signals underlying Inner Mongolia Cashmere goat hair follicle initiation. ALL LIFE 2023. [DOI: 10.1080/26895293.2023.2169363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Lele Wang
- Ulanqab of Medical College, Ulanqab, People’s Republic of China
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Gaofeng Wang
- Ulanqab Center for Animal Disease Control and Prevention, Ulanqab, People’s Republic of China
| | - Meng Zhao
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, People’s Republic of China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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3
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Amaya-Garrido A, Brunet M, Buffin-Meyer B, Piedrafita A, Grzesiak L, Agbegbo E, Del Bello A, Ferrandiz I, Ardeleanu S, Bermudez-Lopez M, Fedou C, Camus M, Burlet-Schiltz O, Massines J, Buléon M, Feuillet G, Alves M, Neau E, Casemayou A, Breuil B, Saulnier-Blache JS, Denis C, Voelkl J, Glorieux G, Hobson S, Arefin S, Rahman A, Kublickiene K, Stenvinkel P, Bascands JL, Faguer S, Valdivielso JM, Schanstra JP, Klein J. Calprotectin is a contributor to and potential therapeutic target for vascular calcification in chronic kidney disease. Sci Transl Med 2023; 15:eabn5939. [PMID: 37672568 DOI: 10.1126/scitranslmed.abn5939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/17/2023] [Indexed: 09/08/2023]
Abstract
Vascular calcification is an important risk factor for cardiovascular (CV) mortality in patients with chronic kidney disease (CKD). It is also a complex process involving osteochondrogenic differentiation of vascular smooth muscle cells (VSMCs) and abnormal deposition of minerals in the vascular wall. In an observational, multicenter European study, including 112 patients with CKD from Spain and 171 patients on dialysis from France, we used serum proteome analysis and further validation by ELISA to identify calprotectin, a circulating damage-associated molecular pattern protein, as being independently associated with CV outcome and mortality. This was confirmed in an additional cohort of 170 patients with CKD from Sweden, where increased serum calprotectin concentrations correlated with increased vascular calcification. In primary human VSMCs and mouse aortic rings, calprotectin exacerbated calcification. Treatment with paquinimod, a calprotectin inhibitor, as well as pharmacological inhibition of the receptor for advanced glycation end products and Toll-like receptor 4 inhibited the procalcifying effect of calprotectin. Paquinimod also ameliorated calcification induced by the sera of uremic patients in primary human VSMCs. Treatment with paquinimod prevented vascular calcification in mice with chronic renal failure induced by subtotal nephrectomy and in aged apolipoprotein E-deficient mice as well. These observations identified calprotectin as a key contributor of vascular calcification, and increased circulating calprotectin was strongly and independently associated with calcification, CV outcome, and mortality in patients with CKD. Inhibition of calprotectin might therefore be a promising strategy to prevent vascular calcification in patients with CKD.
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Affiliation(s)
- Ana Amaya-Garrido
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Manon Brunet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Bénédicte Buffin-Meyer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Alexis Piedrafita
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Lucile Grzesiak
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Ezechiel Agbegbo
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Arnaud Del Bello
- Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, Centre Hospitalo-Universitaire de Toulouse, 31400 Toulouse, France
| | - Inés Ferrandiz
- Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, Centre Hospitalo-Universitaire de Toulouse, 31400 Toulouse, France
| | - Serban Ardeleanu
- AURAR Saint Louis Dialysis Center, 97421 Saint Louis, La Réunion, France
| | - Marcelino Bermudez-Lopez
- Vascular and Renal Translational Research Group, UDETMA, REDinREN del ISCIII, IRBLleida, 25198 Lleida, Spain
| | - Camille Fedou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Mylène Camus
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31400 Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31400 Toulouse, France
| | - Jean Massines
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Marie Buléon
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Melinda Alves
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Eric Neau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Audrey Casemayou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
- Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, Centre Hospitalo-Universitaire de Toulouse, 31400 Toulouse, France
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Jean-Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Jakob Voelkl
- Institute for Physiology and Pathophysiology, Johannes Kepler University Linz, 4040 Linz, Austria
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Griet Glorieux
- Nephrology Section, Department of Internal Medicine and Pediatrics, Ghent University Hospital, 9000 Gent, Belgium
| | - Sam Hobson
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Samsul Arefin
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Awahan Rahman
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Karolina Kublickiene
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188, Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97491 Sainte Clotilde, La Réunion, France
| | - Stanislas Faguer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
- Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, Centre Hospitalo-Universitaire de Toulouse, 31400 Toulouse, France
| | - José M Valdivielso
- Vascular and Renal Translational Research Group, UDETMA, REDinREN del ISCIII, IRBLleida, 25198 Lleida, Spain
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
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Baiken Y, Markhametova Z, Ashimova A, Zhulamanova A, Nogaibayeva A, Kozina L, Matkarimov B, Aituov B, Gaipov A, Myngbay A. Elevated Levels of Plasma Collagen Triple Helix Repeat Containing 1 (CTHRC1) Is Strongly Associated with eGFR and Albuminuria in Chronic Kidney Disease. Medicina (B Aires) 2023; 59:medicina59040651. [PMID: 37109608 PMCID: PMC10146339 DOI: 10.3390/medicina59040651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Background: Chronic kidney disease (CKD) has various etiologies, making it impossible to fully understand its complex pathophysiology. Elevated levels of plasma creatinine, proteinuria, and albuminuria and declined eGFR are traits observed in CKD patients. The current study attempts to highlight the collagen triple helix repeat containing 1 (CTHRC1) protein as a putative blood biomarker for CKD in addition to existing recognized indicators of CKD progression. Methods: A total of 26 CKD patients and 18 healthy controls were enrolled in this study. Clinical characteristics and complete blood and biochemical analyses were collected, and human ELISA kits were used to detect possible CKD biomarkers. Results: The study’s findings showed that CTHRC1 correlates with key clinical markers of kidney function such as 24 h urine total protein, creatinine, urea, and uric acid. In addition, CTHRC1 demonstrated a strong significant difference (p ≤ 0.0001) between the CKD and control group. Conclusions: Our research demonstrates that the plasma level of CTHRC1 can distinguish between those with CKD and healthy patients. Plasma CTHRC1 levels may aid in the diagnosis of CKD given the current state of knowledge, and these results call for further investigation in a wider, more diverse patient group.
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5
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Dai D, Cheng Z, Feng S, Zhu Z, Yu J, Zhang W, Lu H, Zhang R, Zhu J. Quantitative Data-Independent Acquisition Mass Spectrometry Proteomics and Weighted Correlation Network Analysis of Plasma Samples for the Discovery of Chronic Kidney Disease-Specific Atherosclerosis Risk Factors. DNA Cell Biol 2022; 41:966-980. [PMID: 36255451 DOI: 10.1089/dna.2022.0200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chronic kidney disease (CKD) accelerates atherosclerosis. The mechanism of CKD-related atherosclerosis is complex, and CKD-specific risk factors may contribute to this process in addition to traditional risk factors such as hypertension, diabetes, and hypercholesterolemia. In the present study, to discover CKD-specific atherosclerosis risk factors, a total of 62 patients with different stages of kidney function were enrolled. All patients underwent coronary angiographies and the severity of coronary atherosclerosis was defined by the SYNTAX score. Patients were divided into different groups according to their kidney function levels and coronary atherosclerosis severity. Data-independent acquisition mass spectrometry was used to identify differentially expressed proteins (DEPs) in the plasma samples, and weighted correlation network analysis (WGCNA) was employed to identify significant protein modules and hub proteins related to CKD-specific atherosclerosis. The results showed that 10 DEPs associated with atherosclerosis were found in the comparative groups with modest and severe CKD. Through WGCNA, 1768 proteins were identified and 8 protein modules were established. Enrichment analyses of protein modules revealed functional clusters mainly associated with inflammation and the complement and coagulation cascade as atherosclerosis developed under CKD conditions. The results may help to better understand the mechanisms of CKD-related atherosclerosis and guide future research on developing treatments for CKD-related atherosclerosis.
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Affiliation(s)
- Daopeng Dai
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiwei Cheng
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics and Data Science, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Feng
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengbin Zhu
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiwei Yu
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenli Zhang
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Lu
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics and Data Science, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruiyan Zhang
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinzhou Zhu
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Kasprzak Ł, Twardawa M, Formanowicz P, Formanowicz D. The Mutual Contribution of 3-NT, IL-18, Albumin, and Phosphate Foreshadows Death of Hemodialyzed Patients in a 2-Year Follow-Up. Antioxidants (Basel) 2022; 11:antiox11020355. [PMID: 35204237 PMCID: PMC8868576 DOI: 10.3390/antiox11020355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023] Open
Abstract
Patients with chronic kidney disease (CKD), especially those who are hemodialyzed (HD), are at significantly high risk of contracting cardiovascular disease and having increased mortality. This study aimed to find potential death predictors, the measurement of which may reflect increased mortality in HD patients, and then combine the most promising ones in frames of a simple death risk assessment model. For this purpose, HD patients (n=71) with acute myocardial infarction in the last year (HD group) and healthy people (control group) as a comparative group (n=32) were included in the study. Various laboratory determinations and non-invasive cardiovascular tests were performed. Next, patients were followed for two years, and data on cardiovascular (CV) deaths were collected. On this basis, two HD groups were formed: patients who survived (HD-A, n=51) and patients who died (HD-D, n=20). To model HD mortality, 21 out of 90 potential variables collected or calculated from the raw data were selected. The best explanatory power (95.5%) was reached by a general linear model with four variables: interleukin 18, 3-nitrotyrosine, albumin, and phosphate. The interplay between immuno-inflammatory processes, nitrosative and oxidative stress, malnutrition, and calcium-phosphate disorders has been indicated to be essential in predicting CV-related mortality in studied HD patients. ClinicalTrials.gov Identifier: NCT05214872.
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Affiliation(s)
- Łukasz Kasprzak
- Department of Nephrology with Dialysis Unit, Provincial Hospital in Leszno, 64-100 Leszno, Poland;
| | - Mateusz Twardawa
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland; (M.T.); (P.F.)
- ICT Security Department, Poznan Supercomputing and Networking Center Affiliated to the Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-139 Poznan, Poland
| | - Piotr Formanowicz
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland; (M.T.); (P.F.)
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Dorota Formanowicz
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence:
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Cruz A, Condinho M, Carvalho B, Arraiano CM, Pobre V, Pinto SN. The Two Weapons against Bacterial Biofilms: Detection and Treatment. Antibiotics (Basel) 2021; 10:1482. [PMID: 34943694 PMCID: PMC8698905 DOI: 10.3390/antibiotics10121482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms are defined as complex aggregates of bacteria that grow attached to surfaces or are associated with interfaces. Bacteria within biofilms are embedded in a self-produced extracellular matrix made of polysaccharides, nucleic acids, and proteins. It is recognized that bacterial biofilms are responsible for the majority of microbial infections that occur in the human body, and that biofilm-related infections are extremely difficult to treat. This is related with the fact that microbial cells in biofilms exhibit increased resistance levels to antibiotics in comparison with planktonic (free-floating) cells. In the last years, the introduction into the market of novel compounds that can overcome the resistance to antimicrobial agents associated with biofilm infection has slowed down. If this situation is not altered, millions of lives are at risk, and this will also strongly affect the world economy. As such, research into the identification and eradication of biofilms is important for the future of human health. In this sense, this article provides an overview of techniques developed to detect and imaging biofilms as well as recent strategies that can be applied to treat biofilms during the several biofilm formation steps.
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Affiliation(s)
- Adriana Cruz
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Manuel Condinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Beatriz Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Sandra N. Pinto
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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8
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Applying Proteomics and Integrative "Omics" Strategies to Decipher the Chronic Kidney Disease-Related Atherosclerosis. Int J Mol Sci 2021; 22:ijms22147492. [PMID: 34299112 PMCID: PMC8305100 DOI: 10.3390/ijms22147492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Patients with chronic kidney disease (CKD) are at increased risk of atherosclerosis and premature mortality, mainly due to cardiovascular events. However, well-known risk factors, which promote “classical” atherosclerosis are alone insufficient to explain the high prevalence of atherosclerosis-related to CKD (CKD-A). The complexity of the molecular mechanisms underlying the acceleration of CKD-A is still to be defied. To obtain a holistic picture of these changes, comprehensive proteomic approaches have been developed including global protein profiling followed by functional bioinformatics analyses of dysregulated pathways. Furthermore, proteomics surveys in combination with other “omics” techniques, i.e., transcriptomics and metabolomics as well as physiological assays provide a solid ground for interpretation of observed phenomena in the context of disease pathology. This review discusses the comprehensive application of various “omics” approaches, with emphasis on proteomics, to tackle the molecular mechanisms underlying CKD-A progression. We summarize here the recent findings derived from global proteomic approaches and underline the potential of utilizing integrative systems biology, to gain a deeper insight into the pathogenesis of CKD-A and other disorders.
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9
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Coimbra S, Reis F, Valente MJ, Rocha S, Catarino C, Rocha-Pereira P, Sameiro-Faria M, Bronze-da-Rocha E, Belo L, Santos-Silva A. Subpopulations of High-Density Lipoprotein: Friends or Foes in Cardiovascular Disease Risk in Chronic Kidney Disease? Biomedicines 2021; 9:554. [PMID: 34065648 PMCID: PMC8157071 DOI: 10.3390/biomedicines9050554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022] Open
Abstract
Dyslipidemia is a major traditional risk factor for cardiovascular disease (CVD) in chronic kidney disease (CKD) patients, although the altered lipid profile does not explain the number and severity of CVD events. High-density lipoprotein (HDL) is a heterogeneous (size, composition, and functionality) population of particles with different atherogenic or atheroprotective properties. HDL-cholesterol concentrations per se may not entirely reflect a beneficial or a risk profile for CVD. Large HDL in CKD patients may have a unique proteome and lipid composition, impairing their cholesterol efflux capacity. This lack of HDL functionality may contribute to the paradoxical coexistence of increased large HDL and enhanced risk for CVD events. Moreover, CKD is associated with inflammation, oxidative stress, diabetes, and/or hypertension that are able to interfere with the anti-inflammatory, antioxidative, and antithrombotic properties of HDL subpopulations. How these changes interfere with HDL functions in CKD is still poorly understood. Further studies are warranted to fully clarify if different HDL subpopulations present different functionalities and/or atheroprotective effects. To achieve this goal, the standardization of techniques would be valuable.
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Affiliation(s)
- Susana Coimbra
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
- CESPU, Institute of Research and Advanced Training in Health Sciences and Technologies (IINFACTS), 4585-116 Gandra-Paredes, Portugal
| | - Flávio Reis
- Institute of Pharmacology & Experimental Therapeutics, & Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal;
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
| | - Maria João Valente
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
| | - Susana Rocha
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Cristina Catarino
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
| | - Petronila Rocha-Pereira
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
- Chemistry Department, University of Beira Interior, 6201-001 Covilhã, Portugal
| | - Maria Sameiro-Faria
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
- Hemodialysis Clinic Hospital Agostinho Ribeiro, 4610-106 Felgueiras, Portugal
| | - Elsa Bronze-da-Rocha
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
| | - Luís Belo
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
| | - Alice Santos-Silva
- UCIBIO\REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.J.V.); (C.C.); (P.R.-P.); (M.S.-F.); (E.B.-d.-R.); (L.B.); (A.S.-S.)
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10
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Zhou F, Luo Q, Han L, Shen G, Huang L, Ye H. Proteomics reveals urine apolipoprotein A-I as a potential biomarker of acute kidney injury following percutaneous coronary intervention in elderly patients. Exp Ther Med 2021; 22:745. [PMID: 34046095 PMCID: PMC8141962 DOI: 10.3892/etm.2021.10177] [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: 12/18/2019] [Accepted: 04/14/2021] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to investigate how changes in the lipid composition are involved in early stages of acute kidney injury (AKI) following percutaneous coronary intervention (PCI-AKI) in elderly patients. A prospective nested case-control study was performed. Alterations in the urine protein accumulation were investigated in patients with and without PCI-AKI using isobaric tags for relative and absolute quantitation (iTRAQ). In addition, differentially expressed proteins (DEPs) related to lipids were confirmed using parallel reaction monitoring (PRM)-based targeted proteomics. From the cohort of elderly patients (>60 years of age), 14 (12.28%) developed AKI within 48 h after PCI. No significant differences were detected between the AKI and control (CON) groups for serum creatinine at 24 h following treatment (P=0.27). Among the DEPs that overlapped in both the AKI-24 h/AKI-Pre (AKI group at 24 h post-PCI vs. pre-PCI) and AKI-24 h/CON-24 h groups (AKI group vs. CON group at 24 h post-PCI), only apolipoprotein A-I (apoA-I) was related to lipids, which displayed a significant upregulation in expression levels. The protein expression levels of apoA-I displayed a 5.98-fold increase at 24 h after PCI from the baseline and a 2.09-fold increase compared with the control group as determined using PRM, which exhibited a similar trend to the iTRAQ results. Using protein-protein interaction analyses, apoA-I was determined to be functionally linked to the complement and coagulation cascades, the renin-angiotensin system and the hypoxia-inducible factor-1 signaling pathway. Using the pathway analysis tool from the Kyoto Encyclopedia of Genes and Genomes, several pathways were identified to be associated with apoA-I, including fat digestion and absorption, vitamin digestion and absorption, as well as the peroxisome proliferator activated receptor signaling pathway. In conclusion, apoA-I may be a promising biomarker for the early diagnosis of PCI-AKI in elderly patients. The role of apoA-I in the pathobiology of PCI-AKI requires further exploration.
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Affiliation(s)
- Fangfang Zhou
- Department of Nephrology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
| | - Qun Luo
- Department of Nephrology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
| | - Lina Han
- Department of Nephrology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
| | - Gen Shen
- Department of Cardiology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
| | - Lulu Huang
- Department of Nephrology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
| | - Honghua Ye
- Department of Cardiology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010, P.R. China
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11
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Tracz J, Handschuh L, Lalowski M, Marczak Ł, Kostka-Jeziorny K, Perek B, Wanic-Kossowska M, Podkowińska A, Tykarski A, Formanowicz D, Luczak M. Proteomic Profiling of Leukocytes Reveals Dysregulation of Adhesion and Integrin Proteins in Chronic Kidney Disease-Related Atherosclerosis. J Proteome Res 2021; 20:3053-3067. [PMID: 33939431 DOI: 10.1021/acs.jproteome.0c00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A progressive loss of functional nephrons defines chronic kidney disease (CKD). Complications related to cardiovascular disease (CVD) are the principal causes of mortality in CKD; however, the acceleration of CVD in CKD remains unresolved. Our study used a complementary proteomic approach to assess mild and advanced CKD patients with different atherosclerosis stages and two groups of patients with different classical CVD progression but without renal dysfunction. We utilized a label-free approach based on LC-MS/MS and functional bioinformatic analyses to profile CKD and CVD leukocyte proteins. We revealed dysregulation of proteins involved in different phases of leukocytes' diapedesis process that is very pronounced in CKD's advanced stage. We also showed an upregulation of apoptosis-related proteins in CKD as compared to CVD. The differential abundance of selected proteins was validated by multiple reaction monitoring, ELISA, Western blotting, and at the mRNA level by ddPCR. An increased rate of apoptosis was then functionally confirmed on the cellular level. Hence, we suggest that the disturbances in leukocyte extravasation proteins may alter cell integrity and trigger cell death, as demonstrated by flow cytometry and microscopy analyses. Our proteomics data set has been deposited to the ProteomeXchange Consortium via the PRIDE repository with the data set identifier PXD018596.
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Affiliation(s)
- Joanna Tracz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Luiza Handschuh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Lalowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.,Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, 00100 Helsinki, Finland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Kostka-Jeziorny
- Department of Hypertension, Angiology and Internal Disease, Poznan University of Medical Sciences, Długa 1/2, 61-848, Poznan, Poland
| | - Bartłomiej Perek
- Department of Cardiac Surgery and Transplantology, Poznan University of Medical Sciences, Długa 1/2, 61-848, Poznan, Poland
| | - Maria Wanic-Kossowska
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznan, Poland
| | - Alina Podkowińska
- Dialysis Station Dravis sp. z o.o., Dojazd 34, 60-631 Poznan, Poland
| | - Andrzej Tykarski
- Department of Hypertension, Angiology and Internal Disease, Poznan University of Medical Sciences, Długa 1/2, 61-848, Poznan, Poland
| | - Dorota Formanowicz
- Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, Rokietnicka 8, 60-806 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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12
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Marczak L, Idkowiak J, Tracz J, Stobiecki M, Perek B, Kostka-Jeziorny K, Tykarski A, Wanic-Kossowska M, Borowski M, Osuch M, Formanowicz D, Luczak M. Mass Spectrometry-Based Lipidomics Reveals Differential Changes in the Accumulated Lipid Classes in Chronic Kidney Disease. Metabolites 2021; 11:275. [PMID: 33925471 PMCID: PMC8146808 DOI: 10.3390/metabo11050275] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic kidney disease (CKD) is characterized by the progressive loss of functional nephrons. Although cardiovascular disease (CVD) complications and atherosclerosis are the leading causes of morbidity and mortality in CKD, the mechanism by which the progression of CVD accelerates remains unclear. To reveal the molecular mechanisms associated with atherosclerosis linked to CKD, we applied a shotgun lipidomics approach fortified with standard laboratory analytical methods and gas chromatography-mass spectrometry technique on selected lipid components and precursors to analyze the plasma lipidome in CKD and classical CVD patients. The MS-based lipidome profiling revealed the upregulation of triacylglycerols in CKD and downregulation of cholesterol/cholesteryl esters, sphingomyelins, phosphatidylcholines, phosphatidylethanolamines and ceramides as compared to CVD group and controls. We have further observed a decreased abundance of seven fatty acids in CKD with strong inter-correlation. In contrast, the level of glycerol was elevated in CKD in comparison to all analyzed groups. Our results revealed the putative existence of a functional causative link-the low cholesterol level correlated with lower estimated glomerular filtration rate and kidney dysfunction that supports the postulated "reverse epidemiology" theory and suggest that the lipidomic background of atherosclerosis-related to CKD is unique and might be associated with other cellular factors, i.e., inflammation.
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Affiliation(s)
- Lukasz Marczak
- Department of Natural Products Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (J.I.); (M.S.)
| | - Jakub Idkowiak
- Department of Natural Products Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (J.I.); (M.S.)
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, 532 10 Pardubice, Czech Republic
| | - Joanna Tracz
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland;
| | - Maciej Stobiecki
- Department of Natural Products Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (J.I.); (M.S.)
| | - Bartłomiej Perek
- Department of Cardiac Surgery and Transplantology, Poznan University of Medical Sciences, 61-001 Poznan, Poland;
| | - Katarzyna Kostka-Jeziorny
- Department of Hypertension, Angiology and Internal Disease, Poznan University of Medical Sciences, 61-001 Poznan, Poland; (K.K.-J.); (A.T.)
| | - Andrzej Tykarski
- Department of Hypertension, Angiology and Internal Disease, Poznan University of Medical Sciences, 61-001 Poznan, Poland; (K.K.-J.); (A.T.)
| | - Maria Wanic-Kossowska
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland;
| | - Marcin Borowski
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland;
| | - Marcin Osuch
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland;
| | - Dorota Formanowicz
- Chair and Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
| | - Magdalena Luczak
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland;
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13
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Chen WL, Tain YL, Chen HE, Hsu CN. Cardiovascular Disease Risk in Children With Chronic Kidney Disease: Impact of Apolipoprotein C-II and Apolipoprotein C-III. Front Pediatr 2021; 9:706323. [PMID: 34458211 PMCID: PMC8397580 DOI: 10.3389/fped.2021.706323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/08/2021] [Indexed: 01/28/2023] Open
Abstract
Cardiovascular disease (CVD) is an evolving process that begins in the early stages of chronic kidney disease (CKD) in children. Several surrogate markers, such as ambulatory blood pressure monitoring (ABPM), left ventricular (LV) mass, and arterial stiffness assessment, allow for the early detection of subclinical CVD in pediatric CKD. Four groups of plasma samples (n = 3/group) from congenital anomalies of the kidney and urinary tract (CAKUT), as well as non-CAKUT patients with or without BP abnormalities, were studied to screen differentially expressed proteins using isobaric tags for relative and absolute protein quantification (iTRAQ)-based proteomics. As a result, 20 differentially expressed proteins associated with hypertension in children with CKD were discovered. Among them, apolipoprotein C-II (apoC-II) was found to have the highest abundance among the CKD patients with hypertension. As such, we hypothesized that apoC-II and apolipoprotein C-III (apoC-III) levels were related to BP abnormalities and CVD in children suffering from mild-to-moderate CKD. We examined their associations with surrogate markers of CV risk in 88 pediatric patients with CKD stages G1-G4. Children with CKD stages G2-G4 had a higher plasma apoC-II level than G1 patients (6.35 vs. 5.05 mg/dl, p < 0.05). We observed that ABPM abnormalities, LV mass, and arterial stiffness parameters were greater in CKD children who had stages G2-G4 than in those who had stage G1 (all p < 0.05). Plasma levels of apoC-II and apoC-III were positively correlated with total cholesterol, triglyceride, and low-density lipoprotein (LDL) (all p < 0.001). In multivariate linear regression analyses, apoC-II was correlated with a high LV mass index and an abnormal ABPM profile, and apoC-III was correlated with 24-h hypertension (r = 0.303, p = 0.003) and asleep hypertension (r = 0.379, p < 0.001). Early evaluations of apoC-II and apoC-III, ABPM, and surrogate markers of CV risk will aid in early preventative interventions to reduce the risk of CV in youths suffering from CKD.
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Affiliation(s)
- Wei-Ling Chen
- Division of Pediatric Nephrology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - You-Lin Tain
- Division of Pediatric Nephrology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Hung-En Chen
- Division of Pediatric Nephrology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Ning Hsu
- Department of Pharmacy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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14
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Romanova Y, Laikov A, Markelova M, Khadiullina R, Makseev A, Hasanova M, Rizvanov A, Khaiboullina S, Salafutdinov I. Proteomic Analysis of Human Serum from Patients with Chronic Kidney Disease. Biomolecules 2020; 10:biom10020257. [PMID: 32046176 PMCID: PMC7072325 DOI: 10.3390/biom10020257] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic kidney disease (CKD) is an important public health problem in the world. The aim of our research was to identify novel potential serum biomarkers of renal injury. ELISA assay showed that cytokines and chemokines IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12 (p70), IL-13, IL-15, IL-17, Eotaxin, FGFb, G-CSF, GM-CSF, IP-10, MCP-1, MIP-1α, MIP-1β, PDGF-1bb, RANTES, TNF-α and VEGF were significantly higher (R > 0.6, p value < 0.05) in the serum of patients with CKD compared to healthy subjects, and they were positively correlated with well-established markers (urea and creatinine). The multiple reaction monitoring (MRM) quantification method revealed that levels of HSP90B2, AAT, IGSF22, CUL5, PKCE, APOA4, APOE, APOA1, CCDC171, CCDC43, VIL1, Antigen KI-67, NKRF, APPBP2, CAPRI and most complement system proteins were increased in serum of CKD patients compared to the healthy group. Among complement system proteins, the C8G subunit was significantly decreased three-fold in patients with CKD. However, only AAT and HSP90B2 were positively correlated with well-established markers and, therefore, could be proposed as potential biomarkers for CKD.
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Affiliation(s)
- Yulia Romanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
- Correspondence: (Y.R.); (I.S.); Tel.: +7-927-418-90-02 (Y.R.); +7-917-867-43-60 (I.S.)
| | - Alexander Laikov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
| | - Maria Markelova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
| | - Rania Khadiullina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
| | - Alfiz Makseev
- Republican Clinical Hospital Ministry of Health Republic of Tatarstan, 420064 Kazan, Tatarstan, Russia; (A.M.); (M.H.)
| | - Milausha Hasanova
- Republican Clinical Hospital Ministry of Health Republic of Tatarstan, 420064 Kazan, Tatarstan, Russia; (A.M.); (M.H.)
- Department of Urology and Nephrology, Kazan State Medical Academy, 420012 Kazan, Tatarstan, Russia
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
| | - Svetlana Khaiboullina
- Department of Microbiology and Immunology, University of Nevada, Reno, NV 89557, USA;
| | - Ilnur Salafutdinov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Tartastan, Russia; (A.L.); (M.M.); (R.K.); (A.R.)
- Correspondence: (Y.R.); (I.S.); Tel.: +7-927-418-90-02 (Y.R.); +7-917-867-43-60 (I.S.)
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15
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Chen H, Lin H, Xu M, Xu G, Fang X, He L, Chen Z, Wu Z, Geng H. Quantitative Urinary Proteome Reveals Potential Biomarkers for Ureteropelvic Junction Obstruction. Proteomics Clin Appl 2018; 13:e1800101. [PMID: 30471240 DOI: 10.1002/prca.201800101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/08/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Honghao Chen
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Houwei Lin
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Maosheng Xu
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Guofeng Xu
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Xiaoliang Fang
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Lei He
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Zhoutong Chen
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
| | - Zhixiang Wu
- Department of Pediatric SurgeryXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Hongquan Geng
- Department of Pediatric UrologyXinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine 200092 Shanghai China
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16
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Analytical techniques for characterization of biological molecules - proteins and aptamers/oligonucleotides. Bioanalysis 2018; 11:103-117. [PMID: 30475073 DOI: 10.4155/bio-2018-0225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
With the advent of the high-throughput technologies and exciting times for biology, the discipline of analytical methodology is experiencing a surge in the growth and the scope. Over the years, multitude of analytical techniques have evolved from a work-intensive, low sensitivity and high volume of reagent and sample consumption endeavor to automated, better selectivity, lower limit of quantification and cost-effective techniques for biological research. In this review, we give an overview of the currently available wide range of cell-based and noncell based and structural based analytical techniques, their principle and biological applications. The analytical techniques discussed in this paper includes surface plasmon resonance, electrophoresis, enzyme linked immunosorbent assay, Western blotting, flow cytometry, fluorescence activated cell sorting, mass spectrometry, nuclear magnetic resonance and x-ray crystallography.
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17
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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18
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Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel) 2018; 9:E61. [PMID: 29370075 PMCID: PMC5852557 DOI: 10.3390/genes9020061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
A plethora of genetic association analyses have identified several genetic risk loci. Technological and statistical advancements have now led to the identification of not only common genetic variants, but also low-frequency variants, structural variants, and environmental factors, as well as multi-omics variations that affect the phenotypic variance of complex traits in a population, thus referred to as complex trait architecture. The concept of heritability, or the proportion of phenotypic variance due to genetic inheritance, has been studied for several decades, but its application is mainly in addressing the narrow sense heritability (or additive genetic component) from Genome-Wide Association Studies (GWAS). In this commentary, we reflect on our perspective on the complexity of understanding heritability for human traits in comparison to model organisms, highlighting another round of clues beyond GWAS and an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.
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Affiliation(s)
- Shefali Setia Verma
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marylyn D Ritchie
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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Zdarta A, Tracz J, Luczak M, Guzik U, Kaczorek E. Hydrocarbon-induced changes in proteins and fatty acids profiles of Raoultella ornithinolytica M03. J Proteomics 2017; 164:43-51. [DOI: 10.1016/j.jprot.2017.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Accepted: 05/31/2017] [Indexed: 01/04/2023]
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