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Lerink LJS, Sutton CW, Otten HG, Faro LL, Ploeg RJ, Lindeman JHN, Shaheed S. Using established biorepositories for emerging research questions: a feasibility study. Clin Proteomics 2024; 21:54. [PMID: 39154002 PMCID: PMC11330044 DOI: 10.1186/s12014-024-09504-6] [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: 04/24/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Proteomics and metabolomics offer substantial potential for advancing kidney transplant research by providing versatile opportunities for gaining insights into the biomolecular processes occurring in donors, recipients, and grafts. To achieve this, adequate quality and numbers of biological samples are required. Whilst access to donor samples is facilitated by initiatives such as the QUOD biobank, an adequately powered biobank allowing exploration of recipient-related aspects in long-term transplant outcomes is missing. Rich, yet unverified resources of recipient material are the serum repositories present in the immunological laboratories of kidney transplant centers that prospectively collect recipient sera for immunological monitoring. However, it is yet unsure whether these samples are also suitable for -omics applications, since such clinical samples are collected and stored by individual centers using non-uniform protocols and undergo an undocumented number of freeze-thaw cycles. Whilst these handling and storage aspects may affect individual proteins and metabolites, it was reasoned that incidental handling/storage artifacts will have a limited effect on a theoretical network (pathway) analysis. To test the potential of such long-term stored clinical serum samples for pathway profiling, we submitted these samples to discovery proteomics and metabolomics. METHODS A mass spectrometry-based shotgun discovery approach was used to obtain an overview of proteins and metabolites in clinical serum samples from the immunological laboratories of the Dutch PROCARE consortium. Parallel analyses were performed with material from the strictly protocolized QUOD biobank. RESULTS Following metabolomics, more than 800 compounds could be identified in both sample groups, of which 163 endogenous metabolites were found in samples from both biorepositories. Proteomics yielded more than 600 proteins in both groups. Despite the higher prevalence of fragments in the clinical, non-uniformly collected samples compared to the biobanked ones (42.5% vs 26.5% of their proteomes, respectively), these fragments could still be connected to their parent proteins. Next, the proteomic and metabolomic profiles were successfully mapped onto theoretical pathways through integrated pathway analysis, which showed significant enrichment of 79 pathways. CONCLUSIONS This feasibility study demonstrated that long-term stored serum samples from clinical biorepositories can be used for qualitative proteomic and metabolomic pathway analysis, a notion with far-reaching implications for all biomedical, long-term outcome-dependent research questions and studies focusing on rare events.
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Affiliation(s)
- Lente J S Lerink
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Surgery, Transplant Centre, Leiden University Medical Centre, Leiden, The Netherlands
| | | | | | - Letizia Lo Faro
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Rutger J Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Surgery, Transplant Centre, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jan H N Lindeman
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Surgery, Transplant Centre, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sadr Shaheed
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- Central Diagnostic Laboratory/Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
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Mizuno H, Murakami N. Multi-omics Approach in Kidney Transplant: Lessons Learned from COVID-19 Pandemic. CURRENT TRANSPLANTATION REPORTS 2023; 10:173-187. [PMID: 38152593 PMCID: PMC10751044 DOI: 10.1007/s40472-023-00410-8] [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] [Accepted: 08/09/2023] [Indexed: 12/29/2023]
Abstract
Purpose of Review Multi-omics approach has advanced our knowledge on transplantation-associated clinical outcomes, such as acute rejection and infection, and emerging omics data are becoming available in kidney transplant and COVID-19. Herein, we discuss updated findings of multi-omics data on kidney transplant outcomes, as well as COVID-19 and kidney transplant. Recent Findings Transcriptomics, proteomics, and metabolomics revealed various inflammation pathways associated with kidney transplantation-related outcomes and COVID-19. Although multi-omics data on kidney transplant and COVID-19 is limited, activation of innate immune pathways and suppression of adaptive immune pathways were observed in the active phase of COVID-19 in kidney transplant recipients. Summary Multi-omics analysis has led us to a deeper exploration and a more comprehensive understanding of key biological pathways in complex clinical settings, such as kidney transplantation and COVID-19. Future multi-omics analysis leveraging multi-center biobank collaborative will further advance our knowledge on the precise immunological responses to allograft and emerging pathogens.
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Affiliation(s)
- Hiroki Mizuno
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
- Dvision of Nephrology and Rheumatology, Toranomon Hospital, Tokyo, Japan
| | - Naoka Murakami
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
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Xiao N, Ruan S, Mo Q, Zhao M, Feng F. The Effect of Sodium Benzoate on Host Health: Insight into Physiological Indexes and Gut Microbiota. Foods 2023; 12:4081. [PMID: 38002138 PMCID: PMC10670719 DOI: 10.3390/foods12224081] [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: 10/04/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Sodium benzoate (SB) is a common food preservative widely used in the food industry. However, the effects of SB intake on host health at different stages were still unclear. Hence, we investigated the impact of SB with three concentrations (150 mg/kg, 500 mg/kg and 1000 mg/kg) and at three stages (intake for 5-weeks, intake for 10-weeks and removal for 5 weeks) on host health in normal mice. The results showed that SB intake for 5 weeks slightly changed gut microbiota composition, but it significantly increased TG (only 150 mg/kg and 1000 mg/kg) and blood glucose levels (only 500 mg/kg) and promoted the secretion of interleukin (IL)-1β and IL-6 (p < 0.01). However, SB intake for 10 weeks mostly maintained normal glucolipid metabolism; although, IL-1β (p < 0.01) and IL-6 (p < 0.05) levels were also significantly increased and positively regulated the gut microbiota by significantly increasing the relative abundance of Lactobacillus and significantly decreasing the relative abundance of Ileibacterium. Meanwhile, the safety of SB for host metabolism and gut microbiota was also confirmed via a fecal microbiota transplantation experiment. In addition, we found that SB removal after 10 weeks of intake significantly increased the levels of blood glucose, insulin and HOMA-IR index, which might be attributed to gut microbiota dysbiosis. Mechanistically, these positive effects and negative effects had no close relationship with the concentration of short-chain fatty acids in the gut, which might be associated with metabolites of SB or special bacterial strains. In short, this work provided positive evidence for the safety of SB consumption within the recommended range.
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Affiliation(s)
- Nanhai Xiao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (N.X.); (S.R.); (Q.M.); (M.Z.)
| | - Shengyue Ruan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (N.X.); (S.R.); (Q.M.); (M.Z.)
| | - Qiufen Mo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (N.X.); (S.R.); (Q.M.); (M.Z.)
| | - Minjie Zhao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (N.X.); (S.R.); (Q.M.); (M.Z.)
| | - Fengqin Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (N.X.); (S.R.); (Q.M.); (M.Z.)
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou 450001, China
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Iske J, Cao Y, Roesel MJ, Shen Z, Nian Y. Metabolic reprogramming of myeloid-derived suppressor cells in the context of organ transplantation. Cytotherapy 2023; 25:789-797. [PMID: 37204374 DOI: 10.1016/j.jcyt.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 05/20/2023]
Abstract
Myeloid-derived suppressor cells (MDSCs) are naturally occurring leukocytes that develop from immature myeloid cells under inflammatory conditions that were discovered initially in the context of tumor immunity. Because of their robust immune inhibitory activities, there has been growing interest in MDSC-based cellular therapies for transplant tolerance induction. Indeed, various pre-clinical studies have introduced in vivo expansion or adoptive transfer of MDSC as a promising therapeutic strategy leading to a profound extension of allograft survival due to suppression of alloreactive T cells. However, several limitations of cellular therapies using MDSCs remain to be addressed, including their heterogeneous nature and limited expansion capacity. Metabolic reprogramming plays a crucial role for differentiation, proliferation and effector function of immune cells. Notably, recent reports have focused on a distinct metabolic phenotype underlying the differentiation of MDSCs in an inflammatory microenvironment representing a regulatory target. A better understanding of the metabolic reprogramming of MDSCs may thus provide novel insights for MDSC-based treatment approaches in transplantation. In this review, we will summarize recent, interdisciplinary findings on MDSCs metabolic reprogramming, dissect the underlying molecular mechanisms and discuss the relevance for potential treatment approaches in solid-organ transplantation.
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Affiliation(s)
- Jasper Iske
- Department of Cardiothoracic and Vascular Surgery, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yu Cao
- Research Institute of Transplant Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Maximilian J Roesel
- Department of Cardiothoracic and Vascular Surgery, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Zhongyang Shen
- Research Institute of Transplant Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Yeqi Nian
- Research Institute of Transplant Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China.
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Hu C, Song X, Shao Z, Liu Y, Wang J, Sun B. Untargeted Metabolite Profiling of Adipose Tissue in Rats Exposed to Mepiquat. Foods 2023; 12:867. [PMID: 36832941 PMCID: PMC9956293 DOI: 10.3390/foods12040867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Mepiquat (Mep) is a contaminant produced by Maillard reaction with reducing sugar, free lysine and an alkylating agent under typical roasting conditions, particularly in the range of 200-240 °C. It has been reported that exposure to Mep is harmful to rats. However, its metabolic mechanism is still not clear. In this study, untargeted metabolomics was used to reveal the effect of Mep on the metabolic profile of adipose tissue in Sprague-Dawley rats. Twenty-six differential metabolites were screened out. Eight major perturbed metabolic pathways were found, which were linoleic acid metabolism, Phenylalanine, tyrosine, and tryptophan biosynthesis, phenylalanine metabolism, arachidonic acid metabolism, Glycine, serine, and threonine metabolism, glycerolipid metabolism, Alanine, aspartate, and glutamate metabolism, and glyoxylate and dicarboxylic acid metabolism. This study lays a solid foundation for clarifying the toxic mechanism of Mep.
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Affiliation(s)
| | | | | | | | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Laboratory for Food Quality and Safety, Beijing Technology and Business University (BTBU), 11 Fucheng Road, Beijing 100048, China
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Gao Z, Zhou W, Lv X, Wang X. Metabolomics as a Critical Tool for Studying Clinical Surgery. Crit Rev Anal Chem 2023; 54:2245-2258. [PMID: 36592066 DOI: 10.1080/10408347.2022.2162810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metabolomics enables the analysis of metabolites within an organism, which offers the closest direct measurement of the physiological activity of the organism, and has advanced efforts to characterize metabolic states, identify biomarkers, and investigate metabolic pathways. A high degree of innovation in analytical techniques has promoted the application of metabolomics, especially in the study of clinical surgery. Metabolomics can be employed as a clinical testing method to maximize therapeutic outcomes, and has been applied in rapid diagnosis of diseases, timely postoperative monitoring, prognostic assessment, and personalized medicine. This review focuses on the use of mass spectrometry and nuclear magnetic resonance-based metabolomics in clinical surgery, including identifying metabolic changes before and after surgery, finding disease-associated biomarkers, and exploring the potential of personalized therapy. Challenges and opportunities of metabolomics in organ transplantation are also discussed, with a particular emphasis on metabolomics in donor organ evaluation and protection, prognostic outcome prediction, as well as postoperative adverse reaction monitoring. In the end, current limitations of metabolomics in clinical surgery and future research directions are presented.
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Affiliation(s)
- Zhenye Gao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenxiu Zhou
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xiaoyuan Lv
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xin Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, P. R. China
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7
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De Favari Signini É, Castro A, Rehder-Santos P, Cristina Millan-Mattos J, Magalhães de Oliveira J, Minatel V, Bianca Falasco Pantoni C, Sobreiro Selistre de Araújo H, Fabrizzi F, Porta A, Gilberto Ferreira A, Vincenzi Oliveira R, Maria Catai A. Integrative perspective of the healthy aging process considering the metabolome, cardiac autonomic modulation and cardiorespiratory fitness evaluated in age groups. Sci Rep 2022; 12:21314. [PMID: 36494472 PMCID: PMC9734749 DOI: 10.1038/s41598-022-25747-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The aging process causes changes at all organic levels. Although metabolism, cardiac autonomic modulation (CAM), and cardiorespiratory fitness (CRF) are widely studied as a function of age, they are mainly studied in isolation, thus making it difficult to perceive their concomitant variations. This study aimed to investigate the integrated changes that occur in the metabolome, CAM, and CRF throughout aging in apparently healthy individuals. The subjects (n = 118) were divided into five groups according to age (20-29, 30-39, 40-49, 50-59, and 60-70 years old) and underwent blood collection, autonomic assessment, and a cardiopulmonary exercise test for metabolomics analysis using mass spectrometry and nuclear magnetic resonance, cardiac autonomic modulation analysis, and CRF by peak oxygen consumption analysis, respectively. The Tukey's post hoc and effect size with confidence interval were used for variables with a significant one-way ANOVA effect (P < 0.01). The main changes were in the oldest age group, where the CRF, valine, leucine, isoleucine, 3-hydroxyisobutyrate, and CAM reduced and hippuric acid increased. The results suggest significant changes in the metabolome, CAM, and CRF after the age of sixty as a consequence of aging impairments, but with some changes in the metabolic profile that may be favorable to mitigate the aging deleterious effects.
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Affiliation(s)
- Étore De Favari Signini
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Alex Castro
- grid.411247.50000 0001 2163 588XDepartment of Chemistry, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Patrícia Rehder-Santos
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Juliana Cristina Millan-Mattos
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Juliana Magalhães de Oliveira
- grid.411247.50000 0001 2163 588XDepartment of Chemistry, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Vinicius Minatel
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Camila Bianca Falasco Pantoni
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil ,grid.411247.50000 0001 2163 588XDepartment of Gerontology, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | | | - Fernando Fabrizzi
- Penápolis Educational Foundation (FUNEPE), Penápolis, São Paulo Brazil
| | - Alberto Porta
- grid.4708.b0000 0004 1757 2822Department of Biomedical Sciences for Health, University of Milan, Milan, Italy ,Department of Cardiothoracic, Vascular Anesthesia and Intensive Care, Policlinico San Donato, San Donato Milanese, Milan Italy
| | - Antônio Gilberto Ferreira
- grid.411247.50000 0001 2163 588XDepartment of Chemistry, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Regina Vincenzi Oliveira
- grid.411247.50000 0001 2163 588XDepartment of Chemistry, Federal University of São Carlos, São Carlos, São Paulo Brazil
| | - Aparecida Maria Catai
- grid.411247.50000 0001 2163 588XDepartment of Physiotherapy, Federal University of São Carlos, São Carlos, São Paulo Brazil ,grid.411247.50000 0001 2163 588XCardiovascular Physical Therapy Laboratory, Department of Physical Therapy, Nucleus of Research in Physical Exercise, Federal University of São Carlos, Via Washington Luiz, Km 235, CP: 676, São Carlos, SP 13565-905 Brazil
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8
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Lepoittevin M, Giraud S, Kerforne T, Allain G, Thuillier R, Hauet T. How to improve results after DCD (donation after circulation death). Presse Med 2022; 51:104143. [PMID: 36216034 DOI: 10.1016/j.lpm.2022.104143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
The shortage of organs for transplantation has led health professionals to look for alternative sources of donors. One of the avenues concerns donors who have died after circulatory arrest. This is a special situation because the organs from these donors are exposed to warm ischaemia-reperfusion lesions that are unavoidable during the journey of the organs from the donor to the moment of transplantation in the recipient. We will address and discuss the key issues from the perspective of team organization, legislation and its evolution, and the ethical framework. In a second part, the avenues to improve the quality of organs will be presented following the itinerary of the organs between the donor and the recipient. The important moments from the point of view of therapeutic strategy will be put into perspective. New connections between key players involved in pathophysiological mechanisms and implications for innate immunity and injury processes are among the avenues to explore. Technological developments to improve the quality of organs from these recipients will be analyzed, such as perfusion techniques with new modalities of temperatures and oxygenation. New molecules are being investigated for their potential role in protecting these organs and an analysis of potential prospects will be proposed. Finally, the important perspectives that seem to be favored will be discussed in order to reposition the use of deceased donors after circulatory arrest. The use of these organs has become a routine procedure and improving their quality and providing the means for their evaluation is absolutely inevitable.
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Affiliation(s)
- Maryne Lepoittevin
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France
| | - Sébastien Giraud
- Unité UMR U1082, F-86000 Poitiers, France; Service de Biochimie, Pôle Biospharm, Centre Hospitalier Universitaire, 2 rue de la Milétrie, CS 90577, 86021 Poitiers Cedex, France
| | - Thomas Kerforne
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; CHU Poitiers, Service de Réanimation Chirurgie Cardio-Thoracique et Vasculaire, Coordination des P.M.O., F-86021 Poitiers, France
| | - Géraldine Allain
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; CHU Poitiers, Service de Chirurgie Cardiothoracique et Vasculaire, F-86021 Poitiers, France
| | - Raphaël Thuillier
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; Service de Biochimie, Pôle Biospharm, Centre Hospitalier Universitaire, 2 rue de la Milétrie, CS 90577, 86021 Poitiers Cedex, France
| | - Thierry Hauet
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; Fédération Hospitalo-Universitaire « Survival Optimization in Organ Transplantation », CHU de Poitiers, 2 rue de la Milétrie - CS 90577, 86021 Poitiers Cedex, France.
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Molecular Markers of Kidney Transplantation Outcome: Current Omics Tools and Future Developments. Int J Mol Sci 2022; 23:ijms23116318. [PMID: 35682996 PMCID: PMC9181061 DOI: 10.3390/ijms23116318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
Purpose of review: The emerging field of molecular predictive medicine is aiming to change the traditional medical approach in renal transplantation. Many studies have explored potential biomarker molecules with predictive properties in renal transplantation, issued from omics research. Herein, we review the biomarker molecules of four technologies (i.e., Genomics, Transcriptomics, Proteomics, and Metabolomics) associated with favorable kidney transplant outcomes. Recent findings: Several panels of molecules have been associated with the outcome that the majority of markers are related to inflammation and immune response; although. other molecular ontologies are also represented, such as proteasome, growth, regeneration, and drug metabolism. Throughout this review, we highlight the lack of properly validated statistical demonstration. Indeed, the most preeminent molecular panels either remain at the limited size study stage or are not confirmed during large-scale studies. At the core of this problem, we identify the methodological shortcomings and propose a comprehensive workflow for discovery and validation of molecular biomarkers that aims to improve the relevance of these tools in the future. Summary: Overall, adopting a patient management through omics approach could bring remarkable improvement to transplantation success. An increased effort and investment between scientists, medical biologists, and clinicians seem to be the path toward a proper solution.
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Debik J, Sangermani M, Wang F, Madssen TS, Giskeødegård GF. Multivariate analysis of NMR-based metabolomic data. NMR IN BIOMEDICINE 2022; 35:e4638. [PMID: 34738674 DOI: 10.1002/nbm.4638] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows for simultaneous detection of a wide range of metabolites and lipids. As metabolites act together in complex metabolic networks, they are often highly correlated, and optimal biological insight is achieved when using methods that take the correlation into account. For this reason, latent-variable-based methods, such as principal component analysis and partial least-squares discriminant analysis, are widely used in metabolomic studies. However, with increasing availability of larger population cohorts, and a shift from analysis of spectral data to using quantified metabolite levels, both more traditional statistical approaches and alternative machine learning methods have become more widely used. This review aims at providing an overview of the current state-of-the-art multivariate methods for the analysis of NMR-based metabolomic data as well as alternative methods, highlighting their strengths and limitations.
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Affiliation(s)
- Julia Debik
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Matteo Sangermani
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Feng Wang
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital HF, Trondheim, Norway
| | - Torfinn S Madssen
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
| | - Guro F Giskeødegård
- Clinic of Surgery, St. Olavs Hospital HF, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
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Paluszkiewicz P, Martuszewski A, Zaręba N, Wala K, Banasik M, Kepinska M. The Application of Nanoparticles in Diagnosis and Treatment of Kidney Diseases. Int J Mol Sci 2021; 23:ijms23010131. [PMID: 35008556 PMCID: PMC8745391 DOI: 10.3390/ijms23010131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Nanomedicine is currently showing great promise for new methods of diagnosing and treating many diseases, particularly in kidney disease and transplantation. The unique properties of nanoparticles arise from the diversity of size effects, used to design targeted nanoparticles for specific cells or tissues, taking renal clearance and tubular secretion mechanisms into account. The design of surface particles on nanoparticles offers a wide range of possibilities, among which antibodies play an important role. Nanoparticles find applications in encapsulated drug delivery systems containing immunosuppressants and other drugs, in imaging, gene therapies and many other branches of medicine. They have the potential to revolutionize kidney transplantation by reducing and preventing ischemia-reperfusion injury, more efficiently delivering drugs to the graft site while avoiding systemic effects, accurately localizing and visualising the diseased site and enabling continuous monitoring of graft function. So far, there are known nanoparticles with no toxic effects on human tissue, although further studies are still needed to confirm their safety.
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Affiliation(s)
- Patrycja Paluszkiewicz
- Department of Emergency Medical Service, Wroclaw Medical University, Bartla 5, 50-367 Wroclaw, Poland;
| | - Adrian Martuszewski
- Department of Population Health, Division of Environmental Health and Occupational Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 7, 50-368 Wroclaw, Poland;
| | - Natalia Zaręba
- Department of Pharmaceutical Biochemistry, Division of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
| | - Kamila Wala
- Faculty of Medicine, Wroclaw Medical University, Pasteura 1, 50-367 Wroclaw, Poland;
| | - Mirosław Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland
- Correspondence: (M.B.); (M.K.); Tel.: +48-71-733-2500 (M.B.); +48-71-784-0171 (M.K.)
| | - Marta Kepinska
- Department of Pharmaceutical Biochemistry, Division of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wrocław, Poland;
- Correspondence: (M.B.); (M.K.); Tel.: +48-71-733-2500 (M.B.); +48-71-784-0171 (M.K.)
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Ma C, He J, Lai L, Chen Y, Xue W, Chen J, Dai W, Tang D, Yan Q, Dai Y. Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation. Mol Omics 2021; 17:985-996. [PMID: 34676841 DOI: 10.1039/d1mo00279a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Renal transplantation is the most effective treatment for end-stage renal disease, but the long-term prognosis of organs after transplantation is not ideal. In recent years, the importance of gut microbes and metabolites in the study of disease mechanisms has gradually received attention. However, the coordination between gut microbes and the metabolism of renal transplant patients needs further study. We integrated 16s sequencing and metabolomics data to describe the changes in the serum and fecal metabolites of renal transplant patients. Our data revealed that the gut microbial diversity decreased and the relative abundance of many bacteria, such as Enterococcus and Streptococcus, significantly changed after transplantation. In addition, a large number of amino acids and peptides in serum and feces significantly changed, suggesting an abnormal amino acid metabolism after transplantation. Spearman's correlation analysis revealed the changes in the co-metabolism pattern between gut microbes and the host metabolism after transplantation. Furthermore, Enterococcus was found to be correlated with renal functions and metabolites reflecting renal damage. This study provides potential gut microbes and metabolites impacting renal health, which helps in understanding the renal damage in patients with kidney transplantation.
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Affiliation(s)
- Chiyu Ma
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Jingquan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Liusheng Lai
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Yumei Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Wen Xue
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Jieping Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Donge Tang
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Qiang Yan
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China.
| | - Yong Dai
- Guangxi Key Laboratory of Metabolic Disease Research, Nephrology Department, Central Laboratory of Guilin, NO. 924 Hospital, Guilin, 541002, China. .,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
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Schultheiss UT, Kosch R, Kotsis F, Altenbuchinger M, Zacharias HU. Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses. Metabolites 2021; 11:460. [PMID: 34357354 PMCID: PMC8304377 DOI: 10.3390/metabo11070460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Kidney diseases still pose one of the biggest challenges for global health, and their heterogeneity and often high comorbidity load seriously hinders the unraveling of their underlying pathomechanisms and the delivery of optimal patient care. Metabolomics, the quantitative study of small organic compounds, called metabolites, in a biological specimen, is gaining more and more importance in nephrology research. Conducting a metabolomics study in human kidney disease cohorts, however, requires thorough knowledge about the key workflow steps: study planning, sample collection, metabolomics data acquisition and preprocessing, statistical/bioinformatics data analysis, and results interpretation within a biomedical context. This review provides a guide for future metabolomics studies in human kidney disease cohorts. We will offer an overview of important a priori considerations for metabolomics cohort studies, available analytical as well as statistical/bioinformatics data analysis techniques, and subsequent interpretation of metabolic findings. We will further point out potential research questions for metabolomics studies in the context of kidney diseases and summarize the main results and data availability of important studies already conducted in this field.
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Affiliation(s)
- Ulla T. Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Robin Kosch
- Computational Biology, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany; (U.T.S.); (F.K.)
- Department of Medicine IV—Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Altenbuchinger
- Institute of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany;
| | - Helena U. Zacharias
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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Buszewska-Forajta M, Pomastowski P, Monedeiro F, Walczak-Skierska J, Markuszewski M, Matuszewski M, Markuszewski MJ, Buszewski B. Lipidomics as a Diagnostic Tool for Prostate Cancer. Cancers (Basel) 2021; 13:cancers13092000. [PMID: 33919225 PMCID: PMC8122642 DOI: 10.3390/cancers13092000] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 01/31/2023] Open
Abstract
The main goal of this study was to explore the phospholipid alterations associated with the development of prostate cancer (PCa) using two imaging methods: matrix-assisted laser desorption ionization with time-of-flight mass spectrometer (MALDI-TOF/MS), and electrospray ionization with triple quadrupole mass spectrometer (ESI-QqQ/MS). For this purpose, samples of PCa tissue (n = 40) were evaluated in comparison to the controls (n = 40). As a result, few classes of compounds, namely phosphatidylcholines (PCs), lysophosphatidylcholines (LPCs), sphingomyelins (SMs), and phosphatidylethanolamines (PEs), were determined. The obtained results were evaluated by univariate (Mann-Whitney U-test) and multivariate statistical analysis (principal component analysis, correlation analysis, volcano plot, artificial neural network, and random forest algorithm), in order to select the most discriminative features and to search for the relationships between the responses of these groups of substances, also in terms of the used analytical technique. Based on previous literature and our results, it can be assumed that PCa is linked with both the synthesis of fatty acids and lipid oxidation. Among the compounds, phospholipids, namely PC 16:0/16:1, PC 16:0/18:2, PC 18:0/22:5, PC 18:1/18:2, PC 18:1/20:0, PC 18:1/20:4, and SM d18:1/24:0, were assigned as metabolites with the best discriminative power for the tested groups. Based on the results, lipidomics can be found as alternative diagnostic tool for CaP diagnosis.
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Affiliation(s)
- Magdalena Buszewska-Forajta
- Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy, Medical University of Gdańsk, Aleja Generała Józefa Hallera 107, 80-416 Gdańsk, Poland;
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Toruń, Poland
- Correspondence: ; Tel.: +44-(58)-3491493
| | - Paweł Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (P.P.); (F.M.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Fernanda Monedeiro
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (P.P.); (F.M.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Justyna Walczak-Skierska
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland;
| | - Marcin Markuszewski
- Department of Urology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214 Gdańsk, Poland; (M.M.); (M.M.)
| | - Marcin Matuszewski
- Department of Urology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214 Gdańsk, Poland; (M.M.); (M.M.)
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy, Medical University of Gdańsk, Aleja Generała Józefa Hallera 107, 80-416 Gdańsk, Poland;
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (P.P.); (F.M.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland;
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Martuszewski A, Paluszkiewicz P, Król M, Banasik M, Kepinska M. Donor-Derived Cell-Free DNA in Kidney Transplantation as a Potential Rejection Biomarker: A Systematic Literature Review. J Clin Med 2021; 10:jcm10020193. [PMID: 33430458 PMCID: PMC7827757 DOI: 10.3390/jcm10020193] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Kidney transplantation (KTx) is the best treatment method for end-stage kidney disease. KTx improves the patient's quality of life and prolongs their survival time; however, not all patients benefit fully from the transplantation procedure. For some patients, a problem is the premature loss of graft function due to immunological or non-immunological factors. Circulating cell-free DNA (cfDNA) is degraded deoxyribonucleic acid fragments that are released into the blood and other body fluids. Donor-derived cell-free DNA (dd-cfDNA) is cfDNA that is exogenous to the patient and comes from a transplanted organ. As opposed to an invasive biopsy, dd-cfDNA can be detected by a non-invasive analysis of a sample. The increase in dd-cfDNA concentration occurs even before the creatinine level starts rising, which may enable early diagnosis of transplant injury and adequate treatment to avoid premature graft loss. In this paper, we summarise the latest promising results related to cfDNA in transplant patients.
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Affiliation(s)
- Adrian Martuszewski
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Patrycja Paluszkiewicz
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Magdalena Król
- Students Scientific Association, Department of Biomedical and Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Mirosław Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (A.M.); (P.P.); (M.B.)
| | - Marta Kepinska
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
- Correspondence: ; Tel.: +48-71-784-0171
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