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Glavan MR, Socaciu C, Socaciu AI, Gadalean F, Cretu OM, Vlad A, Muntean DM, Bob F, Milas O, Suteanu A, Jianu DC, Stefan M, Balint L, Ienciu S, Petrica L. Untargeted Metabolomics by Ultra-High-Performance Liquid Chromatography Coupled with Electrospray Ionization-Quadrupole-Time of Flight-Mass Spectrometry Analysis Identifies a Specific Metabolomic Profile in Patients with Early Chronic Kidney Disease. Biomedicines 2023; 11:biomedicines11041057. [PMID: 37189675 DOI: 10.3390/biomedicines11041057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Chronic kidney disease (CKD) has emerged as one of the most progressive diseases with increased mortality and morbidity. Metabolomics offers new insights into CKD pathogenesis and the discovery of new biomarkers for the early diagnosis of CKD. The aim of this cross-sectional study was to assess metabolomic profiling of serum and urine samples obtained from CKD patients. Untargeted metabolomics followed by multivariate and univariate analysis of blood and urine samples from 88 patients with CKD, staged by estimated glomerular filtration rate (eGFR), and 20 healthy control subjects was performed using ultra-high-performance liquid chromatography coupled with electrospray ionization-quadrupole-time of flight-mass spectrometry. Serum levels of Oleoyl glycine, alpha-lipoic acid, Propylthiouracil, and L-cysteine correlated directly with eGFR. Negative correlations were observed between serum 5-Hydroxyindoleacetic acid, Phenylalanine, Pyridoxamine, Cysteinyl glycine, Propenoylcarnitine, Uridine, and All-trans retinoic acid levels and eGFR. In urine samples, the majority of molecules were increased in patients with advanced CKD as compared with early CKD patients and controls. Amino acids, antioxidants, uremic toxins, acylcarnitines, and tryptophane metabolites were found in all CKD stages. Their dual variations in serum and urine may explain their impact on both glomerular and tubular structures, even in the early stages of CKD. Patients with CKD display a specific metabolomic profile. Since this paper represents a pilot study, future research is needed to confirm our findings that metabolites can serve as indicators of early CKD.
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Affiliation(s)
- Mihaela-Roxana Glavan
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Carmen Socaciu
- Research Center for Applied Biotechnology and Molecular Therapy BIODIATECH, SC Proplanta, 400478 Cluj-Napoca, Romania
| | - Andreea Iulia Socaciu
- Department of Occupational Health, University of Medicine and Pharmacy “Iuliu Haţieganu”, 400347 Cluj-Napoca, Romania
| | - Florica Gadalean
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Octavian M. Cretu
- Department of Surgery—Surgical Semiotics, “Victor Babeş” University of Medicine and Pharmacy, 300041 Timişoara, Romania
| | - Adrian Vlad
- Department of Internal Medicine II—Diabetes and Metabolic Diseases, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Danina M. Muntean
- Department of Functional Sciences—Pathophysiology, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Center for Translational Research and Systems Medicine, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Flaviu Bob
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Oana Milas
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Anca Suteanu
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Dragos Catalin Jianu
- Deptartment of Neurosciences—Neurology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Cognitive Research in Neuropsychiatric Pathology, Clinical County Emergency Hospital, Victor Babeș” University of Medicine and Pharmacy, 300723 Timișoara, Romania
| | - Maria Stefan
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Lavinia Balint
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Silvia Ienciu
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
| | - Ligia Petrica
- Department of Internal Medicine II—Nephrology, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
- Centre for Molecular Research in Nephrology and Vascular Disease, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy, 300041 Timișoara, Romania
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2
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Correia MJ, Pimpão AB, Fernandes DGF, Morello J, Sequeira CO, Calado J, Antunes AMM, Almeida MS, Branco P, Monteiro EC, Vicente JB, Serpa J, Pereira SA. Cysteine as a Multifaceted Player in Kidney, the Cysteine-Related Thiolome and Its Implications for Precision Medicine. Molecules 2022; 27:1416. [PMID: 35209204 PMCID: PMC8874463 DOI: 10.3390/molecules27041416] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
In this review encouraged by original data, we first provided in vivo evidence that the kidney, comparative to the liver or brain, is an organ particularly rich in cysteine. In the kidney, the total availability of cysteine was higher in cortex tissue than in the medulla and distributed in free reduced, free oxidized and protein-bound fractions (in descending order). Next, we provided a comprehensive integrated review on the evidence that supports the reliance on cysteine of the kidney beyond cysteine antioxidant properties, highlighting the relevance of cysteine and its renal metabolism in the control of cysteine excess in the body as a pivotal source of metabolites to kidney biomass and bioenergetics and a promoter of adaptive responses to stressors. This view might translate into novel perspectives on the mechanisms of kidney function and blood pressure regulation and on clinical implications of the cysteine-related thiolome as a tool in precision medicine.
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Affiliation(s)
- Maria João Correia
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - António B. Pimpão
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Dalila G. F. Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), 2780-157 Oeiras, Portugal; (D.G.F.F.); (J.B.V.)
| | - Judit Morello
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Catarina O. Sequeira
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - Joaquim Calado
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal;
- Nephrology Department, Centro Hospitalar Universitário de Lisboa Central, 1069-166 Lisboa, Portugal
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, 1049-001 Lisboa, Portugal;
| | - Manuel S. Almeida
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Hospital de Santa Cruz, Centro Hospitalar de Lisboa Ocidental, 2790-134 Carnaxide, Portugal
| | - Patrícia Branco
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Hospital de Santa Cruz, Centro Hospitalar de Lisboa Ocidental, 2790-134 Carnaxide, Portugal
| | - Emília C. Monteiro
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), 2780-157 Oeiras, Portugal; (D.G.F.F.); (J.B.V.)
| | - Jacinta Serpa
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), 1099-023 Lisboa, Portugal
| | - Sofia A. Pereira
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal; (M.J.C.); (A.B.P.); (J.M.); (C.O.S.); (M.S.A.); (P.B.); (E.C.M.); (J.S.)
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Abstract
Cysteine is a conditionally essential amino acid required for the synthesis of proteins and many important intracellular metabolites. Cysteine depletion can trigger iron-dependent nonapoptotic cell death-ferroptosis. Despite this, cysteine itself is normally maintained at relatively low levels within the cell, and many mechanisms that could act to buffer cysteine depletion do not appear to be especially effective or active, at least in cancer cells. How do we reconcile these seemingly paradoxical features? Here, we describe the regulation of cysteine and its contribution to ferroptosis and speculate about how the levels of this amino acid are controlled to govern nonapoptotic cell death.
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Affiliation(s)
| | - Scott J. Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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Na I, Meng F, Kurgan L, Uversky VN. Autophagy-related intrinsically disordered proteins in intra-nuclear compartments. MOLECULAR BIOSYSTEMS 2017; 12:2798-817. [PMID: 27377881 DOI: 10.1039/c6mb00069j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent analyses indicated that autophagy can be regulated via some nuclear transcriptional networks and many important players in the autophagy and other forms of programmed cell death are known to be intrinsically disordered. To this end, we analyzed similarities and differences in the intrinsic disorder distribution of nuclear and non-nuclear proteins related to autophagy. We also looked at the peculiarities of the distribution of the intrinsically disordered autophagy-related proteins in various intra-nuclear organelles, such as the nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinucleolar compartment. This analysis revealed that the autophagy-related proteins constitute about 2.5% of the non-nuclear proteins and 3.3% of the nuclear proteins, which corresponds to a substantial enrichment by about 32% in the nucleus. Curiously, although, in general, the autophagy-related proteins share similar characteristics of disorder with a generic set of all non-nuclear proteins, chromatin and nuclear speckles are enriched in the intrinsically disordered autophagy proteins (29 and 37% of these proteins are disordered, respectively) and have high disorder content at 0.24 and 0.27, respectively. Therefore, our data suggest that some of the nuclear disordered proteins may play important roles in autophagy.
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Affiliation(s)
- Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Fanchi Meng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23219, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA. and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia and Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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Arutyunov D, Schmalhausen E, Orlov V, Rahuel-Clermont S, Nagradova N, Branlant G, Muronetz V. An unusual effect of NADP+ on the thermostability of the nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans. Biochem Cell Biol 2013; 91:295-302. [PMID: 24032678 DOI: 10.1139/bcb-2012-0104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Adiabatic differential scanning calorimetry was used to investigate the effect of NADP+ on the irreversible thermal denaturation of the nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Streptococcus mutans. The GAPN-NADP+ binary complex showed a strongly decreased thermal stability, with a difference of about 20 °C between the temperatures of the thermal transition peak maxima of the complex and the free protein. This finding was similar to the previously described thermal destabilization of GAPN upon binding of inorganic phosphate to the substrate binding site and can be interpreted as the shift of the equilibrium between 2 conformers of tetrameric GAPN upon addition of the coenzyme. Single amino acid substitution, known to abolish the NADP+ binding, cancelled the calorimetric effect of the coenzyme. GAPN thermal inactivation was considerably decelerated in the presence of NADP+ showing that the apparent change in stability of the active centre can be the opposite to that of the whole protein molecule. NADP+ could also reactivate the inactive GAPN* species, obtained by the heating of the apoenzyme below the thermal denaturation transition temperature. These effects may reflect a mechanism that provides GAPN the sufficient flexibility for the earlier observed profound active site reorganizations required during the catalytic cycle. The elevated thermal stability of the apoenzyme may, in turn, be important for maintaining a constant level of active GAPN--an enzyme that is known to be crucial for the effective supply of the reducing equivalents in S. mutans and its ability to grow under aerobic conditions.
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Affiliation(s)
- Denis Arutyunov
- a Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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