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Oluwatoba DS, Safoah HA, Do TD. The rise and fall of adenine clusters in the gas phase: a glimpse into crystal growth and nucleation. Anal Bioanal Chem 2024:10.1007/s00216-024-05442-2. [PMID: 39031229 DOI: 10.1007/s00216-024-05442-2] [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: 05/24/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/22/2024]
Abstract
The emergence of a crystal nucleus from disordered states is a critical and challenging aspect of the crystallization process, primarily due to the extremely short length and timescales involved. Methods such as liquid-cell or low-dose focal-series transmission electron microscopy (TEM) are often employed to probe these events. In this study, we demonstrate that ion mobility spectrometry-mass spectrometry (IMS-MS) offers a complementary and insightful perspective on the nucleation process by examining the sizes and shapes of small clusters, specifically those ranging from n = 2 to 40. Our findings reveal the significant role of sulfate ions in the growth of adeninediium sulfate clusters, which are the precursors to the formation of single crystals. Specifically, sulfate ions stabilize adenine clusters at the 1:1 ratio. In contrast, guanine sulfate forms smaller clusters with varied ratios, which become stable as they approach the 1:2 ratio. The nucleation size is predicted to be between n = 8 and 14, correlating well with the unit cell dimensions of adenine crystals. This correlation suggests that IMS-MS can identify critical nucleation sizes and provide valuable structural information consistent with established crystallographic data. We also discuss the strengths and limitations of IMS-MS in this context. IMS-MS offers rapid and robust experimental protocols, making it a valuable tool for studying the effects of various additives on the assembly of small molecules. Additionally, it aids in elucidating nucleation processes and the growth of different crystal polymorphs.
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Affiliation(s)
| | - Happy Abena Safoah
- Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA.
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Liu W, Liang W, Zhang C, Liu H, Li H, Zhou L, Zhou L. LncR-GAS5 decrease in adenine phosphoribosyltransferase expresssion via binding TAF1 to increase kidney damage created by CIH. Heliyon 2024; 10:e33084. [PMID: 38994083 PMCID: PMC11238052 DOI: 10.1016/j.heliyon.2024.e33084] [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: 01/16/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
Objective Chronic kidney disease (CKD) related to obstructive sleep apnea-hypopnea syndrome (OSAHS) mainly results from chronic intermittent hypoxia (CIH)-induced renal injury. This study aimed to explore the interaction between the long noncoding RNA (lncRNA) growth arrest-specific transcript 5 (GAS5) and recombinant adenine phosphoribosyltransferase (APRT) in CIH-induced renal injury. Methods A rat intermittent hypoxia model was constructed, total RNA was extracted from kidney tissue, and transcriptome sequencing was performed using high-throughput sequencing technology. CIH rat models were established and injected with sh-GAS5 or OE-APRT plasmid, the serum levels of blood urea nitrogen (BUN) and creatinine amidohydrolase were measured, and the expression of oxidative stress-related factors was detected. Hematoxylin and eosin (H&E) and Masson's trichrome staining were used for morphological observations, and cell apoptosis was determined by TUNEL staining. Interactions between GAS5, TATA-box binding protein-associated factor 1 (TAF1), and APRT were predicted and verified. After transfection of HK-2 cells, the expression of GAS5, TAF1, APRT, Bax, Bcl-2, apoptosis-related factors, fibrosis-related factors (collagen I and Ⅳ), and autophagy-related proteins (LC3-Ⅱ, LC3-Ⅰ, p62, and Beclin-1) was measured by RT-qPCR and western blotting. Results Sequencing results revealed that TAF1 was significantly increased and APRT was significantly decreased in the CIH group. RNA was significantly involved in the biological process of kidney injury mediated by CIH. CIH rats injected with GAS5 suppression or APRT overexpression plasmids showed decreased GAS5 and elevated APRT expression, along with suppressed serum levels of BUN and creatinine amidohydrolase. Meanwhile, GAS5 suppression or APRT overexpression attenuated apoptosis and fibrosis, suppressed oxidative stress, and promoted autophagy in CIH-induced renal tubular epithelial cells. The RNA pull-down assay and RIP verified the binding and interaction of GAS5 and TAF1. Chip immunoprecipitation (ChIP) identified TAF1 regulation of the APRT promoter. GAS5 and TAF1 negatively regulated APRT expression. Conclusion The lncRNA GAS5 can bind TAF1 to suppress APRT transcription, thereby enhancing CIH-induced renal injury in rats.
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Affiliation(s)
- Wei Liu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Wukaiyang Liang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - CunTai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Huiguo Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hai Li
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Lun Zhou
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Ling Zhou
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Leow EH, Chong SL, Tan ES, Koh AL, Cham BWM, Yap CJY, Ng YH. Adenine phosphoribosyl transferase (APRT) deficiency and a novel sequence variant in APRT with phenotypic diversity and a literature review. Nephrology (Carlton) 2023; 28:649-654. [PMID: 37619970 DOI: 10.1111/nep.14232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Adenine phosphoribosyl transferase (APRT) deficiency is an autosomal recessive disorder and a rare cause of urolithiasis due to mutations in APRT (OMIM #102600). APRT deficiency results in increased urinary excretion of 2,8-dihydroxyadenine (DHA) which can cause urolithiasis and kidney failure. However, with prompt diagnosis, patients with APRT deficiency can be treated with xanthine oxidoreductase inhibitors which decrease urinary DHA excretion and improve outcomes. We report a pair of siblings, an 11-year-old brother and his 14-year-old sister with compound heterozygous variants c.270del (p.Lys91Serfs*46) and c.484_486del (p.Leu162del) in APRT with variable clinical presentation of APRT deficiency. The brother presented at 17 months of age with urolithiasis and severe acute kidney injury. His elder sister remained well and asymptomatic with normal kidney function and did not develop renal calculi. Brownish disk or sphere-like crystals with both concentric and radial markings were reported on urine microscopy in the sister on screening. The sister's diagnosis was confirmed with further laboratory evidence of absent red cell lysate APRT activity with corresponding elevated levels of urinary DHA. In conclusion, we identified a novel mutation in the APRT gene in a pair of siblings with greater phenotypic severity in the male.
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Affiliation(s)
- Esther Huimin Leow
- Nephrology Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Siew Le Chong
- Nephrology Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Ee Shien Tan
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Ai Ling Koh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Breana Wen Min Cham
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Celeste Jia Ying Yap
- Nephrology Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Yong Hong Ng
- Nephrology Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
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Schumann A, Schultheiss UT, Ferreira CR, Blau N. Clinical and biochemical footprints of inherited metabolic diseases. XIV. Metabolic kidney diseases. Mol Genet Metab 2023; 140:107683. [PMID: 37597335 DOI: 10.1016/j.ymgme.2023.107683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
Kidney disease is a global health burden with high morbidity and mortality. Causes of kidney disease are numerous, extending from common disease groups like diabetes and arterial hypertension to rare conditions including inherited metabolic diseases (IMDs). Given its unique anatomy and function, the kidney is a target organ in about 10% of known IMDs, emphasizing the relevant contribution of IMDs to kidney disease. The pattern of injury affects all segments of the nephron including glomerular disease, proximal and distal tubular damage, kidney cyst formation, built-up of nephrocalcinosis and stones as well as severe malformations. We revised and updated the list of known metabolic etiologies associated with kidney involvement and found 190 relevant IMDs. This represents the 14th of a series of educational articles providing a comprehensive and revised list of metabolic differential diagnoses according to system involvement.
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Affiliation(s)
- Anke Schumann
- Department of General Paediatrics, Adolescent Medicine and Neonatology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
| | - Ulla T Schultheiss
- Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine, and Medical Center, University of Freiburg, Institute of Genetic Epidemiology, Freiburg, Germany.
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA.
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital, Zürich, Switzerland.
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A case of 2,8-DHA crystalline nephropathy caused by adenine phosphoribosyltransferase deficiency: diagnosis and treatment. CEN Case Rep 2022:10.1007/s13730-022-00768-1. [PMID: 36576711 PMCID: PMC10393930 DOI: 10.1007/s13730-022-00768-1] [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: 08/06/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022] Open
Abstract
Adenine phosphoribosyltransferase (APRT) deficiency is a rare autosomal recessive disorder that leads to the accumulation of poorly soluble 2,8-dihydroxyadenine (DHA) in the kidneys, resulting in a variety of renal presentations including nephrolithiasis, acute kidney injury, and chronic kidney disease (CKD) caused by crystal nephropathy. Here, we report a case of a 43-year-old man with 2,8-DHA crystalline nephropathy caused by APRT deficiency strongly suspected by renal biopsy results and definitively diagnosed by a urine gas chromatography-mass spectrometry (GC/MS)-based plasma metabolomic assessment. This case represents the importance of awareness and recognition of the signs and symptoms of this rare condition and its progression to CKD, which can be prevented by the early administration of xanthine oxidoreductase inhibitors.
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Adenine overload induces ferroptosis in human primary proximal tubular epithelial cells. Cell Death Dis 2022; 13:104. [PMID: 35110539 PMCID: PMC8810935 DOI: 10.1038/s41419-022-04527-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022]
Abstract
The pathogenesis of crystal nephropathy involves deposition of intratubular crystals, tubular obstruction and cell death. The deposition of 8-dihydroxyadenine (DHA) crystals within kidney tubules, for instance, is caused by a hereditary deficiency of adenine phosphoribosyl transferase in humans or adenine overload in preclinical models. However, the downstream pathobiological patterns of tubular cell attrition in adenine/DHA-induced nephropathy remain poorly understood. In this study, we investigated: (i) the modes of adenine-induced tubular cell death in an experimental rat model and in human primary proximal tubular epithelial cells (PTEC); and (ii) the therapeutic effect of the flavonoid baicalein as a novel cell death inhibitor. In a rat model of adenine diet-induced crystal nephropathy, significantly elevated levels of tubular iron deposition and lipid peroxidation (4-hydroxynonenal; 4-HNE) were detected. This phenotype is indicative of ferroptosis, a novel form of regulated necrosis. In cultures of human primary PTEC, adenine overload-induced significantly increased mitochondrial superoxide levels, mitochondrial depolarisation, DNA damage and necrotic cell death compared with untreated PTEC. Molecular interrogation of adenine-stimulated PTEC revealed a significant reduction in the lipid repair enzyme glutathione peroxidase 4 (GPX4) and the significant increase in 4-HNE compared with untreated PTEC, supporting the concept of ferroptotic cell death. Moreover, baicalein treatment inhibited ferroptosis in adenine-stimulated PTEC by selectively modulating the mitochondrial antioxidant enzyme superoxide dismutase 2 (SOD2) and thus, suppressing mitochondrial superoxide production and DNA damage. These data identify ferroptosis as the primary pattern of PTEC necrosis in adenine-induced nephropathy and establish baicalein as a potential therapeutic tool for the clinical management of ferroptosis-associated crystal nephropathies (e.g., DHA nephropathy, oxalate nephropathy).
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Koyun M, Sancaktar M, Aksoy GK, Çomak E, Kaçar A, Adar M, Berdeli A, Akman S. A rare cause of urolithiasis in an infant: Answers. Pediatr Nephrol 2021; 36:2067-2068. [PMID: 33459934 DOI: 10.1007/s00467-020-04910-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Mustafa Koyun
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey.
| | - Muhammet Sancaktar
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
| | - Gülşah Kaya Aksoy
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
| | - Elif Çomak
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
| | - Ayla Kaçar
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
| | - Mehtap Adar
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
| | - Afig Berdeli
- Faculty of Medicine, Department of Pediatrics, Molecular Medicine Laboratory, Ege University, Izmir, Turkey
| | - Sema Akman
- Faculty of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Akdeniz University, 07070, Antalya, Turkey
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Klinkhammer BM, Djudjaj S, Kunter U, Palsson R, Edvardsson VO, Wiech T, Thorsteinsdottir M, Hardarson S, Foresto-Neto O, Mulay SR, Moeller MJ, Jahnen-Dechent W, Floege J, Anders HJ, Boor P. Cellular and Molecular Mechanisms of Kidney Injury in 2,8-Dihydroxyadenine Nephropathy. J Am Soc Nephrol 2020; 31:799-816. [PMID: 32086278 DOI: 10.1681/asn.2019080827] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hereditary deficiency of adenine phosphoribosyltransferase causes 2,8-dihydroxyadenine (2,8-DHA) nephropathy, a rare condition characterized by formation of 2,8-DHA crystals within renal tubules. Clinical relevance of rodent models of 2,8-DHA crystal nephropathy induced by excessive adenine intake is unknown. METHODS Using animal models and patient kidney biopsies, we assessed the pathogenic sequelae of 2,8-DHA crystal-induced kidney damage. We also used knockout mice to investigate the role of TNF receptors 1 and 2 (TNFR1 and TNFR2), CD44, or alpha2-HS glycoprotein (AHSG), all of which are involved in the pathogenesis of other types of crystal-induced nephropathies. RESULTS Adenine-enriched diet in mice induced 2,8-DHA nephropathy, leading to progressive kidney disease, characterized by crystal deposits, tubular injury, inflammation, and fibrosis. Kidney injury depended on crystal size. The smallest crystals were endocytosed by tubular epithelial cells. Crystals of variable size were excreted in urine. Large crystals obstructed whole tubules. Medium-sized crystals induced a particular reparative process that we term extratubulation. In this process, tubular cells, in coordination with macrophages, overgrew and translocated crystals into the interstitium, restoring the tubular luminal patency; this was followed by degradation of interstitial crystals by granulomatous inflammation. Patients with adenine phosphoribosyltransferase deficiency showed similar histopathological findings regarding crystal morphology, crystal clearance, and renal injury. In mice, deletion of Tnfr1 significantly reduced tubular CD44 and annexin two expression, as well as inflammation, thereby ameliorating the disease course. In contrast, genetic deletion of Tnfr2, Cd44, or Ahsg had no effect on the manifestations of 2,8-DHA nephropathy. CONCLUSIONS Rodent models of the cellular and molecular mechanisms of 2,8-DHA nephropathy and crystal clearance have clinical relevance and offer insight into potential future targets for therapeutic interventions.
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Affiliation(s)
| | | | | | | | | | - Thorsten Wiech
- Institute of Pathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany; and
| | | | - Sverrir Hardarson
- Department of Pathology Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Shrikant R Mulay
- Division of Nephrology, Klinikum der Universität, LMU München, Munich, Germany
| | | | | | | | - Hans-Joachim Anders
- Division of Nephrology, Klinikum der Universität, LMU München, Munich, Germany
| | - Peter Boor
- Institute of Pathology, .,Division of Nephrology and Immunology.,Department of Electron Microscopy, RWTH University Hospital Aachen, Aachen, Germany
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