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Cañadas-Garre M, Baños-Jaime B, Maqueda JJ, Smyth LJ, Cappa R, Skelly R, Hill C, Brennan EP, Doyle R, Godson C, Maxwell AP, McKnight AJ. Genetic variants affecting mitochondrial function provide further insights for kidney disease. BMC Genomics 2024; 25:576. [PMID: 38858654 PMCID: PMC11163707 DOI: 10.1186/s12864-024-10449-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a complex disorder that has become a high prevalence global health problem, with diabetes being its predominant pathophysiologic driver. Autosomal genetic variation only explains some of the predisposition to kidney disease. Variations in the mitochondrial genome (mtDNA) and nuclear-encoded mitochondrial genes (NEMG) are implicated in susceptibility to kidney disease and CKD progression, but they have not been thoroughly explored. Our aim was to investigate the association of variation in both mtDNA and NEMG with CKD (and related traits), with a particular focus on diabetes. METHODS We used the UK Biobank (UKB) and UK-ROI, an independent collection of individuals with type 1 diabetes mellitus (T1DM) patients. RESULTS Fourteen mitochondrial variants were associated with estimated glomerular filtration rate (eGFR) in UKB. Mitochondrial variants and haplogroups U, H and J were associated with eGFR and serum variables. Mitochondrial haplogroup H was associated with all the serum variables regardless of the presence of diabetes. Mitochondrial haplogroup X was associated with end-stage kidney disease (ESKD) in UKB. We confirmed the influence of several known NEMG on kidney disease and function and found novel associations for SLC39A13, CFL1, ACP2 or ATP5G1 with serum variables and kidney damage, and for SLC4A1, NUP210 and MYH14 with ESKD. The G allele of TBC1D32-rs113987180 was associated with higher risk of ESKD in patients with diabetes (OR:9.879; CI95%:4.440-21.980; P = 2.0E-08). In UK-ROI, AGXT2-rs71615838 and SURF1-rs183853102 were associated with diabetic nephropathies, and TFB1M-rs869120 with eGFR. CONCLUSIONS We identified novel variants both in mtDNA and NEMG which may explain some of the missing heritability for CKD and kidney phenotypes. We confirmed the role of MT-ND5 and mitochondrial haplogroup H on renal disease (serum variables), and identified the MT-ND5-rs41535848G variant, along with mitochondrial haplogroup X, associated with higher risk of ESKD. Despite most of the associations were independent of diabetes, we also showed potential roles for NEMG in T1DM.
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Affiliation(s)
- Marisa Cañadas-Garre
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK.
- Genomic Oncology Area, Centre for Genomics and Oncological Research: Pfizer, GENYO, University of Granada-Andalusian Regional Government, PTS Granada. Avenida de La Ilustración 114, 18016, Granada, Spain.
- Hematology Department, Hospital Universitario Virgen de Las Nieves, Avenida de Las Fuerzas Armadas 2, 18014, Granada, Spain.
- Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Avda. de Madrid, 15, 18012, Granada, Spain.
| | - Blanca Baños-Jaime
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja (cicCartuja), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla, Avda. Américo Vespucio 49, 41092, Seville, Spain
| | - Joaquín J Maqueda
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Experimental Oncology Laboratory, IRCCS Rizzoli Orthopaedic Institute, 40136, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Laura J Smyth
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ruaidhri Cappa
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ryan Skelly
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Claire Hill
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Eoin P Brennan
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ross Doyle
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
- Mater Misericordiae University Hospital, Eccles St, Dublin, D07 R2WY, Ireland
| | - Catherine Godson
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Level 11Lisburn Road, Belfast, BT9 7AB, UK
| | - Amy Jayne McKnight
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
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Cox RM, Papoulas O, Shril S, Lee C, Gardner T, Battenhouse AM, Lee M, Drew K, McWhite CD, Yang D, Leggere JC, Durand D, Hildebrandt F, Wallingford JB, Marcotte EM. Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595818. [PMID: 38853926 PMCID: PMC11160598 DOI: 10.1101/2024.05.26.595818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
All eukaryotes share a common ancestor from roughly 1.5 - 1.8 billion years ago, a single-celled, swimming microbe known as LECA, the Last Eukaryotic Common Ancestor. Nearly half of the genes in modern eukaryotes were present in LECA, and many current genetic diseases and traits stem from these ancient molecular systems. To better understand these systems, we compared genes across modern organisms and identified a core set of 10,092 shared protein-coding gene families likely present in LECA, a quarter of which are uncharacterized. We then integrated >26,000 mass spectrometry proteomics analyses from 31 species to infer how these proteins interact in higher-order complexes. The resulting interactome describes the biochemical organization of LECA, revealing both known and new assemblies. We analyzed these ancient protein interactions to find new human gene-disease relationships for bone density and congenital birth defects, demonstrating the value of ancestral protein interactions for guiding functional genetics today.
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Affiliation(s)
- Rachael M Cox
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ophelia Papoulas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tynan Gardner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anna M Battenhouse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - David Yang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Janelle C Leggere
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue Pittsburgh, PA 15213, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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Li X, Shang J, Li S, Wang Y. Identification of a Novel Mitochondrial tRNA Mutation in Chinese Family with Type 2 Diabetes Mellitus. Pharmgenomics Pers Med 2024; 17:149-161. [PMID: 38645701 PMCID: PMC11032666 DOI: 10.2147/pgpm.s438978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/29/2024] [Indexed: 04/23/2024] Open
Abstract
Background Mutations in mitochondrial tRNA (mt-tRNA) could be the origin of some type 2 diabetes mellitus (T2DM) cases, but the mechanism remained largely unknown. Aim The aim of this study was to assess the impact of a novel mitochondrial tRNACys/tRNATyr A5826G mutation on the development and progression of T2DM. Methods A four-generation Han Chinese family with maternally inherited diabetes underwent clinical, genetic and biochemical analyses. The mitochondrial DNA (mtDNA) mutations of three matrilineal relatives were screened by PCR-Sanger sequencing. Furthermore, to see whether m.A5826G mutations affected mitochondrial functions, the cybrid cell lines were derived from three subjects with m.A5826G mutation and three controls without this mutation. ATP was evaluated by luminescent cell viability assay, mitochondrial membrane potential (MMP), and reactive oxygen species (ROS) were determined by flow cytometry. The student's two-tailed, unpaired t-test was used to assess the statistical significance between the control and mutant results. Results The age at onset of diabetes in this pedigree varied from 40 to 63 years, with an average of 54 years. Mutational analysis of mitochondrial genomes revealed the presence of a novel m.A5826G mutation. Interestingly, the m.A5826G mutation occurred at the conjunction between tRNACys and tRNATyr, a very conserved position that was critical for tRNAs processing and functions. Using trans-mitochondrial cybrid cells, we found that mutant cells carrying the m.A5826G showed approximately 36.5% and 22.4% reductions in ATP and MMP, respectively. By contrast, mitochondrial ROS levels increased approximately 33.3%, as compared with the wild type cells. Conclusion A novel m.A5826G mutation was identified in a pedigree with T2DM, and this mutation would lead to mitochondrial dysfunction. Thus, the genetic spectrum of mitochondrial diabetes was expanded by including m.A5826G mutation in tRNACys/tRNATyr, our study provided novel insight into the molecular pathogenesis, early diagnosis, prevention and clinical treatment for mitochondrial diabetes.
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Affiliation(s)
- Xing Li
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Jinyao Shang
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Shuang Li
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Yue Wang
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
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Garcia-Gaona E, García-Gregorio A, García-Jiménez C, López-Olaiz MA, Mendoza-Ramírez P, Fernandez-Guzman D, Pillado-Sánchez RA, Soto-Pacheco AD, Yareni-Zuñiga L, Sánchez-Parada MG, González-Santiago AE, Román-Pintos LM, Castañeda-Arellano R, Hernández-Ortega LD, Mercado-Sesma AR, Orozco-Luna FDJ, Villa-Angulo C, Villa-Angulo R, Baptista-Rosas RC. mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes. Curr Issues Mol Biol 2023; 45:8716-8732. [PMID: 37998725 PMCID: PMC10670651 DOI: 10.3390/cimb45110548] [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: 09/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Type 2 diabetes (T2D) is a chronic systemic disease with a complex etiology, characterized by insulin resistance and mitochondrial dysfunction in various cell tissues. To explore this relationship, we conducted a secondary analysis of complete mtDNA sequences from 1261 T2D patients and 1105 control individuals. Our findings revealed significant associations between certain single-nucleotide polymorphisms (SNPs) and T2D. Notably, the variants m.1438A>G (rs2001030) (controls: 32 [27.6%], T2D: 84 [72.4%]; OR: 2.46; 95%CI: 1.64-3.78; p < 0.001), m.14766C>T (rs193302980) (controls: 498 [36.9%], T2D: 853 [63.1%]; OR: 2.57, 95%CI: 2.18-3.04, p < 0.001), and m.16519T>C (rs3937033) (controls: 363 [43.4%], T2D: 474 [56.6%]; OR: 1.24, 95%CI: 1.05-1.47, p = 0.012) were significantly associated with the likelihood of developing diabetes. The variant m.16189T>C (rs28693675), which has been previously documented in several studies across diverse populations, showed no association with T2D in our analysis (controls: 148 [13.39] T2D: 171 [13.56%]; OR: 1.03; 95%CI: 0.815-1.31; p = 0.83). These results provide evidence suggesting a link between specific mtDNA polymorphisms and T2D, possibly related to association rules, topological patterns, and three-dimensional conformations associated with regions where changes occur, rather than specific point mutations in the sequence.
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Affiliation(s)
- Enrique Garcia-Gaona
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | - Alhelí García-Gregorio
- Facultad de Enfermería Región Poza Rica-Tuxpan, Universidad Veracruzana, Veracruz 91700, Mexico;
| | - Camila García-Jiménez
- Facultad de Ciencias Médicas y Biológicas “Dr. Ignacio Chávez”, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58000, Mexico;
| | | | - Paola Mendoza-Ramírez
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | | | | | - Axel David Soto-Pacheco
- Facultad de Medicina Extensión Los Mochis, Universidad Autónoma de Sinaloa, Sinaloa 81223, Mexico; (R.A.P.-S.); (A.D.S.-P.)
| | - Laura Yareni-Zuñiga
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
| | - María Guadalupe Sánchez-Parada
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Ana Elizabeth González-Santiago
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Miguel Román-Pintos
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Rolando Castañeda-Arellano
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Daniel Hernández-Ortega
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Arieh Roldán Mercado-Sesma
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | | | - Carlos Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Rafael Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Raúl C. Baptista-Rosas
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
- Hospital General de Occidente, Secretaría de Salud Jalisco, Zapopan 45170, Mexico
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Hill C, Duffy S, Coulter T, Maxwell AP, McKnight AJ. Harnessing Genomic Analysis to Explore the Role of Telomeres in the Pathogenesis and Progression of Diabetic Kidney Disease. Genes (Basel) 2023; 14:609. [PMID: 36980881 PMCID: PMC10048490 DOI: 10.3390/genes14030609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The prevalence of diabetes is increasing globally, and this trend is predicted to continue for future decades. Research is needed to uncover new ways to manage diabetes and its co-morbidities. A significant secondary complication of diabetes is kidney disease, which can ultimately result in the need for renal replacement therapy, via dialysis or transplantation. Diabetic kidney disease presents a substantial burden to patients, their families and global healthcare services. This review highlights studies that have harnessed genomic, epigenomic and functional prediction tools to uncover novel genes and pathways associated with DKD that are useful for the identification of therapeutic targets or novel biomarkers for risk stratification. Telomere length regulation is a specific pathway gaining attention recently because of its association with DKD. Researchers are employing both observational and genetics-based studies to identify telomere-related genes associated with kidney function decline in diabetes. Studies have also uncovered novel functions for telomere-related genes beyond the immediate regulation of telomere length, such as transcriptional regulation and inflammation. This review summarises studies that have revealed the potential to harness therapeutics that modulate telomere length, or the associated epigenetic modifications, for the treatment of DKD, to potentially slow renal function decline and reduce the global burden of this disease.
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Affiliation(s)
- Claire Hill
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Seamus Duffy
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Tiernan Coulter
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
| | - Alexander Peter Maxwell
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University of Belfast, Belfast BT12 6BA, UK
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6
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Ito M, Gurumani MZ, Merscher S, Fornoni A. Glucose- and Non-Glucose-Induced Mitochondrial Dysfunction in Diabetic Kidney Disease. Biomolecules 2022; 12:biom12030351. [PMID: 35327540 PMCID: PMC8945149 DOI: 10.3390/biom12030351] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial dysfunction plays an important role in the pathogenesis and progression of diabetic kidney disease (DKD). In this review, we will discuss mitochondrial dysfunction observed in preclinical models of DKD as well as in clinical DKD with a focus on oxidative phosphorylation (OXPHOS), mitochondrial reactive oxygen species (mtROS), biogenesis, fission and fusion, mitophagy and urinary mitochondrial biomarkers. Both glucose- and non-glucose-induced mitochondrial dysfunction will be discussed. In terms of glucose-induced mitochondrial dysfunction, the energetic shift from OXPHOS to aerobic glycolysis, called the Warburg effect, occurs and the resulting toxic intermediates of glucose metabolism contribute to DKD-induced injury. In terms of non-glucose-induced mitochondrial dysfunction, we will review the roles of lipotoxicity, hypoxia and vasoactive pathways, including endothelin-1 (Edn1)/Edn1 receptor type A signaling pathways. Although the relative contribution of each of these pathways to DKD remains unclear, the goal of this review is to highlight the complexity of mitochondrial dysfunction in DKD and to discuss how markers of mitochondrial dysfunction could help us stratify patients at risk for DKD.
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Affiliation(s)
| | | | - Sandra Merscher
- Correspondence: (S.M.); (A.F.); Tel.: +1-305-243-6567 (S.M.); +1-305-243-7745 (A.F.)
| | - Alessia Fornoni
- Correspondence: (S.M.); (A.F.); Tel.: +1-305-243-6567 (S.M.); +1-305-243-7745 (A.F.)
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Blood biomarkers for assessment of mitochondrial dysfunction: An expert review. Mitochondrion 2021; 62:187-204. [PMID: 34740866 DOI: 10.1016/j.mito.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022]
Abstract
Although mitochondrial dysfunction is the known cause of primary mitochondrial disease, mitochondrial dysfunction is often difficult to measure and prove, especially when biopsies of affected tissue are not available. In order to identify blood biomarkers of mitochondrial dysfunction, we reviewed studies that measured blood biomarkers in genetically, clinically or biochemically confirmed primary mitochondrial disease patients. In this way, we were certain that there was an underlying mitochondrial dysfunction which could validate the biomarker. We found biomarkers of three classes: 1) functional markers measured in blood cells, 2) biochemical markers of serum/plasma and 3) DNA markers. While none of the reviewed single biomarkers may perfectly reveal all underlying mitochondrial dysfunction, combining biomarkers that cover different aspects of mitochondrial impairment probably is a good strategy. This biomarker panel may assist in the diagnosis of primary mitochondrial disease patients. As mitochondrial dysfunction may also play a significant role in the pathophysiology of multifactorial disorders such as Alzheimer's disease and glaucoma, the panel may serve to assess mitochondrial dysfunction in complex multifactorial diseases as well and enable selection of patients who could benefit from therapies targeting mitochondria.
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Cañadas-Garre M, Anderson K, Cappa R, Skelly R, Smyth LJ, McKnight AJ, Maxwell AP. Genetic Susceptibility to Chronic Kidney Disease - Some More Pieces for the Heritability Puzzle. Front Genet 2019; 10:453. [PMID: 31214239 PMCID: PMC6554557 DOI: 10.3389/fgene.2019.00453] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Chronic kidney disease (CKD) is a major global health problem with an increasing prevalence partly driven by aging population structure. Both genomic and environmental factors contribute to this complex heterogeneous disease. CKD heritability is estimated to be high (30-75%). Genome-wide association studies (GWAS) and GWAS meta-analyses have identified several genetic loci associated with CKD, including variants in UMOD, SHROOM3, solute carriers, and E3 ubiquitin ligases. However, these genetic markers do not account for all the susceptibility to CKD, and the causal pathways remain incompletely understood; other factors must be contributing to the missing heritability. Less investigated biological factors such as telomere length; mitochondrial proteins, encoded by nuclear genes or specific mitochondrial DNA (mtDNA) encoded genes; structural variants, such as copy number variants (CNVs), insertions, deletions, inversions and translocations are poorly covered and may explain some of the missing heritability. The sex chromosomes, often excluded from GWAS studies, may also help explain gender imbalances in CKD. In this review, we outline recent findings on molecular biomarkers for CKD (telomeres, CNVs, mtDNA variants, sex chromosomes) that typically have received less attention than gene polymorphisms. Shorter telomere length has been associated with renal dysfunction and CKD progression, however, most publications report small numbers of subjects with conflicting findings. CNVs have been linked to congenital anomalies of the kidney and urinary tract, posterior urethral valves, nephronophthisis and immunoglobulin A nephropathy. Information on mtDNA biomarkers for CKD comes primarily from case reports, therefore the data are scarce and diverse. The most consistent finding is the A3243G mutation in the MT-TL1 gene, mainly associated with focal segmental glomerulosclerosis. Only one GWAS has found associations between X-chromosome and renal function (rs12845465 and rs5987107). No loci in the Y-chromosome have reached genome-wide significance. In conclusion, despite the efforts to find the genetic basis of CKD, it remains challenging to explain all of the heritability with currently available methods and datasets. Although additional biomarkers have been investigated in less common suspects such as telomeres, CNVs, mtDNA and sex chromosomes, hidden heritability in CKD remains elusive, and more comprehensive approaches, particularly through the integration of multiple -"omics" data, are needed.
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Affiliation(s)
- Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Ruaidhri Cappa
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Ryan Skelly
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Laura Jane Smyth
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen’s University of Belfast, Belfast, United Kingdom
- Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
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9
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Mitochondrial Haplogroup and the Risk of Acute Kidney Injury Following Cardiac Bypass Surgery. Sci Rep 2019; 9:2279. [PMID: 30783114 PMCID: PMC6381211 DOI: 10.1038/s41598-018-37944-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/11/2018] [Indexed: 02/02/2023] Open
Abstract
Although mitochondrial dysfunction plays a key role in the pathophysiology of acute kidney injury (AKI), the influence of mitochondrial genetic variability in this process remains unclear. We explored the association between the risk of post-cardiac bypass AKI and mitochondrial haplotype - inherited mitochondrial genomic variations of potentially functional significance. Our single-centre study recruited consecutive patients prior to surgery. Exclusions included stage 5 CKD, non-Caucasian race and subsequent off-pump surgery. Haplogroup analysis allowed characterisation of the study population using the common mutations and by phylogenetic supergroup (WXI and HV). Chi-square tests for association allowed the identification of potential predictors of AKI for use in logistic regression analysis. AKI occurred in 12.8% of the study population (n = 881; male 69.6%, non-diabetic 78.5%, median (interquartile range) age 68.0 (61.0-75.0) years). The haplogroup profile comprised H (42.7%), J (12.1%), T (10.9%), U (14.4%) and K (7.6%). Although the regression model was statistically significant (χ2 = 95.483, p < 0.0005), neither the phylogenetic supergroups nor any individual haplogroup was a significant contributor. We found no significant association between common European haplogroups and the risk of post-cardiac bypass AKI. However, given the major role of mitochondrial dysfunction in AKI, there is a need to replicate our findings in other cohorts and with other aetiologies of AKI.
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10
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Corbin KD, Driscoll KA, Pratley RE, Smith SR, Maahs DM, Mayer-Davis EJ. Obesity in Type 1 Diabetes: Pathophysiology, Clinical Impact, and Mechanisms. Endocr Rev 2018; 39:629-663. [PMID: 30060120 DOI: 10.1210/er.2017-00191] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
There has been an alarming increase in the prevalence of obesity in people with type 1 diabetes in recent years. Although obesity has long been recognized as a major risk factor for the development of type 2 diabetes and a catalyst for complications, much less is known about the role of obesity in the initiation and pathogenesis of type 1 diabetes. Emerging evidence suggests that obesity contributes to insulin resistance, dyslipidemia, and cardiometabolic complications in type 1 diabetes. Unique therapeutic strategies may be required to address these comorbidities within the context of intensive insulin therapy, which promotes weight gain. There is an urgent need for clinical guidelines for the prevention and management of obesity in type 1 diabetes. The development of these recommendations will require a transdisciplinary research strategy addressing metabolism, molecular mechanisms, lifestyle, neuropsychology, and novel therapeutics. In this review, the prevalence, clinical impact, energy balance physiology, and potential mechanisms of obesity in type 1 diabetes are described, with a special focus on the substantial gaps in knowledge in this field. Our goal is to provide a framework for the evidence base needed to develop type 1 diabetes-specific weight management recommendations that account for the competing outcomes of glycemic control and weight management.
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Affiliation(s)
- Karen D Corbin
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - Kimberly A Driscoll
- Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, Colorado.,Barbara Davis Center for Diabetes, Aurora, Colorado
| | - Richard E Pratley
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - David M Maahs
- Division of Pediatric Endocrinology, Department of Pediatrics, Stanford University, Stanford, California
| | - Elizabeth J Mayer-Davis
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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11
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Li Y, Zhu M, Huo Y, Zhang X, Liao M. Anti-fibrosis activity of combination therapy with epigallocatechin gallate, taurine and genistein by regulating glycolysis, gluconeogenesis, and ribosomal and lysosomal signaling pathways in HSC-T6 cells. Exp Ther Med 2018; 16:4329-4338. [PMID: 30542382 PMCID: PMC6257822 DOI: 10.3892/etm.2018.6743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/21/2017] [Indexed: 12/24/2022] Open
Abstract
A previous study by our group indicated that combined treatment with taurine, epigallocatechin gallate (EGCG) and genistein protects against liver fibrosis. The aim of the present study was to elucidate the antifibrotic mechanism of this combination treatment using isobaric tag for relative and absolute quantification (iTRAQ)-based proteomics in an activated rat hepatic stellate cell (HSC) line. In the present study, HSC-T6 cells were incubated with taurine, EGCG and genistein, and cellular proteins were extracted and processed for iTRAQ labeling. Quantification and identification of proteins was performed using two-dimensional liquid chromatography coupled with tandem mass spectrometry. Proteomic analysis indicated that the expression of 166 proteins were significantly altered in response to combination treatment with taurine, EGCG and genistein. A total 76 of these proteins were upregulated and 90 were downregulated. Differentially expressed proteins were grouped according to their association with specific Kyoto Encyclopedia of Genes and Genomes pathways. The results indicated that the differentially expressed proteins hexokinase-2 and lysosome-associated membrane glycoprotein 1 were associated with glycolysis, gluconeogenesis and lysosome signaling pathways. The expression of these proteins was validated using western blot analysis; the expression of hexokinase-2 was significantly decreased and the expression of lysosome-associated membrane glycoprotein 1 was significantly increased in HSC-T6 cells treated with taurine, EGCG and genistein compared with the control, respectively (P<0.05). These results were in accordance with the changes in protein expression identified using the iTRAQ approach. Therefore, the antifibrotic effect of combined therapy with taurine, EGCG and genistein may be associated with the activation of several pathways in HSCs, including glycolysis, gluconeogenesis, and the ribosome and lysosome signaling pathways. The differentially expressed proteins identified in the current study may be useful for treatment of liver fibrosis in the future.
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Affiliation(s)
- Yan Li
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Min Zhu
- Guangxi University Library, Guangxi University, Nanning, Guangxi 530004, P.R. China
| | - Yani Huo
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Xuerong Zhang
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
| | - Ming Liao
- Medical Scientific Research Centre, Key Laboratory of High-Incidence-Tumor Prevention and Treatment, Guangxi Medical University, Ministry of Education, Nanning, Guangxi 530021, P.R. China
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12
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Abstract
Globally, diabetes is the leading cause of chronic kidney disease and end-stage renal disease, which are major risk factors for cardiovascular disease and death. Despite this burden, the factors that precipitate the development and progression of diabetic kidney disease (DKD) remain to be fully elucidated. Mitochondrial dysfunction is associated with kidney disease in nondiabetic contexts, and increasing evidence suggests that dysfunctional renal mitochondria are pathological mediators of DKD. These complex organelles have a broad range of functions, including the generation of ATP. The kidneys are mitochondrially rich, highly metabolic organs that require vast amounts of ATP for their normal function. The delivery of metabolic substrates for ATP production, such as fatty acids and oxygen, is altered by diabetes. Changes in metabolic fuel sources in diabetes to meet ATP demands result in increased oxygen consumption, which contributes to renal hypoxia. Inherited factors including mutations in genes that impact mitochondrial function and/or substrate delivery may also be important risk factors for DKD. Hence, we postulate that the diabetic milieu and inherited factors that underlie abnormalities in mitochondrial function synergistically drive the development and progression of DKD.
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Affiliation(s)
- Josephine M Forbes
- Glycation and Diabetes Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia.,Mater Clinical School, School of Medicine, The University of Queensland, St Lucia, Queensland, Australia.,Departments of Medicine and Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - David R Thorburn
- Departments of Medicine and Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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13
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Hsieh AR, Chen DP, Chattopadhyay AS, Li YJ, Chang CC, Fann CSJ. A non-threshold region-specific method for detecting rare variants in complex diseases. PLoS One 2017; 12:e0188566. [PMID: 29190701 PMCID: PMC5708778 DOI: 10.1371/journal.pone.0188566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/09/2017] [Indexed: 11/23/2022] Open
Abstract
A region-specific method, NTR (non-threshold rare) variant detection method, was developed—it does not use the threshold for defining rare variants and accounts for directions of effects. NTR also considers linkage disequilibrium within the region and accommodates common and rare variants simultaneously. NTR weighs variants according to minor allele frequency and odds ratio to combine the effects of common and rare variants on disease occurrence into a single score and provides a test statistic to assess the significance of the score. In the simulations, under different effect sizes, the power of NTR increased as the effect size increased, and the type I error of our method was controlled well. Moreover, NTR was compared with several other existing methods, including the combined multivariate and collapsing method (CMC), weighted sum statistic method (WSS), sequence kernel association test (SKAT), and its modification, SKAT-O. NTR yields comparable or better power in simulations, especially when the effects of linkage disequilibrium between variants were at least moderate. In an analysis of diabetic nephropathy data, NTR detected more confirmed disease-related genes than the other aforementioned methods. NTR can thus be used as a complementary tool to help in dissecting the etiology of complex diseases.
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Affiliation(s)
- Ai-Ru Hsieh
- Graduate Institute of Biostatistics, China Medical University, Taichung, Taiwan
| | - Dao-Peng Chen
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Ying-Ju Li
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chien-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan
| | - Cathy S. J. Fann
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
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14
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Buzzetti R, Prudente S, Copetti M, Dauriz M, Zampetti S, Garofolo M, Penno G, Trischitta V. Clinical worthlessness of genetic prediction of common forms of diabetes mellitus and related chronic complications: A position statement of the Italian Society of Diabetology. Nutr Metab Cardiovasc Dis 2017; 27:99-114. [PMID: 28063875 DOI: 10.1016/j.numecd.2016.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/01/2016] [Accepted: 08/13/2016] [Indexed: 02/08/2023]
Abstract
AIM We are currently facing several attempts aimed at marketing genetic data for predicting multifactorial diseases, among which diabetes mellitus is one of the more prevalent. The present document primarily aims at providing to practicing physicians a summary of available data regarding the role of genetic information in predicting diabetes and its chronic complications. DATA SYNTHESIS Firstly, general information about characteristics and performance of risk prediction tools will be presented in order to help clinicians to get acquainted with basic methodological information related to the subject at issue. Then, as far as type 1 diabetes is concerned, available data indicate that genetic information and counseling may be useful only in families with many affected individuals. However, since no disease prevention is possible, the utility of predicting this form of diabetes is at question. In the case of type 2 diabetes, available data really question the utility of adding genetic information on top of well performing, easy available and inexpensive non-genetic markers. Finally, the possibility of using the few available genetic data on diabetic complications for improving our ability to predict them will also be presented and discussed. For cardiovascular complication, the addition of genetic information to models based on clinical features does not translate in a substantial improvement in risk discrimination. For all other diabetic complications genetic information are currently very poor and cannot, therefore, be used for improving risk stratification. CONCLUSIONS In all, nowadays the use of genetic testing for predicting diabetes and its chronic complications is definitively of little value in clinical practice.
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Affiliation(s)
- R Buzzetti
- Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy; UOC Diabetology, Polo Pontino, "Sapienza" University of Rome, Rome, Italy
| | - S Prudente
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - M Copetti
- Unit of Biostatistics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - M Dauriz
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Verona School of Medicine and Hospital Trust of Verona, Verona, Italy
| | - S Zampetti
- Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy; UOC Diabetology, Polo Pontino, "Sapienza" University of Rome, Rome, Italy
| | - M Garofolo
- Section of Diabetes and Metabolic Disease, Department of Clinical and Experimental Medicine, University of Pisa and Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - G Penno
- Section of Diabetes and Metabolic Disease, Department of Clinical and Experimental Medicine, University of Pisa and Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - V Trischitta
- Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy; Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy; Research Unit of Diabetes and Endocrine Diseases, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
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15
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MnTBAP Therapy Attenuates Renal Fibrosis in Mice with 5/6 Nephrectomy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:7496930. [PMID: 26989454 PMCID: PMC4773577 DOI: 10.1155/2016/7496930] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/20/2016] [Indexed: 11/18/2022]
Abstract
Renal fibrosis is a common pathological feature of all kinds of chronic kidney diseases (CKDs) with uncertain mechanisms. Accumulating evidence demonstrated an important role of oxidative stress in the pathogenesis of CKD. Here we hypothesized that MnTBAP (manganese (III) tetrakis (4-benzoic acid)porphyrin chloride), a cell-permeable mimic of superoxide dismutase (SOD), may protect against the fibrotic response in CKD by antagonizing oxidative stress. To verify this hypothesis, we performed experiments in tubular epithelial cells and mice with 5/6 nephrectomy (Nx). In mouse tubular epithelial cells, TGF-β1 induced a significant transition to fibrotic phenotype in line with a remarkable mitochondrial dysfunction, which was markedly improved by MnTBAP (1.14 μM) pretreatment. In remnant kidneys of 5/6 Nx mice, tubulointerstitial fibrosis occurred in parallel with mitochondrial abnormality in renal tubular cells. Administration of MnTBAP significantly attenuated the deposition of extracellular matrix as evidenced by the blocked expressions of fibronectin, collagen I, and collagen III. Masson staining also displayed an ameliorated accumulation of collagenous matrix in MnTBAP-treated mice. Moreover, MnTBAP also significantly improved the severity of proteinuria without altering CKD-related hypertension. Collectively, MnTBAP therapy served as a promising strategy in preventing renal fibrosis in CKDs possibly via antagonizing mitochondrial-derived oxidative stress and subsequent protection of mitochondrial function.
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16
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Swan EJ, Maxwell AP, McKnight AJ. Distinct methylation patterns in genes that affect mitochondrial function are associated with kidney disease in blood-derived DNA from individuals with Type 1 diabetes. Diabet Med 2015; 32:1110-5. [PMID: 25850930 DOI: 10.1111/dme.12775] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 12/18/2022]
Abstract
AIMS Epigenetic modifications, such as DNA methylation, can influence the risk of developing kidney disease. We studied methylation profiles in genes related to mitochondrial function to assess whether differences in these epigenetic features were associated with diabetic kidney disease in people with Type 1 diabetes. METHODS A case-control association study was undertaken (n = 196 individuals with diabetic kidney disease vs. n = 246 individuals without renal disease). Participants were White and diagnosed with Type 1 diabetes before 31 years of age. Genes that encode mitochondrial proteins (n = 780) were downloaded from mitoproteome.org. DNA methylation profiles from blood-derived DNA were generated using the Illumina Infinium HumanMethylation450 (262 samples) and Illumina Infinium HumanMethylation27 (192 samples) arrays. Beta values (β) were calculated and quality control was conducted, including evaluating blind duplicate DNA samples. RESULTS Fifty-four Cytosine-phosphate-Guanine probes across 51 unique genes were significantly associated (P ≤ 10(-8) ) with diabetic kidney disease across both the 450K and the 27K methylation arrays. A subanalysis, employing the 450K array, identified 755 Cytosine-phosphate-Guanine probes in 374 genes that were significantly associated (P ≤ 10(-8) ) with end-stage renal disease. Forty-six of the top-ranked variants for diabetic kidney disease were also identified as being differentially methylated in individuals with end-stage renal disease. The largest change in methylation (Δβ = 0.2) was observed for cg03169527 in the TAMM41 gene, chromosome 3p25.2. Three genes, PMPCB, TSFM and AUH, were observed with differential methylation at multiple Cytosine-phosphate-Guanine sites each (P < 10(-12) ). CONCLUSIONS Differential methylation in genes that influence mitochondrial function are associated with kidney disease in individuals with Type 1 diabetes.
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Affiliation(s)
- E J Swan
- Centre for Public Health, Queen's University of Belfast
| | - A P Maxwell
- Centre for Public Health, Queen's University of Belfast
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A J McKnight
- Centre for Public Health, Queen's University of Belfast
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17
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Abstract
The global prevalence of diabetic nephropathy is rising in parallel with the increasing incidence of diabetes in most countries. Unfortunately, up to 40 % of persons diagnosed with diabetes may develop kidney complications. Diabetic nephropathy is associated with substantially increased risks of cardiovascular disease and premature mortality. An inherited susceptibility to diabetic nephropathy exists, and progress is being made unravelling the genetic basis for nephropathy thanks to international research collaborations, shared biological resources and new analytical approaches. Multiple epidemiological studies have highlighted the clinical heterogeneity of nephropathy and the need for better phenotyping to help define important subgroups for analysis and increase the power of genetic studies. Collaborative genome-wide association studies for nephropathy have reported unique genes, highlighted novel biological pathways and suggested new disease mechanisms, but progress towards clinically relevant risk prediction models for diabetic nephropathy has been slow. This review summarises the current status, recent developments and ongoing challenges elucidating the genetics of diabetic nephropathy.
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Affiliation(s)
- Amy Jayne McKnight
- Nephrology Research Group, Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK,
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