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Yamamoto T, Isaka Y. Pathological mechanisms of kidney disease in ageing. Nat Rev Nephrol 2024; 20:603-615. [PMID: 39025993 DOI: 10.1038/s41581-024-00868-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
The kidney is a metabolically active organ that requires energy to drive processes such as tubular reabsorption and secretion, and shows a decline in function with advancing age. Various molecular mechanisms, including genomic instability, telomere attrition, inflammation, autophagy, mitochondrial function, and changes to the sirtuin and Klotho signalling pathways, are recognized regulators of individual lifespan and pivotal factors that govern kidney ageing. Thus, mechanisms that contribute to ageing not only dictate renal outcomes but also exert a substantial influence over life expectancy. Conversely, kidney dysfunction, in the context of chronic kidney disease (CKD), precipitates an expedited ageing trajectory in individuals, leading to premature ageing and a disconnect between biological and chronological age. As CKD advances, age-related manifestations such as frailty become increasingly conspicuous. Hence, the pursuit of healthy ageing necessitates not only the management of age-related complications but also a comprehensive understanding of the processes and markers that underlie systemic ageing. Here, we examine the hallmarks of ageing, focusing on the mechanisms by which they affect kidney health and contribute to premature organ ageing. We also review diagnostic methodologies and interventions for premature ageing, with special consideration given to the potential of emerging therapeutic avenues to target age-related kidney diseases.
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Affiliation(s)
- Takeshi Yamamoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan.
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2
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Gigliotti G, Joshi R, Khalid A, Widmer D, Boccellino M, Viggiano D. Epigenetics, Microbiome and Personalized Medicine: Focus on Kidney Disease. Int J Mol Sci 2024; 25:8592. [PMID: 39201279 PMCID: PMC11354516 DOI: 10.3390/ijms25168592] [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: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024] Open
Abstract
Personalized medicine, which involves modifying treatment strategies/drug dosages based on massive laboratory/imaging data, faces large statistical and study design problems. The authors believe that the use of continuous multidimensional data, such as those regarding gut microbiota, or binary multidimensional systems properly transformed into a continuous variable, such as the epigenetic clock, offer an advantageous scenario for the design of trials of personalized medicine. We will discuss examples focusing on kidney diseases, specifically on IgA nephropathy. While gut dysbiosis can provide a treatment strategy to restore the standard gut microbiota using probiotics, transforming epigenetic omics data into epigenetic clocks offers a promising tool for personalized acute and chronic kidney disease care. Epigenetic clocks involve a complex transformation of DNA methylome data into estimated biological age. These clocks can identify people at high risk of developing kidney problems even before symptoms appear. Some of the effects of both the epigenetic clock and microbiota on kidney diseases seem to be mediated by endothelial dysfunction. These "big data" (epigenetic clocks and microbiota) can help tailor treatment plans by pinpointing patients likely to experience rapid declines or those who might not need overly aggressive therapies.
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Affiliation(s)
| | - Rashmi Joshi
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | - Anam Khalid
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | | | - Mariarosaria Boccellino
- Department Experimental Medicine, University of Campania, 81100 Naples, Italy
- Department Life Sciences, Health and Health Professions, Link University, 00165 Rome, Italy
| | - Davide Viggiano
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
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García-García I, Grisotto G, Heini A, Gibertoni S, Nusslé S, Gonseth Nusslé S, Donica O. Examining nutrition strategies to influence DNA methylation and epigenetic clocks: a systematic review of clinical trials. FRONTIERS IN AGING 2024; 5:1417625. [PMID: 39077104 PMCID: PMC11284312 DOI: 10.3389/fragi.2024.1417625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/18/2024] [Indexed: 07/31/2024]
Abstract
Nutrition has powerful impacts on our health and longevity. One of the mechanisms by which nutrition might influence our health is by inducing epigenetic modifications, modulating the molecular mechanisms that regulate aging. Observational studies have provided evidence of a relationship between nutrition and differences in DNA methylation. However, these studies are limited in that they might not provide an accurate control of the interactions between different nutrients, or between nutrition and other lifestyle behaviors. Here we systematically reviewed clinical studies examining the impact of nutrition strategies on DNA methylation. We examined clinical studies in community-dwelling adults testing the effects of nutrition interventions on i) global DNA methylation and its proxies, and ii) epigenetic clocks. We included 21 intervention studies that focused on the effects of healthy nutrition patterns, specific foods or nutrients, as well as the effect of multivitamin or multimineral supplements. In four studies on the methylation effects of healthy dietary patterns, as defined by being rich in vegetables, fruits, whole-grains, and nuts and reduced in the intake of added sugars, saturated fat, and alcohol, two of them suggested that a healthy diet, is associated with lower epigenetic age acceleration, one of them reported increases in global DNA methylation, while another one found no diet effects. Studies examining epigenetic effects of specific foods, nutrients, or mixtures of nutrients were scarce. For both folic acid and polyunsaturated fatty acids, the available independent studies produced conflicting findings. Although more evidence is still needed to draw firm conclusions, results begin to suggest that healthy dietary patterns have positive effects on DNA methylation. Additional evidence from large randomized-controlled clinical trials is needed to support the effects of healthy nutrition on the DNA methylome.
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Affiliation(s)
| | | | - Adrian Heini
- Clinique la Prairie, Clarens-Montreux, Vaud, Switzerland
| | | | | | | | - Olga Donica
- Clinique la Prairie, Clarens-Montreux, Vaud, Switzerland
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LaHue SC, Fuentealba M, Roa Diaz S, Seetharaman S, Garcia T, Furman D, Lai JC, Newman JC. Association of biological aging with frailty and post-transplant outcomes among adults with cirrhosis. GeroScience 2024; 46:3287-3295. [PMID: 38246968 PMCID: PMC11009173 DOI: 10.1007/s11357-024-01076-5] [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: 10/26/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
Frailty is classically associated with advanced age but is also an important predictor of clinical outcomes in comparatively young adults with cirrhosis. We examined the association of biological aging with frailty and post-transplant outcomes in a pilot of adults with cirrhosis undergoing liver transplantation (LT). Frailty was measured via the Liver Frailty Index (LFI). The primary epigenetic clock DNA methylation (DNAm) PhenoAge was calculated from banked peripheral blood mononuclear cells; we secondarily explored two first-generation clocks (Hannum; Horvath) and two additional second-generation clocks (GrimAge; GrimAge2). Twelve adults were included: seven frail (LFI ≥ 4.4, mean age 55 years) and five robust (LFI < 3.2, mean age 55 years). Mean PhenoAge age acceleration (AgeAccel) was + 2.5 years (P = 0.23) for frail versus robust subjects. Mean PhenoAge AgeAccel was + 2.7 years (P = 0.19) for subjects who were readmitted or died within 30 days of discharge post-LT versus those without this outcome. When compared with first-generation clocks, the second-generation clocks demonstrated greater average AgeAccel for subjects with frailty or poor post-LT outcomes. Measuring biological age using DNAm-derived epigenetic clocks is feasible in adults undergoing LT. While frail and robust subjects had the same average chronological age, average biological age as measured by second-generation epigenetic clocks tended to be accelerated among those who were frail or experienced a poor post-LT outcome. These results suggest that frailty in these relatively young subjects with cirrhosis may involve similar aging mechanisms as frailty classically observed in chronologically older adults and warrant validation in a larger cohort.
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Affiliation(s)
- Sara C LaHue
- Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA.
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, 505 Parnassus Ave, Box 0114, San Francisco, CA, 94143, USA.
- Buck Institute for Research On Aging, Novato, CA, USA.
| | | | - Stephanie Roa Diaz
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | - Srilakshmi Seetharaman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Thelma Garcia
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | - David Furman
- Buck Institute for Research On Aging, Novato, CA, USA
- Instituto de Investigaciones en Medicina Traslacional, Universidad Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, 1629, Pilar, Argentina
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer C Lai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - John C Newman
- Buck Institute for Research On Aging, Novato, CA, USA
- Division of Geriatrics, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
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Sagy N, Meyrom N, Beckerman P, Pleniceanu O, Bar DZ. Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression. Clin Epigenetics 2024; 16:27. [PMID: 38347603 PMCID: PMC10863297 DOI: 10.1186/s13148-024-01642-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Chronological and biological age correlate with DNA methylation levels at specific sites in the genome. Linear combinations of multiple methylation sites, termed epigenetic clocks, can inform us the chronological age and predict multiple health-related outcomes. However, why some sites correlating with lifespan, healthspan, or specific medical conditions remain poorly understood. Kidney fibrosis is the common pathway for chronic kidney disease, which affects 10% of European and US populations. RESULTS Here we identify epigenetic clocks and methylation sites that correlate with kidney function. Moreover, we identify methylation sites that have a unique methylation signature in the kidney. Methylation levels in majority of these sites correlate with kidney state and function. When kidney function deteriorates, all of these sites regress toward the common methylation pattern observed in other tissues. Interestingly, while the majority of sites are less methylated in the kidney and become more methylated with loss of function, a fraction of the sites are highly methylated in the kidney and become less methylated when kidney function declines. These methylation sites are enriched for specific transcription-factor binding sites. In a large subset of sites, changes in methylation patterns are accompanied by changes in gene expression in kidneys of chronic kidney disease patients. CONCLUSIONS These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines. However, this information loss is not random, but guided toward a baseline that is dependent on the genomic loci. SIGNIFICANCE STATEMENT DNA methylation at specific sites accurately reflects chronological and biological age. We identify sites that have a unique methylation pattern in the kidney. Methylation levels in the majority of these sites correlate with kidney state and function. Moreover, when kidney function deteriorates, all of these sites regress toward the common methylation pattern observed in other tissues. Thus, the unique methylation signature of the kidney is degraded, and epigenetic information is lost, when kidney disease progresses. These methylation sites are enriched for specific and methylation-sensitive transcription-factor binding sites, and associated genes show disease-dependent changes in expression. These results support the information theory of aging, and the hypothesis that the unique tissue identity, as captured by methylation patterns, is lost as tissue function declines.
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Affiliation(s)
- Naor Sagy
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Noa Meyrom
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Pazit Beckerman
- Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel-Hashomer and The Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel-Hashomer and The Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Daniel Z Bar
- Department of Oral Biology, Goldschleger School of Dental Medicine, The Faculty of Medical and Health Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
- The AI and Data Science Center (TAD), Tel Aviv University, 69978, Tel Aviv, Israel.
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