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Xi YJ, Guo Q, Zhang R, Duan GS, Zhang SX. Identifying cellular senescence associated genes involved in the progression of end-stage renal disease as new biomarkers. BMC Nephrol 2023; 24:231. [PMID: 37553608 PMCID: PMC10408218 DOI: 10.1186/s12882-023-03285-0] [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: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Cellular senescence plays an essential role in the development and progression of end-stage renal disease (ESRD). However, the detailed mechanisms phenomenon remains unclear. METHODS The mRNA expression profiling dataset GSE37171 was taken from the Gene Expression Omnibus (GEO) database. The cell senescence-associated hub genes were selected by applying protein-protein interaction (PPI), followed by correlation analysis, gene interaction analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We next explored the relationships of hub genes with miRNAs, TFs, and diseases. The absolute abundance of eight immune cells and two stromal cells were calculated by MCPcount and the correlation of hub genes with these ten cells was analyzed. Lasso was used to selecting for trait genes. ROC curves and DCA decision curves were used to assess the accuracy and predictive power of the trait genes. RESULTS A total of 65 cellular senescence signature genes were identified among patients and controls. The PPI network screened out ten hub genes. GO and KEGG indicated that ten hub genes were associated with ESRD progression. Transcription factor gene interactions and common regulatory networks of miRNAs were also identified in the datasets. The hub genes were significantly correlated with immune cells and stromal cells. Then the lasso model was constructed to screen out the five most relevant signature genes (FOS, FOXO3, SIRT1, TP53, SMARCA4). The area under the ROC curve (AUC) showed that these five characteristic genes have good resolving power for the diagnostic model. CONCLUSIONS Our findings suggested that cellular senescence-associated genes played an important role in the development of ESRD and immune regulation.
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Affiliation(s)
- Yu-Jia Xi
- Department of Urology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi Province, China
| | - Qiang Guo
- Department of Urology, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Ran Zhang
- School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Guo-Sheng Duan
- Fifth School of Clinical Medicine, Shanxi Provincial People's Hospital, Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Sheng-Xiao Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi Province, China.
- Department of Rheumatology, Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, 030001, Shanxi Province, China.
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Makievskaya CI, Popkov VA, Andrianova NV, Liao X, Zorov DB, Plotnikov EY. Ketogenic Diet and Ketone Bodies against Ischemic Injury: Targets, Mechanisms, and Therapeutic Potential. Int J Mol Sci 2023; 24:2576. [PMID: 36768899 PMCID: PMC9916612 DOI: 10.3390/ijms24032576] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
The ketogenic diet (KD) has been used as a treatment for epilepsy since the 1920s, and its role in the prevention of many other diseases is now being considered. In recent years, there has been an intensive investigation on using the KD as a therapeutic approach to treat acute pathologies, including ischemic ones. However, contradictory data are observed for the effects of the KD on various organs after ischemic injury. In this review, we provide the first systematic analysis of studies conducted from 1980 to 2022 investigating the effects and main mechanisms of the KD and its mimetics on ischemia-reperfusion injury of the brain, heart, kidneys, liver, gut, and eyes. Our analysis demonstrated a high diversity of both the composition of the used KD and the protocols for the treatment of animals, which could be the reason for contradictory effects in different studies. It can be concluded that a true KD or its mimetics, such as β-hydroxybutyrate, can be considered as positive exposure, protecting the organ from ischemia and its negative consequences, whereas the shift to a rather similar high-calorie or high-fat diet leads to the opposite effect.
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Affiliation(s)
- Ciara I. Makievskaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vasily A. Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Nadezda V. Andrianova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Xinyu Liao
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Dmitry B. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Egor Y. Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
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3
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Chang ZS, He ZM, Xia JB. FoxO3 Regulates the Progress and Development of Aging and Aging-Related Diseases. Curr Mol Med 2023; 23:991-1006. [PMID: 36239722 DOI: 10.2174/1566524023666221014140817] [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: 06/20/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/22/2022]
Abstract
Aging is an inevitable risk factor for many diseases, including cardiovascular diseases, neurodegenerative diseases, cancer, and diabetes. Investigation into the molecular mechanisms involved in aging and longevity will benefit the treatment of age-dependent diseases and the development of preventative medicine for agingrelated diseases. Current evidence has revealed that FoxO3, encoding the transcription factor (FoxO)3, a key transcription factor that integrates different stimuli in the intrinsic and extrinsic pathways and is involved in cell differentiation, protein homeostasis, stress resistance and stem cell status, plays a regulatory role in longevity and in age-related diseases. However, the precise mechanisms by which the FoxO3 transcription factor modulates aging and promotes longevity have been unclear until now. Here, we provide a brief overview of the mechanisms by which FoxO3 mediates signaling in pathways involved in aging and aging-related diseases, as well as the current knowledge on the role of the FoxO3 transcription factor in the human lifespan and its clinical prospects. Ultimately, we conclude that FoxO3 signaling pathways, including upstream and downstream molecules, may be underlying therapeutic targets in aging and age-related diseases.
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Affiliation(s)
- Zao-Shang Chang
- Department of Physiology, School of Basic Medical Sciences, Shaoyang University, Shaoyang 422000, Hunan, China
| | - Zhi-Ming He
- Department of Physiology, School of Basic Medical Sciences, Shaoyang University, Shaoyang 422000, Hunan, China
| | - Jing-Bo Xia
- Guangdong Provincial Key Laboratory of Physical Activity and Health Promotion, Guangzhou Sport University, Guangzhou 510500, Guangdong, China
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5
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Gu X, Yang H, Sheng X, Ko YA, Qiu C, Park J, Huang S, Kember R, Judy RL, Park J, Damrauer SM, Nadkarni G, Loos RJF, My VTH, Chaudhary K, Bottinger EP, Paranjpe I, Saha A, Brown C, Akilesh S, Hung AM, Palmer M, Baras A, Overton JD, Reid J, Ritchie M, Rader DJ, Susztak K. Kidney disease genetic risk variants alter lysosomal beta-mannosidase ( MANBA) expression and disease severity. Sci Transl Med 2021; 13:13/576/eaaz1458. [PMID: 33441424 DOI: 10.1126/scitranslmed.aaz1458] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 04/08/2020] [Accepted: 12/09/2020] [Indexed: 02/05/2023]
Abstract
More than 800 million people in the world suffer from chronic kidney disease (CKD). Genome-wide association studies (GWAS) have identified hundreds of loci where genetic variants are associated with kidney function; however, causal genes and pathways for CKD remain unknown. Here, we performed integration of kidney function GWAS and human kidney-specific expression quantitative trait analysis and identified that the expression of beta-mannosidase (MANBA) was lower in kidneys of subjects with CKD risk genotype. We also show an increased incidence of renal failure in subjects with rare heterozygous loss-of-function coding variants in MANBA using phenome-wide association analysis of 40,963 subjects with exome sequencing data. MANBA is a lysosomal gene highly expressed in kidney tubule cells. Deep phenotyping revealed structural and functional lysosomal alterations in human kidneys from subjects with CKD risk alleles and mice with genetic deletion of Manba Manba heterozygous and knockout mice developed more severe kidney fibrosis when subjected to toxic injury induced by cisplatin or folic acid. Manba loss altered multiple pathways, including endocytosis and autophagy. In the absence of Manba, toxic acute tubule injury induced inflammasome activation and fibrosis. Together, these results illustrate the convergence of common noncoding and rare coding variants in MANBA in kidney disease development and demonstrate the role of the endolysosomal system in kidney disease development.
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Affiliation(s)
- Xiangchen Gu
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Division of Nephrology, Yueyang Hospital of Integrative Traditional Chinese and Western Medicine, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Hongliu Yang
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Division of Nephrology, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xin Sheng
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-An Ko
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chengxiang Qiu
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jihwan Park
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shizheng Huang
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel Kember
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Renae L Judy
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Joseph Park
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.,Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott M Damrauer
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Girish Nadkarni
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Hasso Plattner Institute of Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vy Thi Ha My
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Hasso Plattner Institute of Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ishan Paranjpe
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aparna Saha
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher Brown
- Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Adriana M Hung
- Nashville VA Medical Center, Nashville, TN 37212, USA.,Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Matthew Palmer
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aris Baras
- Regeneron Genetics Center (RGC), 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center (RGC), 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - Jeffrey Reid
- Regeneron Genetics Center (RGC), 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - Marylyn Ritchie
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.,Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.,Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katalin Susztak
- Department of Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. .,Department of Genetics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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