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Tavakolidakhrabadi N, Aulicino F, May CJ, Saleem MA, Berger I, Welsh GI. Genome editing and kidney health. Clin Kidney J 2024; 17:sfae119. [PMID: 38766272 PMCID: PMC11099665 DOI: 10.1093/ckj/sfae119] [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: 02/14/2024] [Indexed: 05/22/2024] Open
Abstract
Genome editing technologies, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas in particular, have revolutionized the field of genetic engineering, providing promising avenues for treating various genetic diseases. Chronic kidney disease (CKD), a significant health concern affecting millions of individuals worldwide, can arise from either monogenic or polygenic mutations. With recent advancements in genomic sequencing, valuable insights into disease-causing mutations can be obtained, allowing for the development of new treatments for these genetic disorders. CRISPR-based treatments have emerged as potential therapies, especially for monogenic diseases, offering the ability to correct mutations and eliminate disease phenotypes. Innovations in genome editing have led to enhanced efficiency, specificity and ease of use, surpassing earlier editing tools such as zinc-finger nucleases and transcription activator-like effector nucleases (TALENs). Two prominent advancements in CRISPR-based gene editing are prime editing and base editing. Prime editing allows precise and efficient genome modifications without inducing double-stranded DNA breaks (DSBs), while base editing enables targeted changes to individual nucleotides in both RNA and DNA, promising disease correction in the absence of DSBs. These technologies have the potential to treat genetic kidney diseases through specific correction of disease-causing mutations, such as somatic mutations in PKD1 and PKD2 for polycystic kidney disease; NPHS1, NPHS2 and TRPC6 for focal segmental glomerulosclerosis; COL4A3, COL4A4 and COL4A5 for Alport syndrome; SLC3A1 and SLC7A9 for cystinuria and even VHL for renal cell carcinoma. Apart from editing the DNA sequence, CRISPR-mediated epigenome editing offers a cost-effective method for targeted treatment providing new avenues for therapeutic development, given that epigenetic modifications are associated with the development of various kidney disorders. However, there are challenges to overcome, including developing efficient delivery methods, improving safety and reducing off-target effects. Efforts to improve CRISPR-Cas technologies involve optimizing delivery vectors, employing viral and non-viral approaches and minimizing immunogenicity. With research in animal models providing promising results in rescuing the expression of wild-type podocin in mouse models of nephrotic syndrome and successful clinical trials in the early stages of various disorders, including cancer immunotherapy, there is hope for successful translation of genome editing to kidney diseases.
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Affiliation(s)
| | - Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, Bristol Royal Hospital for Children
| | - Carl J May
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
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Wang Q, Zou B, Wei X, Lin H, Pang C, Wang L, Zhong J, Chen H, Gao X, Li M, Ong ACM, Yue Z, Sun L. Identification of renal cyst cells of type I Nephronophthisis by single-nucleus RNA sequencing. Front Cell Dev Biol 2023; 11:1192935. [PMID: 37583898 PMCID: PMC10423821 DOI: 10.3389/fcell.2023.1192935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/20/2023] [Indexed: 08/17/2023] Open
Abstract
Background: Nephronophthisis (NPH) is the most common genetic cause of end-stage renal disease (ESRD) in childhood, and NPHP1 is the major pathogenic gene. Cyst formation at the corticomedullary junction is a pathological feature of NPH, but the mechanism underlying cystogenesis is not well understood. The isolation and identification of cystic cell subpopulation could help to identify their origins and provide vital clues to the mechanisms underlying cystogenesis in NPH. Methods: Single-nucleus RNA sequencing (snRNA-seq) was performed to produce an atlas of NPHP1 renal cells. Kidney samples were collected from WT (Nphp1 +/+) mice and NPHP1 (Nphp1 del2-20/del2-20) model mice. Results: A comprehensive atlas of the renal cellular landscape in NPHP1 was generated, consisting of 14 basic renal cell types as well as a subpopulation of DCT cells that was overrepresented in NPHP1 kidneys compared to WT kidneys. GO analysis revealed significant downregulation of genes associated with tubular development and kidney morphogenesis in this subpopulation. Furthermore, the reconstruction of differentiation trajectories of individual cells within this subpopulation confirmed that a specific group of cells in NPHP1 mice become arrested at an early stage of differentiation and proliferate to form cysts. We demonstrate that Niban1 is a specific molecular marker of cystic cells in both mice and human NPHP1. Conclusion: In summary, we report a novel subpopulation of DCT cells, marked by Niban1, that are classified as cystic cells in the NPHP1 mice kidney. These results offer fresh insights into the cellular and molecular basis of cystogenesis in NPH.
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Affiliation(s)
- Qianying Wang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Baojuan Zou
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoya Wei
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongrong Lin
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changmiao Pang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinglin Zhong
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huamu Chen
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuefei Gao
- Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Min Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Albert C. M. Ong
- Kidney Genetics Group, Academic Nephrology Unit, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Zhihui Yue
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liangzhong Sun
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Qiu J, Germino GG, Menezes LF. Mechanisms of Cyst Development in Polycystic Kidney Disease. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:209-219. [PMID: 37088523 PMCID: PMC10289784 DOI: 10.1053/j.akdh.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Autosomal dominant polycystic kidney disease is the most common inherited cause of end-stage kidney disease worldwide. Most cases result from mutation of either of 2 genes, PKD1 and PKD2, which encode proteins that form a probable receptor/channel complex. Studies suggest that a loss of function of the complex below an indeterminate threshold triggers cyst initiation, which ultimately results in dysregulation of multiple metabolic processes and downstream pathways and subsequent cyst growth. Noncell autonomous factors may also promote cyst growth. In this report, we focus primarily on the process of early cyst formation and factors that contribute to its variability with brief consideration of how new studies suggest this process may be reversible.
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Affiliation(s)
- Jiahe Qiu
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | - Gregory G Germino
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD.
| | - Luis F Menezes
- Polycystic Kidney Disease Section, Kidney Disease Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD.
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Kocyigit I, Taheri S, Uysal C, Memis M, Ozayturk SG, Zararsiz G, Rassoulzadegan M. Predicting Progression of Autosomal Dominant Polycystic Kidney Disease by Changes in the Telomeric Epigenome. Cells 2022; 11:cells11203300. [PMID: 36291168 PMCID: PMC9600909 DOI: 10.3390/cells11203300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited cause of chronic kidney disease with Polycystin (PKD) 1 and 2 gene mutation. However, the intra-familial variability in symptoms further suggests a non-Mendelian contribution to the disease. Our goal was to find a marker to track the epigenetic changes common to rapidly progressing forms of the disease. The risk of ADPKD increases with age, and aging shortens the telomere length (TL). Telomeres are a nucleoprotein structure composed mainly of three complexes, shelterin, CST and RNA-containing telomere repeat(TERRA), which protects the ends of chromosomes from degradation and fusion, and plays a role in maintaining cellular stability and in the repair of telomeric damage. TERRAs are transcribed from telomeric regions and a part of them is engaged in a DNA/RNA hybrid (R-loop) at each chromosome end. We tracked TL and TERRA levels in blood samples of 78 patients and 20 healthy control. Our study demonstrates that TL was shortened and TERRA expression levels in the DNA-attached fraction increased in autosomal dominant polycystic kidney patients with mutations in PKD1 and PKD2 compared to the control group. Moreover, it was observed that the expression of TERRA engaged in the R-loop was higher and the length of telomeres shorter in patients with ADPKD who showed rapid disease progression. Intrafamilial variation in TL and TERRA levels with the same mutation would indicate reliable epigenetic potential biomarkers in disease monitoring.
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Affiliation(s)
- Ismail Kocyigit
- Department of Nephrology, Medical School, Erciyes University, 38280 Kayseri, Turkey
- Correspondence:
| | - Serpil Taheri
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
- Department of Medical Biology, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Cihan Uysal
- Department of Nephrology, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Mehmet Memis
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
| | - Salih Guntug Ozayturk
- Department of Internal Medicine, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Minoo Rassoulzadegan
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
- INSERM-CNRS, Université de Nice, 06107 Nice, France
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Agborbesong E, Li LX, Li L, Li X. Molecular Mechanisms of Epigenetic Regulation, Inflammation, and Cell Death in ADPKD. Front Mol Biosci 2022; 9:922428. [PMID: 35847973 PMCID: PMC9277309 DOI: 10.3389/fmolb.2022.922428] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder, which is caused by mutations in the PKD1 and PKD2 genes, characterizing by progressive growth of multiple cysts in the kidneys, eventually leading to end-stage kidney disease (ESKD) and requiring renal replacement therapy. In addition, studies indicate that disease progression is as a result of a combination of factors. Understanding the molecular mechanisms, therefore, should facilitate the development of precise therapeutic strategies for ADPKD treatment. The roles of epigenetic modulation, interstitial inflammation, and regulated cell death have recently become the focuses in ADPKD. Different epigenetic regulators, and the presence of inflammatory markers detectable even before cyst growth, have been linked to cyst progression. Moreover, the infiltration of inflammatory cells, such as macrophages and T cells, have been associated with cyst growth and deteriorating renal function in humans and PKD animal models. There is evidence supporting a direct role of the PKD gene mutations to the regulation of epigenetic mechanisms and inflammatory response in ADPKD. In addition, the role of regulated cell death, including apoptosis, autophagy and ferroptosis, have been investigated in ADPKD. However, there is no consensus whether cell death promotes or delays cyst growth in ADPKD. It is therefore necessary to develop an interactive picture between PKD gene mutations, the epigenome, inflammation, and cell death to understand why inherited PKD gene mutations in patients may result in the dysregulation of these processes that increase the progression of renal cyst formation.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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Xu J, Xue C, Wang X, Zhang L, Mei C, Mao Z. Chromatin Methylation Abnormalities in Autosomal Dominant Polycystic Kidney Disease. Front Med (Lausanne) 2022; 9:921631. [PMID: 35865176 PMCID: PMC9294145 DOI: 10.3389/fmed.2022.921631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease worldwide and is one of the major causes of end-stage renal disease. PKD1 and PKD2 are two genes that mainly contribute to the development and progression of ADPKD. The precise mechanism is not fully understood. In recent years, epigenetic modification has drawn increasing attention. Chromatin methylation is a very important category of PKD epigenetic changes and mostly involves DNA, histone, and RNA methylation. Genome hypomethylation and regional gene hypermethylation coexist in ADPKD. We found that the genomic DNA of ADPKD kidney tissues showed extensive demethylation by whole-genome bisulphite sequencing, while some regional DNA methylation from body fluids, such as blood and urine, can be used as diagnostic or prognostic biomarkers to predict PKD progression. Histone modifications construct the histone code mediated by histone methyltransferases and contribute to aberrant methylation changes in PKD. Considering the complexity of methylation abnormalities occurring in different regions and genes on the PKD epigenome, more specific therapy aiming to restore to the normal genome should lead to the development of epigenetic treatment.
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Affiliation(s)
- Jing Xu
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Cheng Xue
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xiaodong Wang
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Lei Zhang
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Lei Zhang
| | - Changlin Mei
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
- Changlin Mei
| | - Zhiguo Mao
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
- *Correspondence: Zhiguo Mao
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