Child Kidney Dis.  2025 Feb;29(1):4-11. 10.3339/ckd.25.008.

CRISPR-Cas9 system in autosomal dominant polycystic kidney disease: a comprehensive review

Affiliations
  • 1Department of Pharmacology and Toxicology, Molecular Genetics and Microbiology, University of Toronto, Toronto, ON, Canada
  • 2Department of Pediatrics, Changwon Hanmaeum Hospital, Hanyang University College of Medicine, Changwon, Republic of Korea
  • 3Department of Orthopedic Surgery, Yonsei University Health System, Seoul, Republic of Korea
  • 4Department of Internal Medicine IV, Nephrology and Hypertension, Medical University of Innsbruck, Innsbruck, Austria
  • 5Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
  • 6Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
  • 7Severance Underwood Meta-Research Center, Institute of Convergence Science, Yonsei University, Seoul, Republic of Korea

Abstract

Genetic kidney diseases are caused by mutations in specific genes that significantly affect kidney development and function. Although the underlying pathogenic genes of many kidney diseases have been identified, an understanding of their mechanisms and effective treatments remains limited. Gene editing, particularly using clustered regularly interspaced short palindromic repeats (CRISPR), has recently become a promising approach for studying genetic diseases and the CRISPR/CRISPR-associated protein 9 (CRISPR-Cas9) method has become a prominent research method. It has been shown that CRISPR-Cas9 can be targeted to knock out specific genomic sites, which enables researchers to correct gene mutations, prevent inheritance, and better understand the function of genes and the effectiveness of drugs. However, the application of CRISPR-Cas9 technology in the development of therapeutic agents against genetic kidney disease has been overlooked compared with other genetic diseases. In this paper, we provide an overview of the current research advancements in genetic kidney diseases using CRISPR technology, as well as the diverse preclinical research methods implemented, with particular emphasis on autosomal dominant polycystic kidney disease.

Keyword

Autosomal dominant polycystic kidney disease; Clustered regularly interspaced short palindromic repeats; CRISPR-associated protein 9; Gene editing; Kidney

Reference

References

1. Ayme S, Bockenhauer D, Day S, Devuyst O, Guay-Woodford LM, Ingelfinger JR, et al. Common elements in rare kidney diseases: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) controversies conference. Kidney Int. 2017; 92:796–808. DOI: 10.1016/j.kint.2017.10.004. PMID: 29153144.
2. Vivante A, Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease. Nat Rev Nephrol. 2016; 12:133–46. DOI: 10.1038/nrneph.2015.205. PMID: 26750453.
Article
3. Kidney Disease: Improving Global Outcomes (KDIGO) Lupus Nephritis Work Group. KDIGO 2024 clinical practice guideline for the management of LUPUS NEPHRITIS. Kidney Int. 2024; 105(1S):S1–69. DOI: 10.1016/j.kint.2023.09.002. PMID: 38182286.
4. Torra R, Furlano M, Ortiz A, Ars E. Genetic kidney diseases as an underrecognized cause of chronic kidney disease: the key role of international registry reports. Clin Kidney J. 2021; 14:1879–85. DOI: 10.1093/ckj/sfab056. PMID: 34345410.
Article
5. Devuyst O, Knoers NV, Remuzzi G, Schaefer F; Board of the Working Group for Inherited Kidney Diseases of the European Renal Association and European Dialysis and Transplant Association. Rare inherited kidney diseases: challenges, opportunities, and perspectives. Lancet. 2014; 383:1844–59. DOI: 10.1016/s0140-6736(14)60659-0. PMID: 24856029.
Article
6. KDIGO Conference Participants. Genetics in chronic kidney disease: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) controversies conference. Kidney Int. 2022; 101:1126–41. PMID: 35460632.
7. Roth TL, Marson A. Genetic disease and therapy. Annu Rev Pathol. 2021; 16:145–66. DOI: 10.1146/annurev-pathmechdis-012419-032626. PMID: 33497260.
Article
8. Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012; 109:E2579–86. DOI: 10.1073/pnas.1208507109. PMID: 22949671.
Article
9. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337:816–21. DOI: 10.1126/science.1225829. PMID: 22745249.
Article
10. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339:819–23. DOI: 10.1126/science.1231143. PMID: 23287718.
Article
11. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. Elife. 2013; 2:e00471. DOI: 10.7554/elife.00471. PMID: 23386978.
Article
12. Cruz NM, Freedman BS. CRISPR gene editing in the kidney. Am J Kidney Dis. 2018; 71:874–83. DOI: 10.1053/j.ajkd.2018.02.347. PMID: 29606501.
Article
13. Li T, Yang Y, Qi H, Cui W, Zhang L, Fu X, et al. CRISPR/Cas9 therapeutics: progress and prospects. Signal Transduct Target Ther. 2023; 8:36. DOI: 10.1038/s41392-023-01309-7. PMID: 36646687.
Article
14. Safi W, Marco A, Moya D, Prado P, Garreta E, Montserrat N. Assessing kidney development and disease using kidney organoids and CRISPR engineering. Front Cell Dev Biol. 2022; 10:948395. DOI: 10.3389/fcell.2022.948395. PMID: 36120564.
Article
15. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013; 339:823–6. DOI: 10.1126/science.1232033. PMID: 23287722.
Article
16. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011; 471:602–7. DOI: 10.1038/nature09886. PMID: 21455174.
Article
17. Ma H, Marti-Gutierrez N, Park SW, Wu J, Lee Y, Suzuki K, et al. Correction of a pathogenic gene mutation in human embryos. Nature. 2017; 548:413–9. DOI: 10.3410/f.727864756.793535171. PMID: 28783728.
Article
18. Chapman AB, Devuyst O, Eckardt KU, Gansevoort RT, Harris T, Horie S, et al. Autosomal-dominant polycystic kidney disease (ADPKD): executive summary from a Kidney Disease: Improving Global Outcomes (KDIGO) controversies conference. Kidney Int. 2015; 88:17–27. DOI: 10.1038/ki.2015.59. PMID: 25786098.
Article
19. Patel V, Chowdhury R, Igarashi P. Advances in the pathogenesis and treatment of polycystic kidney disease. Curr Opin Nephrol Hypertens. 2009; 18:99–106. DOI: 10.1097/mnh.0b013e3283262ab0. PMID: 19430332.
Article
20. European Polycystic Kidney Disease Consortium. The polycystic kidney disease 1 gene encodes a 14 kb transcript and lies within a duplicated region on chromosome 16. Cell. 1994; 77:881–94. DOI: 10.1016/0092-8674(94)90137-6. PMID: 8004675.
21. Mochizuki T, Wu G, Hayashi T, Xenophontos SL, Veldhuisen B, Saris JJ, et al. PKD2, a gene for polycystic kidney disease that encodes an integral membrane protein. Science. 1996; 272:1339–42. DOI: 10.1126/science.272.5266.1339. PMID: 8650545.
Article
22. Harris PC, Rossetti S. Molecular diagnostics for autosomal dominant polycystic kidney disease. Nat Rev Nephrol. 2010; 6:197–206. DOI: 10.1038/nrneph.2010.18. PMID: 20177400.
Article
23. Ong AC, Harris PC. A polycystin-centric view of cyst formation and disease: the polycystins revisited. Kidney Int. 2015; 88:699–710. DOI: 10.1038/ki.2015.207. PMID: 26200945.
Article
24. Lanktree MB, Haghighi A, di Bari I, Song X, Pei Y. Insights into autosomal dominant polycystic kidney disease from genetic studies. Clin J Am Soc Nephrol. 2021; 16:790–9. DOI: 10.2215/cjn.02320220. PMID: 32690722.
Article
25. Lantinga-van Leeuwen IS, Dauwerse JG, Baelde HJ, Leonhard WN, van de Wal A, Ward CJ, et al. Lowering of Pkd1 expression is sufficient to cause polycystic kidney disease. Hum Mol Genet. 2004; 13:3069–77. DOI: 10.1093/hmg/ddh336. PMID: 15496422.
Article
26. Hopp K, Ward CJ, Hommerding CJ, Nasr SH, Tuan HF, Gainullin VG, et al. Functional polycystin-1 dosage governs autosomal dominant polycystic kidney disease severity. J Clin Invest. 2012; 122:4257–73. DOI: 10.1172/jci64313. PMID: 23064367.
Article
27. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007; 131:861–72. DOI: 10.1016/j.cell.2007.11.019. PMID: 18035408.
Article
28. Pandya H, Shen MJ, Ichikawa DM, Sedlock AB, Choi Y, Johnson KR, et al. Differentiation of human and murine induced pluripotent stem cells to microglia-like cells. Nat Neurosci. 2017; 20:753–9. DOI: 10.1038/nn.4534. PMID: 28253233.
Article
29. Ullah I, Abu-Dawud R, Busch JF, Rabien A, Erguen B, Fischer I, et al. VEGF: supplemented extracellular matrix is sufficient to induce endothelial differentiation of human iPSC. Biomaterials. 2019; 216:119283. DOI: 10.1016/j.biomaterials.2019.119283. PMID: 31247481.
30. Ueda T, Kaneko S. In vitro differentiation of T cell: from CAR-modified T-iPSC. Methods Mol Biol. 2019; 2048:85–91. DOI: 10.1007/978-1-4939-9728-2_10. PMID: 31396933.
Article
31. Wang G, Yang L, Grishin D, Rios X, Ye LY, Hu Y, et al. Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc. 2017; 12:88–103. DOI: 10.1038/nprot.2016.152. PMID: 27929521.
Article
32. Freedman BS, Brooks CR, Lam AQ, Fu H, Morizane R, Agrawal V, et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat Commun. 2015; 6:8715. DOI: 10.1038/ncomms9715. PMID: 26493500.
Article
33. Cruz NM, Song X, Czerniecki SM, Gulieva RE, Churchill AJ, Kim YK, et al. Organoid cystogenesis reveals a critical role of microenvironment in human polycystic kidney disease. Nat Mater. 2017; 16:1112–9. DOI: 10.1038/nmat4994. PMID: 28967916.
34. Huang B, Zeng Z, Li H, Li Z, Chen X, Guo J, et al. Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids. bioRxiv [Preprint] 2023 May 25. https://doi.org/10.1101/2023.05.25.542343.
35. Vishy CE, Thomas C, Vincent T, Crawford DK, Goddeeris MM, Freedman BS. Genetics of cystogenesis in base-edited human organoids reveal therapeutic strategies for polycystic kidney disease. Cell Stem Cell. 2024; 31:537–53.e5. DOI: 10.1016/j.stem.2024.03.005. PMID: 38579684.
Article
36. Taguchi A, Kaku Y, Ohmori T, Sharmin S, Ogawa M, Sasaki H, et al. Redefining the in vivo origin of metanephric nephron progenitors enables generation of complex kidney structures from pluripotent stem cells. Cell Stem Cell. 2014; 14:53–67. DOI: 10.1016/j.stem.2013.11.010. PMID: 24332837.
Article
37. Paul BM, Vanden Heuvel GB. Kidney: polycystic kidney disease. Wiley Interdiscip Rev Dev Biol. 2014; 3:465–87. DOI: 10.1002/wdev.152. PMID: 25186187.
Article
38. Kuraoka S, Tanigawa S, Taguchi A, Hotta A, Nakazato H, Osafune K, et al. PKD1-dependent renal cystogenesis in human induced pluripotent stem cell-derived ureteric bud/collecting duct organoids. J Am Soc Nephrol. 2020; 31:2355–71. DOI: 10.1681/asn.2020030378. PMID: 32747355.
Article
39. Huang B, Zeng Z, Kim S, Fausto CC, Koppitch K, Li H, et al. Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease. Cell Stem Cell. 2024; 31:921–39.e17. DOI: 10.1016/j.stem.2024.04.002. PMID: 38692273.
Article
40. Yang B, Sonawane ND, Zhao D, Somlo S, Verkman AS. Small-molecule CFTR inhibitors slow cyst growth in polycystic kidney disease. J Am Soc Nephrol. 2008; 19:1300–10. DOI: 10.1681/asn.2007070828. PMID: 18385427.
Article
41. Takiar V, Nishio S, Seo-Mayer P, King JD, Li H, Zhang L, et al. Activating AMP-activated protein kinase (AMPK) slows renal cystogenesis. Proc Natl Acad Sci U S A. 2011; 108:2462–7. DOI: 10.1073/pnas.1011498108. PMID: 21262823.
Article
42. Pastor-Soler NM, Li H, Pham J, Rivera D, Ho PY, Mancino V, et al. Metformin improves relevant disease parameters in an autosomal dominant polycystic kidney disease mouse model. Am J Physiol Renal Physiol. 2022; 322:F27–41. DOI: 10.1152/ajprenal.00298.2021. PMID: 34806449.
Article
43. Li LX, Fan LX, Zhou JX, Grantham JJ, Calvet JP, Sage J, et al. Lysine methyltransferase SMYD2 promotes cyst growth in autosomal dominant polycystic kidney disease. J Clin Invest. 2017; 127:2751–64. DOI: 10.1172/jci90921. PMID: 28604386.
Article
44. Li LX, Zhang L, Agborbesong E, Zhang X, Zhou JX, Li X. Cross talk between lysine methyltransferase Smyd2 and TGF-β-Smad3 signaling promotes renal fibrosis in autosomal dominant polycystic kidney disease. Am J Physiol Renal Physiol. 2022; 323:F227–42. DOI: 10.1152/ajprenal.00452.2021. PMID: 35759739.
Article
45. Chumley P, Zhou J, Mrug S, Chacko B, Parant JM, Challa AK, et al. Truncating PKHD1 and PKD2 mutations alter energy metabolism. Am J Physiol Renal Physiol. 2019; 316:F414–25. DOI: 10.1152/ajprenal.00167.2018. PMID: 30566001.
46. Porath B, Gainullin VG, Cornec-Le Gall E, Dillinger EK, Heyer CM, Hopp K, et al. Mutations in GANAB, encoding the glucosidase IIα subunit, cause autosomal-dominant polycystic kidney and liver disease. Am J Hum Genet. 2016; 98:1193–207. DOI: 10.3410/f.726397953.793521825. PMID: 27259053.
47. Combes RD, Balls M. Every silver lining has a cloud: the scientific and animal welfare issues surrounding a new approach to the production of transgenic animals. Altern Lab Anim. 2014; 42:137–45. DOI: 10.1177/026119291404200206.
Article
48. Ayanoglu FB, Elcin AE, Elcin YM. Bioethical issues in genome editing by CRISPR-Cas9 technology. Turk J Biol. 2020; 44:110–20. DOI: 10.3906/biy-1912-52. PMID: 32256147.
Article
49. Andrews KL, Mudd JL, Li C, Miner JH. Quantitative trait loci influence renal disease progression in a mouse model of Alport syndrome. Am J Pathol. 2002; 160:721–30. DOI: 10.1016/s0002-9440(10)64892-4. PMID: 11839593.
Article
50. Cosgrove D, Kalluri R, Miner JH, Segal Y, Borza DB. Choosing a mouse model to study the molecular pathobiology of Alport glomerulonephritis. Kidney Int. 2007; 71:615–8. DOI: 10.1038/sj.ki.5002115. PMID: 17290292.
Article
51. Watanabe M, Umeyama K, Nakano K, Matsunari H, Fukuda T, Matsumoto K, et al. Generation of heterozygous PKD1 mutant pigs exhibiting early-onset renal cyst formation. Lab Invest. 2022; 102:560–9. DOI: 10.1038/s41374-021-00717-z. PMID: 34980882.
Article
52. Tsukiyama T, Kobayashi K, Nakaya M, Iwatani C, Seita Y, Tsuchiya H, et al. Monkeys mutant for PKD1 recapitulate human autosomal dominant polycystic kidney disease. Nat Commun. 2019; 10:5517. DOI: 10.1038/s41467-019-13398-6. PMID: 31822676.
Article
53. Soomro I, Hong A, Li Z, Duncan JS, Skolnik EY. Discoidin domain receptor 1 (DDR1) tyrosine kinase is upregulated in PKD kidneys but does not play a role in the pathogenesis of polycystic kidney disease. PLoS One. 2019; 14:e0211670. DOI: 10.1371/journal.pone.0211670. PMID: 31260458.
Article
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