Epigenetics in acute kidney injury

Current Opinion in Nephrology and Hypertension

Volumn 24, Issue 4, 2015, Pages 351-358

  Tang, Jinhua ^a   Zhuang, Shougang ^a,b  

^a TONGJI UNIVERSITY SCHOOL OF MEDICINE   (China)

^b BROWN UNIVERSITY   (United States)

Author keywords

Acetylation; Acute kidney injury; Epigenetics; Methylation; microRNA

Indexed keywords

HISTONE; MICRORNA; PROTEIN;

ACUTE KIDNEY FAILURE; EPIGENETICS; GENE EXPRESSION; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HUMAN; MOLECULAR PATHOLOGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ACETYLATION; PROTEIN METHYLATION; REVIEW; ANIMAL; GENETIC EPIGENESIS; ISCHEMIA; KIDNEY; METABOLISM; PHYSIOLOGY; PROTEIN PROCESSING; REGENERATION;

ACUTE KIDNEY INJURY; ANIMALS; EPIGENESIS, GENETIC; HUMANS; ISCHEMIA; KIDNEY; PROTEIN PROCESSING, POST-TRANSLATIONAL; REGENERATION;

EID: 84942765600     PISSN: 10624821     EISSN: 14736543     Source Type: Journal    
DOI: 10.1097/MNH.0000000000000140     Document Type: Review

References (67)

1. Bomsztyk K, Denisenko O. Epigenetic alterations in acute kidney injury. Semin Nephrol 2013;33:327-340.
2. Rewa O, Bagshaw SM. Acute kidney injury-epidemiology, outcomes and economics. Nat Rev Nephrol 2014;10:193-207.
3. Bonventre JV, Yang L. Cellular pathophysiology of ischemic acute kidney injury. J Clin Invest 2011;121:4210-4221.
4. Kelly KJ. Acute renal failure: much more than a kidney disease. Semin Nephrol 2006;26:105-113.
5. Wen X, Murugan R, Peng Z, et al. Pathophysiology of acute kidney injury: a new perspective. Contrib Nephrol 2010;165:39-45.
6. Mehta RL, Kellum JA, Shah SV, et al. Acute kidney injury network: report of an initiative to improve outcomes in acute kidney injury. Crit Care 2007;11:R31.
7. Bonventre JV. Dedifferentiation and proliferation of surviving epithelial cells in acute renal failure. J Am Soc Nephrol 2003;14(Suppl 1):S55-S61.
8. He S, Liu N, Bayliss G, et al. EGFR activity is required for renal tubular cell dedifferentiation and proliferation in a murine model of folic acid-induced acute kidney injury. Am J Physiol Renal Physiol 2013;304:F356-F366.
9. Inche AG, La Thangue NB. Chromatin control and cancer-drug discovery: realizing the promise. Drug Discov Today 2006;11:97-109.
10. Bolden JE, Peart MJ, Johnstone RW. Anticancer activities of histone deacetylase inhibitors. Nat Rev Drug Discov 2006;5:769-784.
11. Chen S, Bellew C, Yao X, et al. Histone deacetylase (HDAC) activity is critical for embryonic kidney gene expression, growth, and differentiation. J Biol Chem 2011;286:32775-32789.
12. Majumdar G, Adris P, Bhargava N, et al. Pan-histone deacetylase inhibitors regulate signaling pathways involved in proliferative and pro-inflammatory mechanisms in h9c2 cells. BMC Genom 2012;13:709.
13. Lefevre GM, Patel SR, Kim D, et al. Altering a histone h3k4 methylation pathway in glomerular podocytes promotes a chronic disease phenotype. PLoS genet 2010;6:e1001142.
14. Yuan H, Marmorstein R. Histone acetyltransferases: rising ancient counterparts to protein kinases. Biopolymers 2013;99:98-111.
15. Roth SY, Denu JM, Allis CD. Histone acetyltransferases. Annu Rev Biochem 2001;70:81-120.
16. Thiagalingam S, Cheng KH, Lee HJ, et al. Histone deacetylases: unique players in shaping the epigenetic histone code. Ann NYAcad Sci 2003;983:84-100.
17. Havasi A, Haegele JA, Gall JM, et al. Histone acetyl transferase (HAT) HBO1 and JADE1 in epithelial cell regeneration. Am J Pathol 2013;182:152-162.
18. Bomsztyk K, Flanagin S, Mar. D, et al. Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated TNF-alpha gene in acute kidney injury. PloS one 2013;8:e70322.
19. Tang J, Yan Y, Zhao TC, et al. Class I histone deacetylase activity is required & for proliferation of renal epithelial cells. Am J Physiol Renal Physiol 2013;305:F244-F254. Inhibition of class I HDAC activity with MS-275, or silencing HDAC1, 3, or 8 with small interfering RNA decreases cell proliferation, and reduces expression of cyclin D1 and proliferating cell nuclear antigen in cultured renal proximal tubular cells.
20. Tang J, Yan Y, Zhao TC, et al. Class i HDAC activity is required for renal & protection and regeneration after acute kidney injury. Am J Physiol Renal Physiol 2014;307:F303-F316. In the mouse model of AKI, inhibition of class I HDACs with MS-275 resulted in more severe tubular injury as evidenced by worsening renal dysfunction, increased NGAL expression, and enhanced renal tubular cell apoptosis. MS-275 also impaired renal regeneration as indicated by decreased expression of renal Pax-2, vimentin, and PCNA.
21. Marumo T, Hishikawa K, Yoshikawa M, et al. Epigenetic regulation of BMP7 & in the regenerative response to ischemia. J Am Soc Nephrol 2008;19:1311-1320. I/R of the mouse kidney induces a transient decrease in histone acetylation in proximal tubular cells, which is accompanied by downregulation of HDAC5 and upregulation of BMP7 expression in the recovery phase of AKI. RNAi-mediated HDAC5 knockdown significantly increased histone acetylation and BMP7 expression.
22. Villanueva S, Cespedes C, Vio CP. Ischemic acute renal failure induces the expression of a wide range of nephrogenic proteins. Am J Physiol Regul Integr Comp Physiol 2006;290:R861-R870.
23. Tomita M, Asada M, Asada N, et al. BMP7 maintains undifferentiated kidney progenitor population and determines nephron numbers at birth. PloS one 2013;8:e73554.
24. Hsing CH, Lin CF, So E, et al. Alpha2-adrenoceptor agonistdexmedetomidine protects septic acute kidney injury through increasing BMP-7 and inhibiting HDAC2 and HDAC5. Am J Physiol Renal Physiol 2012;303:F1443-F1453.
25. Novitskaya T, McDermott L, Zhang KX, et al. A PTBA small molecule enhances recovery and reduces postinjury fibrosis after aristolochic acid-induced kidney injury. Am J Physiol Renal Physiol 2014;306:F496-F504.
26. Liu N, He S, Ma L, et al. Blocking the class I histone deacetylase ameliorates renal fibrosis and inhibits renal fibroblast activation via modulating TGF-b and EGFR signaling. PLoS ONE 2013;8:e54001.
27. Pratt JR, Parker MD, Affleck LJ, et al. Ischemic epigenetics and the transplanted kidney. Transplant Proc 2006;38:3344-3346. Cold ischemia and reperfusion resulted in a significant change in the ratio of methylated to unmethylated cytosines at CpG site, suggesting that DNA methylation can modify gene expression posttransplantation.
28. Mehta TK, Hoque MO, Ugarte R, et al. Quantitative detection of promoter hypermethylation as a biomarker of acute kidney injury during transplantation. Transplant Proc 2006;38:3420-3426.
29. Endo K, Kito N, Fukushima Y, et al. A novel biomarker for acute kidney injury using taqman-based unmethylated DNA-specific polymerase chain reaction. Biomed Res 2014;35:207-213.
30. Kang SW, Shih PA, Mathew RO, et al. Renal kallikrein excretion and epigenetics in human acute kidney injury: expression, mechanisms and consequences. BMC Nephrol 2011;12:27.
31. Huang N, Tan L, Xue Z, et al. Reduction of DNA hydroxymethylation in the mouse kidney insulted by ischemia reperfusion. Biochem Biophys Res Commun 2012;422:697-702.
32. Nguyen AT, Zhang Y. The diverse functions of Dot1 and H3K79 methylation. Genes Dev 2011;25:1345-1358.
33. Nelson JD, Denisenko O, Sova P, et al. Fast chromatin immunoprecipitation assay. Nucleic Acids Res 2006;34:e2.
34. Johnson AC, Ware LB, Himmelfarb J, et al. HMG-CoA reductase activation and urinary pellet cholesterol elevations in acute kidney injury. Clin J Am Soc Nephrol 2011;6:2108-2113.
35. Naito M, Bomsztyk K, Zager RA. Endotoxin mediates recruitment of RNA polymerase II to target genes in acute renal failure. J Am Soc Nephrol 2008;19:1321-1330.
36. Whyte WA, Bilodeau S, Orlando DA, et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012;482:221-225.
37. Shen Q, Jin H, Wang X, et al. Epidermal stem cells and their epigenetic regulation. Int J Mol Sci 2013;14:17861-17880.
38. He Y, Yu H, Sun S, et al. Trans-2-phenylcyclopropylamine regulates zebrafish lateral line neuromast development mediated by depression of LSD1 activity. Int J Dev Biol 2013;57:365-373.
39. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010;11:597-610.
40. Huntzinger E, Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 2011;12:99-110.
41. Bartel DP. MicroRNAs. Target recognition and regulatory functions. Cell 2009;136:215-233.
42. Wei Q, Bhatt K, He HZ, et al. Targeted deletion of Dicer from proximal tubules & protects against renal ischemia-reperfusion injury. J Am Soc Nephrol 2010;21:756-761. Deletion of Dicer from renal proximal tubules protected the kidney from injury as indicated by better renal function, less kidney damage, and improved survival compared with their wild-type littermates.
43. Cantaluppi V, Gatti S, Medica D, et al. Microvesicles derived from endothelial progenitor cells protect the kidney from ischemia-reperfusion injury by micro-RNA-dependent reprogramming of resident renal cells. Kidney Int 2012;82:412-427.
44. Lorenzen JM, Kaucsar T, Schauerte C, et al. MicroRNA-24 antagonism prevents renal ischemia reperfusion injury. J Am Soc Nephrol 2014;25:2717-2729.
45. Lan YF, Chen HH, Lai PF, et al. MicroRNA-494 reduces ATF3 expression and promotes AKI. J Am Soc Nephrol 2012;23:2012-2023.
46. Godwin JG, Ge X, Stephan K, et al. Identification of a microRNA signature of renal ischemia reperfusion injury. Proc Natl Acad Sci USA 2010;107:14339-14344.
47. Xu X, Kriegel AJ, Jiao X, et al. miR-21 in ischemia/reperfusion injury: a doubleedged sword? Physiol Genom 2014;46:789-797.
48. Aguado-Fraile E, Ramos E, Saenz-Morales D, et al. Mir-127 protects proximal tubule cells against ischemia/reperfusion: identification of kinesin family member 3b as miR-127 target. PloS ONE 2012;7:e44305.
49. Bhatt K, Wei Q, Pabla N, et al. Microrna-687 induced by hypoxia-inducible & factor-1 targets phosphatase and tensin homolog in renal ischemiareperfusion injury. J Am Soc Nephrol 2015; doi: 10.1681/ASN.2014050463. [Epub ahead of print] Hypoxia-inducible factor-1 mediates upregulation of microRNA 687 (miR-687) in the ischemic kidney and cultured kidney cells exposed to hypoxia. Inhibition of miR-687 preserves PTEN expression and leads to protection against kidney injury in mice.
50. Rossetto D, Avvakumov N, Cote J. Histone phosphorylation: a chromatin modification involved in diverse nuclear events. Epigenetics 2012;7:1098-1108.
51. Zippo A, Serafini R, Rocchigiani M, et al. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 2009;138:1122-1136.
52. Metzger E, Imhof A, Patel D, et al. Phosphorylation of histone H3T6 by PKCbeta (I) controls demethylation at histone h3k4. Nat 2010;464:792-796.
53. Tang J, Liu N, Tolbert E, et al. Sustained activation of EGFR triggers renal fibrogenesis after acute kidney injury. Am J Pathol 2013;183:160-172.
54. Tang J, Liu N, Zhuang S. Role of epidermal growth factor receptor in acute and chronic kidney injury. Kidney Int 2013;83:804-810.
55. Guo C, Wei Q, Su Y, et al. Sumoylation occurs in acute kidney injury and plays a cytoprotective role. Biochim Biophys Acta 2014;1852:482-489.
56. Martins-Marques T, Ribeiro-Rodrigues T, Pereira P, et al. Autophagy and ubiquitination in cardiovascular diseases. DNA Cell Biol 2015;34:243-251.
57. Varol B, Coskun O, Karabulut S, et al. Clinical significance of serum ADP-ribosylation and NAD glycohydrolase activity in patients with colorectal cancer. Tumour Biol 2014;35:5575-5582.
58. Goldstein DS, Sullivan P, Holmes C, et al. A vesicular sequestration to oxidative deamination shift in myocardial sympathetic nerves in Parkinson's disease. J Neurochem 2014; doi: 10.1111/jnc.12766. [Epub ahead of print]
59. Ravida A, Musante L, Kreivi M, et al. Glycosylation patterns of kidney proteins differ in rat diabetic nephropathy. Kidney Int 2015;87:963-974; doi: 10.1038/ki.2014.387. [Epub ahead of print]
60. Lazarus RC, Buonora JE, Jacobowitz DM, et al. Protein carbonylation after traumatic brain injury: cell specificity, regional susceptibility, and gender differences. Free Radic Biol Med 2015;78:89-100.
61. Agirre X, Vilas-Zornoza A, Jimenez-Velasco A, et al. Epigenetic silencing of the tumor suppressor microRNA Hsa-miR-124a regulates CDK6 expression and confers a poor prognosis in acute lymphoblastic leukemia. Cancer Res 2009;69:4443-4453.
62. Brueckner B, Stresemann C, Kuner R, et al. The human let-7a-3 locus contains an epigenetically regulated microRNA gene with oncogenic function. Cancer Res 2007;67:1419-1423.
63. Fabbri M, Garzon R, Cimmino A, et al. Microrna-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3a and 3b. Proc Natl Acad Sci USA 2007;104:15805-15810.
64. Furuta M, Kozaki KI, Tanaka S, et al. miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma. Carcinogenesis 2010;31:766-776.
65. Lujambio A, Ropero S, Ballestar E, et al. Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 2007;67:1424-1429.
66. Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr Res 2007;61:24R-29R.
67. Schiza V, Molina-Serrano D, Kyriakou D, et al. N-alpha-terminal acetylation of histone H4 regulates arginine methylation and ribosomal DNA silencing. PLoS Genet 2013;9:e1003805.