Urine microRNA as potential biomarkers of autosomal dominant polycystic kidney disease progression: Description of miRNA profiles at baseline

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Ben Dov, Iddo Z ^a,e   Tan, Ying Cai ^b,c   Morozov, Pavel ^a   Wilson, Patricia D ^d   Rennert, Hanna ^b,c   Blumenfeld, Jon D ^c   Tuschl, Thomas ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

^d ROYAL FREE AND UNIVERSITY COLLEGE MEDICAL SCHOOL   (United Kingdom)

^e HADASSAH HEBREW UNIVERSITY MEDICAL CENTER   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

LET 7I; MICRORNA; MICRORNA 1; MICRORNA 133A; MICRORNA 133B; MICRORNA 143; MICRORNA 199A; MICRORNA 199B; MICRORNA 205; MICRORNA 223; MICRORNA 3619; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CHRONIC KIDNEY DISEASE; CISTRON; CLINICAL ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; HUMAN; HUMAN CELL; HUMAN TISSUE; KIDNEY POLYCYSTIC DISEASE; MALE; URINALYSIS;

ADULT; AGED; BIOLOGICAL MARKERS; DISEASE PROGRESSION; EPIGENESIS, GENETIC; FEMALE; FETUS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KIDNEY TUBULES; MALE; MICRORNAS; MIDDLE AGED; POLYCYSTIC KIDNEY, AUTOSOMAL DOMINANT; PRIMARY CELL CULTURE; PROGNOSIS; UROTHELIUM;

EID: 84900448037     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086856     Document Type: Article

References (43)

1. Pei Y, Obaji J, Dupuis A, Paterson AD, Magistroni R, et al. (2009) Unified criteria for ultrasonographic diagnosis of ADPKD. J Am Soc Nephrol 20: 205-212.
2. Myrvang H (2011) Polycystic kidney disease: Urinary fingerprints unique to patients with ADPKD. Nat Rev Nephrol 7: 244.
3. Grantham JJ, Torres VE, Chapman AB, Guay-Woodford LM, Bae KT, et al. (2006) Volume progression in polycystic kidney disease. The New England journal of medicine 354: 2122-2130. (Pubitemid 43736612)
4. Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, et al. (2011) Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int 79: 1244-1253.
5. Farazi TA, Horlings HM, Ten Hoeve JJ, Mihailovic A, Halfwerk H, et al. (2011) MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer research 71: 4443-4453.
6. Mullokandov G, Baccarini A, Ruzo A, Jayaprakash AD, Tung N, et al. (2012) High-throughput assessment of microRNA activity and function using micro-RNA sensor and decoy libraries. Nat Meth 9: 840-846.
7. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, et al. (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proceedings of the National Academy of Sciences of the United States of America 108: 5003-5008.
8. Fleissner F, Goerzig Y, Haverich A, Thum T (2012) Microvesicles as novel biomarkers and therapeutic targets in transplantation medicine. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 12: 289-297.
9. Kistler AD, Mischak H, Poster D, Dakna M, Wuthrich RP, et al. (2009) Identification of a unique urinary biomarker profile in patients with autosomal dominant polycystic kidney disease. Kidney international 76: 89-96.
10. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435: 834-838. (Pubitemid 40839735)
11. Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, et al. (2008) MicroRNAs accurately identify cancer tissue origin. Nature biotechnology 26: 462-469. (Pubitemid 351501813)
12. Wilson PD (1991) Monolayer cultures of microdissected renal tubule epithelial segments. J Tiss Culture Methods 13: 137-142.
13. Wilson PD, Dillingham MA, Breckon R, Anderson RJ (1985) Defined human renal tubular epithelia in culture: growth, characterization, and hormonal response. The American journal of physiology 248: F436-443. (Pubitemid 15142314)
14. Wilson PD, Schrier RW, Breckon RD, Gabow PA (1986) A new method for studying human polycystic kidney disease epithelia in culture. Kidney Int 30: 371-378. (Pubitemid 16029507)
15. Wilson PD, Devuyst O, Li X, Gatti L, Falkenstein D, et al. (2000) Apical plasma membrane mispolarization of NaK-ATPase in polycystic kidney disease epithelia is associated with aberrant expression of the beta2 isoform. Am J Pathol 156: 253-268. (Pubitemid 30644459)
16. Rohatgi R, Battini L, Kim P, Israeli S, Wilson PD, et al. (2008) Mechanoregulation of intracellular Ca2 + in human autosomal recessive polycystic kidney disease cyst-lining renal epithelial cells. Am J Physiol Renal Physiol 294: F890-899.
17. Saleem MA, O'Hare MJ, Reiser J, Coward RJ, Inward CD, et al. (2002) A conditionally immortalized human podocyte cell line demonstrating nephrin and podocin expression. Journal of the American Society of Nephrology : JASN 13: 630-638. (Pubitemid 34183927)
18. Kim YK, Yeo J, Kim B, Ha M, Kim VN (2012) Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Molecular cell 46: 893-895.
19. Williams Z, Ben-Dov IZ, Elias R, Mihailovic A, Brown M, et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proceedings of the National Academy of Sciences of the United States of America 110: 4255-4260.
20. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414. (Pubitemid 46970709)
21. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
22. McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40: 4288-4297.
23. Hafner M, Renwick N, Brown M, Mihailovic A, Holoch D, et al. (2011) RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17: 1697-1712.
24. Muthukumar T, Dadhania D, Ding R, Snopkowski C, Naqvi R, et al. (2005) Messenger RNA for FOXP3 in the Urine of Renal-Allograft Recipients. The New England journal of medicine 353: 2342-2351. (Pubitemid 41713746)
25. Hanke M, Kausch I, Dahmen G, Jocham D, Warnecke JM (2007) Detailed Technical Analysis of Urine RNA-Based Tumor Diagnostics Reveals ETS2/Urokinase Plasminogen Activator to Be a Novel Marker for Bladder Cancer. Clin Chem 53: 2070-2077. (Pubitemid 350197289)
26. Wilson PD (2009) In vitro methods in Renal Research. In: E. D. . Avner, W. . Harmon and P. . Niaudet, editors. Pediatric Nephrology. Lippincott Williams & Wilkins.
27. Wilson PD (2004) Polycystic kidney disease: new understanding in the pathogenesis. The international journal of biochemistry & cell biology 36: 1868-1873.
28. Wilson PD (2001) Polycystin: new aspects of structure, function, and regulation. J Am Soc Nephrol 12: 834-845.
29. Wilson PD (2004) Polycystic kidney disease. The New England journal of medicine 350: 151-164.
30. Burrow CR, Devuyst O, Li X, Gatti L, Wilson PD (1999) Expression of the beta2-subunit and apical localization of Na+-K+-ATPase in metanephric kidney. The American journal of physiology 277: F391-403. (Pubitemid 29459652)
31. Kawakami K, Enokida H, Chiyomaru T, Tatarano S, Yoshino H, et al. (2012) The functional significance of miR-1 and miR-133a in renal cell carcinoma. Eur J Cancer 48: 827-836.
32. Orskov B, Sorensen VR, Feldt-Rasmussen B, Strandgaard S (2012) Changes in causes of death and risk of cancer in Danish patients with autosomal dominant polycystic kidney disease and end-stage renal disease. Nephrol Dial Transplant 27: 1607-1613.
33. Jilg CA, Drendel V, Bacher J, Pisarski P, Neeff H, et al. (2013) Autosomal Dominant Polycystic Kidney Disease: Prevalence of Renal Neoplasias in Surgical Kidney Specimens. Nephron Clin Pract 123: 13-21.
34. Zhao Y, Samal E, Srivastava D (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220. (Pubitemid 41021266)
35. Meder B, Katus HA, Rottbauer W (2008) Right into the heart of microRNA-133a. Genes & development 22: 3227-3231.
36. van Rooij E, Quiat D, Johnson BA, Sutherland LB, Qi X, et al. (2009) A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Developmental cell 17: 662-673.
37. Karihaloo A, Koraishy F, Huen SC, Lee Y, Merrick D, et al. (2011) Macrophages promote cyst growth in polycystic kidney disease. J Am Soc Nephrol 22: 1809-1814.
38. Swanson MS, Dreyfuss G (1988) Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities. Mol Cell Biol 8: 2237-2241.
39. Ta MH, Harris DC, Rangan GK (2013) Role of interstitial inflammation in the pathogenesis of polycystic kidney disease. Nephrology (Carlton) 18: 317-330.
40. Schieren G, Rumberger B, Klein M, Kreutz C, Wilpert J, et al. (2006) Gene profiling of polycystic kidneys. Nephrol Dial Transplant 21: 1816-1824. (Pubitemid 43985708)
41. Zheng D, Wolfe M, Cowley BD Jr, Wallace DP, Yamaguchi T, et al. (2003) Urinary excretion of monocyte chemoattractant protein-1 in autosomal dominant polycystic kidney disease. J Am Soc Nephrol 14: 2588-2595. (Pubitemid 37169344)
42. Meijer E, Boertien WE, Nauta FL, Bakker SJ, van Oeveren W, et al. (2010) Association of urinary biomarkers with disease severity in patients with autosomal dominant polycystic kidney disease: a cross-sectional analysis. Am J Kidney Dis 56: 883-895.
43. Slaby O, Bienertova-Vasku J, Svoboda M, Vyzula R (2012) Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancer. Journal of cellular and molecular medicine 16: 8-21.