Genome-wide identification of microRNA-related variants associated with risk of Alzheimer's disease

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Ghanbari, Mohsen ^a,b   Ikram, M Arfan ^a   De Looper, Hans W J ^a   Hofman, Albert ^a,c   Erkeland, Stefan J ^a   Franco, Oscar H ^a   Dehghan, Abbas ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b MASHHAD UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; LOW DENSITY LIPOPROTEIN RECEPTOR RELATED PROTEIN; MICRORNA; MIRN320 MICRORNA, HUMAN; NECTIN; NECTIN2 PROTEIN, HUMAN; SORL1 PROTEIN, HUMAN;

3' UNTRANSLATED REGION; ALZHEIMER DISEASE; BINDING SITE; BRAIN; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN; METABOLISM; SINGLE NUCLEOTIDE POLYMORPHISM;

3' UNTRANSLATED REGIONS; ALZHEIMER DISEASE; BINDING SITES; BRAIN; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LDL-RECEPTOR RELATED PROTEINS; MEMBRANE TRANSPORT PROTEINS; MICRORNAS; NECTINS; NUCLEIC ACID CONFORMATION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84975847419     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep28387     Document Type: Article

References (60)

1. Brookmeyer, R., Johnson, E., Ziegler-Graham, K. & Arrighi, H. M. Forecasting the global burden of Alzheimer's disease. Alzheimers Dement 3, 186-91 (2007).
2. Schmechel, D. E. et al. Increased amyloid beta-peptide deposition in cerebral cortex as a consequence of apolipoprotein E genotype in late-onset Alzheimer disease. Proc Natl Acad Sci USA 90, 9649-53 (1993).
3. Frankfort, S. V. et al. Amyloid beta protein and tau in cerebrospinal fluid and plasma as biomarkers for dementia: A review of recent literature. Curr Clin Pharmacol 3, 123-31 (2008).
4. Crews, L. & Masliah, E. Molecular mechanisms of neurodegeneration in Alzheimer's disease. Hum Mol Genet 19, R12-20 (2010).
5. Hampel, H. et al. Biomarkers for Alzheimer's disease: Academic, industry and regulatory perspectives. Nat Rev Drug Discov 9, 560-74 (2010).
6. Kivipelto, M. et al. Midlife vascular risk factors and Alzheimer's disease in later life: longitudinal, population based study. BMJ 322, 1447-51 (2001).
7. Geekiyanage, H. & Chan, C. MicroRNA-137/181c regulates serine palmitoyltransferase and in turn amyloid beta, novel targets in sporadic Alzheimer's disease. J Neurosci 31, 14820-30 (2011).
8. Long, J. M. & Lahiri, D. K. MicroRNA-101 downregulates Alzheimer's amyloid-beta precursor protein levels in human cell cultures and is differentially expressed. Biochem Biophys Res Commun 404, 889-95 (2011).
9. Patel, N. et al. MicroRNAs can regulate human APP levels. Mol Neurodegener 3, 10 (2008).
10. Leidinger, P. et al. A blood based 12-miRNA signature of Alzheimer disease patients. Genome Biol 14, R78 (2013).
11. Tan, L., Yu, J. T. & Tan, L. Causes and Consequences of MicroRNA Dysregulation in Neurodegenerative Diseases. Mol Neurobiol 51, 1249-62 (2015).
12. Zi, Y. et al. Circulating MicroRNA as Potential Source for Neurodegenerative Diseases Biomarkers. Mol Neurobiol 52(3), 1494-503 (2014).
13. Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215-33 (2009).
14. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
15. Ghanbari, M. et al. A genetic variant in the seed region of miR-4513 shows pleiotropic effects on lipid and glucose homeostasis, blood pressure, and coronary artery disease. Hum Mutat 35, 1524-31 (2014).
16. Dorn, G. W. 2nd, Matkovich, S. J., Eschenbacher, W. H. & Zhang, Y. A human 3′ miR-499 mutation alters cardiac mRNA targeting and function. Circ Res 110, 958-67 (2012).
17. Georges, M. et al. Polymorphic microRNA-Target interactions: A novel source of phenotypic variation. Cold Spring Harb Symp Quant Biol 71, 343-50 (2006).
18. Ghanbari, M. et al. Genetic Variations in miRNA Binding Sites Affect miRNA-Mediated Regulation of Several Genes Associated with Cardiometabolic Phenotypes. Circ Cardiovasc Genet 8(3), 473-86 (2015).
19. Richardson, K. et al. Gain-of-function lipoprotein lipase variant rs13702 modulates lipid traits through disruption of a microRNA-410 seed site. Am J Hum Genet 92, 5-14 (2013).
20. Ghanbari, M. et al. The association of common polymorphisms in miR-196a2 with waist to hip ratio and miR-1908 with serum lipid and glucose. Obesity (Silver Spring) 23, 495-503 (2015).
21. Landi, D. et al. Polymorphisms within micro-RNA-binding sites and risk of sporadic colorectal cancer. Carcinogenesis 29, 579-84 (2008).
22. Ghanbari, M. et al. Genetic Variants in MicroRNAs and their Binding Sites are Associated with the Risk of Parkinson Disease. Hum Mutat 37(3), 292-300 (2015).
23. Lambert, J. C. et al. Meta-Analysis of 74, 046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet 45, 1452-8 (2013).
24. Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26 (2011).
25. Hollingworth, P. et al. Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet 43, 429-35 (2011).
26. Dweep, H., Sticht, C., Pandey, P. & Gretz, N. miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 44, 839-47 (2011).
27. Kumar, M., Nath, S., Prasad, H. K., Sharma, G. D. & Li, Y. MicroRNAs: A new ray of hope for diabetes mellitus. Protein Cell 3, 726-38 (2012).
28. Chen, L. et al. microRNAs regulate adipocyte differentiation. Cell Biol Int (2013).
29. Qi, L. et al. A SNP site in pri-miR-124 changes mature miR-124 expression but no contribution to Alzheimer's disease in a Mongolian population. Neurosci Lett 515, 1-6 (2012).
30. Saba, R., Medina, S. J. & Booth, S. A. A functional SNP catalog of overlapping miRNA-binding sites in genes implicated in prion disease and other neurodegenerative disorders. Hum Mutat 35, 1233-48 (2014).
31. Berezikov, E., Chung, W. J., Willis, J., Cuppen, E. & Lai, E. C. Mammalian mirtron genes. Mol Cell 28, 328-36 (2007).
32. Cammaerts, S., Strazisar, M., De Rijk, P. & Del Favero, J. Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. Front Genet 6, 186 (2015).
33. Sun, G. et al. SNPs in human miRNA genes affect biogenesis and function. RNA 15, 1640-51 (2009).
34. Ryan, B. M., Robles, A. I. & Harris, C. C. Genetic variation in microRNA networks: The implications for cancer research. Nat Rev Cancer 10, 389-402 (2010).
35. Rogaeva, E. et al. The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat Genet 39, 168-77 (2007).
36. Tong, Y., Xu, Y., Scearce-Levie, K., Ptacek, L. J. & Fu, Y. H. COL25A1 triggers and promotes Alzheimer's disease-like pathology in vivo. Neurogenetics 11, 41-52 (2010).
37. Vardarajan, B. N. et al. Coding mutations in SORL1 and Alzheimer disease. Ann Neurol 77, 215-27 (2015).
38. Nicodemus, K. K. et al. Comprehensive association analysis of APOE regulatory region polymorphisms in Alzheimer disease. Neurogenetics 5, 201-8 (2004).
39. Yu, C. E. et al. Comprehensive analysis of APOE and selected proximate markers for late-onset Alzheimer's disease: patterns of linkage disequilibrium and disease/marker association. Genomics 89, 655-65 (2007).
40. Jeyaseelan, K., Lim, K. Y. & Armugam, A. MicroRNA expression in the blood and brain of rats subjected to transient focal ischemia by middle cerebral artery occlusion. Stroke 39, 959-66 (2008).
41. Naj, A. C. et al. Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet 43, 436-41 (2011).
42. Deng, Y. L. et al. The prevalence of CD33 and MS4A6A variant in Chinese Han population with Alzheimer's disease. Hum Genet 131, 1245-9 (2012).
43. Miyashita, A. et al. SORL1 is genetically associated with late-onset Alzheimer's disease in Japanese, Koreans and Caucasians. PLoS One 8, e58618 (2013).
44. Heman-Ackah, S. M., Hallegger, M., Rao, M. S. & Wood, M. J. RISC in PD: The impact of microRNAs in Parkinson's disease cellular and molecular pathogenesis. Front Mol Neurosci 6, 40 (2013).
45. Alwazzan, M., Newman, E., Hamshere, M. G. & Brook, J. D. Myotonic dystrophy is associated with a reduced level of RNA from the DMWD allele adjacent to the expanded repeat. Hum Mol Genet 8, 1491-7 (1999).
46. Liu, D. Z. et al. Brain and blood microRNA expression profiling of ischemic stroke, intracerebral hemorrhage, and kainate seizures. J Cereb Blood Flow Metab 30, 92-101 (2010).
47. Westerlaken, J. H., Van der Zee, C. E., Peters, W. & Wieringa, B. The DMWD protein from the myotonic dystrophy (DM1) gene region is developmentally regulated and is present most prominently in synapse-dense brain areas. Brain Res 971, 116-27 (2003).
48. Yoshimura, N. et al. Topography of Alzheimer's neurofibrillary change distribution in myotonic dystrophy. Clin Neuropathol 9, 234-9 (1990).
49. Rip, J., Schenk, G. J. & de Boer, A. G. Differential receptor-mediated drug targeting to the diseased brain. Expert Opin Drug Deliv 6, 227-37 (2009).
50. Schenk, G. J. et al. Efficient CRM197-mediated drug targeting to monocytes. J Control Release 158, 139-47 (2012).
51. Bao, L. et al. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 35, D51-4 (2007).
52. Gong, J. et al. Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat 33, 254-63 (2012).
53. Meenhuis, A. et al. MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1-regulated pathways in mice. Blood 118, 916-25 (2011).
54. Agarwal, V., Bell, G. W., Nam, J. W. & Bartel, D. P. Predicting effective microRNA target sites in mammalian mRNAs. Elife 4, (2015).
55. Betel, D., Koppal, A., Agius, P., Sander, C. & Leslie, C. Comprehensive modeling of microRNA targets predicts functional nonconserved and non-canonical sites. Genome Biol 11, R90 (2010).
56. Cogswell, J. P. et al. Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways. J Alzheimers Dis 14, 27-41 (2008).
57. Moreau, M. P., Bruse, S. E., Jornsten, R., Liu, Y. & Brzustowicz, L. M. Chronological changes in microRNA expression in the developing human brain. PLoS One 8, e60480 (2013).
58. Westra, H. J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet (2013).
59. Grundberg, E. et al. Mapping cis-And trans-regulatory effects across multiple tissues in twins. Nat Genet 44, 1084-9 (2012).
60. Kozomara, A. & Griffiths-Jones, S. miRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42, D68-73 (2014).